[aroma.affymetrix] libgsl-0.dll missing error

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[aroma.affymetrix] libgsl-0.dll missing error

Yan Jiao

 

Dear all,

I’m trying to do DNA segmentation,

This is what I’m doing:

ds <- doCRMAv1("Fockens_1", chipType="Mapping50K_Hind240", verbose=TRUE);

###this is done sucessfully

# Segmentation

cbs <- CbsModel(ds);

 

I got error libgsl-0.dll is missing, I think it’s using GLAD, but I’m trying to use DNAcopy for segmentation.

How to change it?

 

Many thanks

 

yan

 

 

 

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Re: [aroma.affymetrix] libgsl-0.dll missing error

Henrik Bengtsson-4
Hi.

On Tue, Nov 23, 2010 at 10:05 AM, Yan Jiao <[hidden email]> wrote:

>
>
> Dear all,
>
> I’m trying to do DNA segmentation,
>
> This is what I’m doing:
>
> ds <- doCRMAv1("Fockens_1", chipType="Mapping50K_Hind240", verbose=TRUE);
>
> ###this is done sucessfully
>
> # Segmentation
>
> cbs <- CbsModel(ds);
>
>
>
> I got error libgsl-0.dll is missing, I think it’s using GLAD, but I’m trying
> to use DNAcopy for segmentation.

Is it really the case that you get that error when you do:

cbs <- CbsModel(ds);

or do you do anything else?  Is suspect you do something more.

Also, after you got the error, could you cut'n'paste the verbose
output including any error messages you get and send it to us?   Also,
make sure to report what print(traceback()) gives immediate after
getting the error.

/Henrik

PS. The 'GLAD' package may indeed be used regardless of segmentation
method because it contains information about cytobands.

>
> How to change it?
>
>
>
> Many thanks
>
>
>
> yan
>
>
>
>
>
>
>
> **********************************************************************
>
> This email and any files transmitted with it are confidential and
>
> intended solely for the use of the individual or entity to whom they
>
> are addressed. If you have received this email in error please notify
>
> the system manager ([hidden email]).
>
> **********************************************************************
>
>
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to [hidden email]
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>

--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.


You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
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RE: [aroma.affymetrix] libgsl-0.dll missing error

Yan Jiao
Hi Henrik,

Sorry, the error is after
cbs <- CbsModel(ds);
ce <- ChromosomeExplorer(cbs);
process(ce, verbose=TRUE);


Generating ChromosomeExplorer report...
Loading required package: Cairo
<simpleError in inDL(x, as.logical(local), as.logical(now), ...): unable
to load shared library
'C:/Users/rmhkyji/R/win64-library/2.11/GLAD/libs/x64/GLAD.dll':
  LoadLibrary failure:  The specified module could not be found.

And there  is a pop out window saying: The program can't start because
libgsl-0.dll I smissing from your computer. Try reinstalling the program
to fix this program.


Yan

-----Original Message-----
From: [hidden email]
[mailto:[hidden email]] On Behalf Of Henrik Bengtsson
Sent: 23 November 2010 18:50
To: aroma-affymetrix
Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error

Hi.

On Tue, Nov 23, 2010 at 10:05 AM, Yan Jiao <[hidden email]> wrote:
>
>
> Dear all,
>
> I'm trying to do DNA segmentation,
>
> This is what I'm doing:
>
> ds <- doCRMAv1("Fockens_1", chipType="Mapping50K_Hind240",
verbose=TRUE);

>
> ###this is done sucessfully
>
> # Segmentation
>
> cbs <- CbsModel(ds);
>
>
>
> I got error libgsl-0.dll is missing, I think it's using GLAD, but I'm
trying
> to use DNAcopy for segmentation.

Is it really the case that you get that error when you do:

cbs <- CbsModel(ds);

or do you do anything else?  Is suspect you do something more.

Also, after you got the error, could you cut'n'paste the verbose
output including any error messages you get and send it to us?   Also,
make sure to report what print(traceback()) gives immediate after
getting the error.

/Henrik

PS. The 'GLAD' package may indeed be used regardless of segmentation
method because it contains information about cytobands.

>
> How to change it?
>
>
>
> Many thanks
>
>
>
> yan
>
>
>
>
>
>
>
> **********************************************************************
>
> This email and any files transmitted with it are confidential and
>
> intended solely for the use of the individual or entity to whom they
>
> are addressed. If you have received this email in error please notify
>
> the system manager ([hidden email]).
>
> **********************************************************************
>
>
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the
latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google
Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to [hidden email]
> To unsubscribe and other options, go to
http://www.aroma-project.org/forum/
>

--
When reporting problems on aroma.affymetrix, make sure 1) to run the
latest version of the package, 2) to report the output of sessionInfo()
and traceback(), and 3) to post a complete code example.


You received this message because you are subscribed to the Google
Groups "aroma.affymetrix" group with website
http://www.aroma-project.org/.
To post to this group, send email to [hidden email]
To unsubscribe and other options, go to
http://www.aroma-project.org/forum/

--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.


You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
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Re: [aroma.affymetrix] libgsl-0.dll missing error

Henrik Bengtsson-4
Hi.

On Tue, Nov 23, 2010 at 11:51 AM, Yan Jiao <[hidden email]> wrote:
> Hi Henrik,
>
> Sorry, the error is after
> cbs <- CbsModel(ds);
> ce <- ChromosomeExplorer(cbs);
> process(ce, verbose=TRUE);

Ok, now the error message makes a bit more sense (it was my suspicion
but I didn't want make guesses).

>
>
> Generating ChromosomeExplorer report...
> Loading required package: Cairo
> <simpleError in inDL(x, as.logical(local), as.logical(now), ...): unable
> to load shared library
> 'C:/Users/rmhkyji/R/win64-library/2.11/GLAD/libs/x64/GLAD.dll':
>  LoadLibrary failure:  The specified module could not be found.
>
> And there  is a pop out window saying: The program can't start because
> libgsl-0.dll I smissing from your computer. Try reinstalling the program
> to fix this program.

I can reproduce this on 64-bit Windows 7 - you get the same error if
you try library("GLAD").  It is because we utilize part of the GLAD
package, if and only if it is *installed*, and otherwise we turn to
backup solutions.  What happens here is that *GLAD is installed but
doesn't load*, which causes the error so that backup solutions doesn't
kick in.   In the next release I'll try to make sure the backup
solutions will also work when there is an error load GLAD.  In
meanwhile, you can do this:

WORKAROUND:

1. Uninstall the GLAD package (it doesn't work anyway):

> remove.packages("GLAD")
Removing package(s) from 'C:\Users\hb\R\win-library\2.12'
(as 'lib' is unspecified)

> library("GLAD")
Error in library("GLAD") : there is no package called 'GLAD'

That should do it.  Let me know if it works for you.

TECHNICAL DETAILS: It happens because the GNU Scientific Library (GSL)
is not installed on the system (hence the 'gsl' part of
'libgsl-0.dll'). There is a hard-to-find note that you need GSL in
order to use the GLAD package, cf.
http://bioconductor.org/packages/release/bioc/html/GLAD.html.  There
exist 32-bit binaries of GSL at
http://gnuwin32.sourceforge.net/packages/gsl.htm.  Unfortunately, it
does not work for the 64-bit version of R on Windows 64-bit.  It works
if you do tricks an run the 32-bit version of R, but that is a rather
inconvenient workaround.

/Henrik

>
>
> Yan
>
> -----Original Message-----
> From: [hidden email]
> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
> Sent: 23 November 2010 18:50
> To: aroma-affymetrix
> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>
> Hi.
>
> On Tue, Nov 23, 2010 at 10:05 AM, Yan Jiao <[hidden email]> wrote:
>>
>>
>> Dear all,
>>
>> I'm trying to do DNA segmentation,
>>
>> This is what I'm doing:
>>
>> ds <- doCRMAv1("Fockens_1", chipType="Mapping50K_Hind240",
> verbose=TRUE);
>>
>> ###this is done sucessfully
>>
>> # Segmentation
>>
>> cbs <- CbsModel(ds);
>>
>>
>>
>> I got error libgsl-0.dll is missing, I think it's using GLAD, but I'm
> trying
>> to use DNAcopy for segmentation.
>
> Is it really the case that you get that error when you do:
>
> cbs <- CbsModel(ds);
>
> or do you do anything else?  Is suspect you do something more.
>
> Also, after you got the error, could you cut'n'paste the verbose
> output including any error messages you get and send it to us?   Also,
> make sure to report what print(traceback()) gives immediate after
> getting the error.
>
> /Henrik
>
> PS. The 'GLAD' package may indeed be used regardless of segmentation
> method because it contains information about cytobands.
>
>>
>> How to change it?
>>
>>
>>
>> Many thanks
>>
>>
>>
>> yan
>>
>>
>>
>>
>>
>>
>>
>> **********************************************************************
>>
>> This email and any files transmitted with it are confidential and
>>
>> intended solely for the use of the individual or entity to whom they
>>
>> are addressed. If you have received this email in error please notify
>>
>> the system manager ([hidden email]).
>>
>> **********************************************************************
>>
>>
>>
>> --
>> When reporting problems on aroma.affymetrix, make sure 1) to run the
> latest
>> version of the package, 2) to report the output of sessionInfo() and
>> traceback(), and 3) to post a complete code example.
>>
>>
>> You received this message because you are subscribed to the Google
> Groups
>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> To post to this group, send email to [hidden email]
>> To unsubscribe and other options, go to
> http://www.aroma-project.org/forum/
>>
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the
> latest version of the package, 2) to report the output of sessionInfo()
> and traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google
> Groups "aroma.affymetrix" group with website
> http://www.aroma-project.org/.
> To post to this group, send email to [hidden email]
> To unsubscribe and other options, go to
> http://www.aroma-project.org/forum/
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to [hidden email]
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>

--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.


You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
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RE: [aroma.affymetrix] libgsl-0.dll missing error

Yan Jiao
Thank you Henrik,
It works now, but I got some warning:

process(ce, verbose=TRUE);
Generating ChromosomeExplorer report...
Loading required package: Cairo
Generating ChromosomeExplorer report...done
[1] TRUE
Warning messages:
1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'Cairo'
2: In method(static, ...) :
  Ghostscript not found. Searched directories: C:/gs, C:\Program Files/gs, /gs, C:\Program Files\Common Files/gs

Are those warning messages serious? Could I ignore them?


Yan

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
Sent: 23 November 2010 21:53
To: aroma-affymetrix
Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error

Hi.

On Tue, Nov 23, 2010 at 11:51 AM, Yan Jiao <[hidden email]> wrote:
> Hi Henrik,
>
> Sorry, the error is after
> cbs <- CbsModel(ds);
> ce <- ChromosomeExplorer(cbs);
> process(ce, verbose=TRUE);

Ok, now the error message makes a bit more sense (it was my suspicion
but I didn't want make guesses).

>
>
> Generating ChromosomeExplorer report...
> Loading required package: Cairo
> <simpleError in inDL(x, as.logical(local), as.logical(now), ...): unable
> to load shared library
> 'C:/Users/rmhkyji/R/win64-library/2.11/GLAD/libs/x64/GLAD.dll':
>  LoadLibrary failure:  The specified module could not be found.
>
> And there  is a pop out window saying: The program can't start because
> libgsl-0.dll I smissing from your computer. Try reinstalling the program
> to fix this program.

I can reproduce this on 64-bit Windows 7 - you get the same error if
you try library("GLAD").  It is because we utilize part of the GLAD
package, if and only if it is *installed*, and otherwise we turn to
backup solutions.  What happens here is that *GLAD is installed but
doesn't load*, which causes the error so that backup solutions doesn't
kick in.   In the next release I'll try to make sure the backup
solutions will also work when there is an error load GLAD.  In
meanwhile, you can do this:

WORKAROUND:

1. Uninstall the GLAD package (it doesn't work anyway):

> remove.packages("GLAD")
Removing package(s) from 'C:\Users\hb\R\win-library\2.12'
(as 'lib' is unspecified)

> library("GLAD")
Error in library("GLAD") : there is no package called 'GLAD'

That should do it.  Let me know if it works for you.

TECHNICAL DETAILS: It happens because the GNU Scientific Library (GSL)
is not installed on the system (hence the 'gsl' part of
'libgsl-0.dll'). There is a hard-to-find note that you need GSL in
order to use the GLAD package, cf.
http://bioconductor.org/packages/release/bioc/html/GLAD.html.  There
exist 32-bit binaries of GSL at
http://gnuwin32.sourceforge.net/packages/gsl.htm.  Unfortunately, it
does not work for the 64-bit version of R on Windows 64-bit.  It works
if you do tricks an run the 32-bit version of R, but that is a rather
inconvenient workaround.

/Henrik

>
>
> Yan
>
> -----Original Message-----
> From: [hidden email]
> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
> Sent: 23 November 2010 18:50
> To: aroma-affymetrix
> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>
> Hi.
>
> On Tue, Nov 23, 2010 at 10:05 AM, Yan Jiao <[hidden email]> wrote:
>>
>>
>> Dear all,
>>
>> I'm trying to do DNA segmentation,
>>
>> This is what I'm doing:
>>
>> ds <- doCRMAv1("Fockens_1", chipType="Mapping50K_Hind240",
> verbose=TRUE);
>>
>> ###this is done sucessfully
>>
>> # Segmentation
>>
>> cbs <- CbsModel(ds);
>>
>>
>>
>> I got error libgsl-0.dll is missing, I think it's using GLAD, but I'm
> trying
>> to use DNAcopy for segmentation.
>
> Is it really the case that you get that error when you do:
>
> cbs <- CbsModel(ds);
>
> or do you do anything else?  Is suspect you do something more.
>
> Also, after you got the error, could you cut'n'paste the verbose
> output including any error messages you get and send it to us?   Also,
> make sure to report what print(traceback()) gives immediate after
> getting the error.
>
> /Henrik
>
> PS. The 'GLAD' package may indeed be used regardless of segmentation
> method because it contains information about cytobands.
>
>>
>> How to change it?
>>
>>
>>
>> Many thanks
>>
>>
>>
>> yan
>>
>>
>>
>>
>>
>>
>>
>> **********************************************************************
>>
>> This email and any files transmitted with it are confidential and
>>
>> intended solely for the use of the individual or entity to whom they
>>
>> are addressed. If you have received this email in error please notify
>>
>> the system manager ([hidden email]).
>>
>> **********************************************************************
>>
>>
>>
>> --
>> When reporting problems on aroma.affymetrix, make sure 1) to run the
> latest
>> version of the package, 2) to report the output of sessionInfo() and
>> traceback(), and 3) to post a complete code example.
>>
>>
>> You received this message because you are subscribed to the Google
> Groups
>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> To post to this group, send email to [hidden email]
>> To unsubscribe and other options, go to
> http://www.aroma-project.org/forum/
>>
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the
> latest version of the package, 2) to report the output of sessionInfo()
> and traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google
> Groups "aroma.affymetrix" group with website
> http://www.aroma-project.org/.
> To post to this group, send email to [hidden email]
> To unsubscribe and other options, go to
> http://www.aroma-project.org/forum/
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to [hidden email]
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>

--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.


You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to [hidden email]
To unsubscribe and other options, go to http://www.aroma-project.org/forum/

--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.


You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to [hidden email]
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Re: [aroma.affymetrix] libgsl-0.dll missing error

Henrik Bengtsson-4
Hi,

great.  Contrary to error messages, warnings are alright to get.

/H

On Wed, Nov 24, 2010 at 2:51 AM, Yan Jiao <[hidden email]> wrote:

> Thank you Henrik,
> It works now, but I got some warning:
>
> process(ce, verbose=TRUE);
> Generating ChromosomeExplorer report...
> Loading required package: Cairo
> Generating ChromosomeExplorer report...done
> [1] TRUE
> Warning messages:
> 1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
>  there is no package called 'Cairo'
> 2: In method(static, ...) :
>  Ghostscript not found. Searched directories: C:/gs, C:\Program Files/gs, /gs, C:\Program Files\Common Files/gs
>
> Are those warning messages serious? Could I ignore them?
>
>
> Yan
>
> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
> Sent: 23 November 2010 21:53
> To: aroma-affymetrix
> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>
> Hi.
>
> On Tue, Nov 23, 2010 at 11:51 AM, Yan Jiao <[hidden email]> wrote:
>> Hi Henrik,
>>
>> Sorry, the error is after
>> cbs <- CbsModel(ds);
>> ce <- ChromosomeExplorer(cbs);
>> process(ce, verbose=TRUE);
>
> Ok, now the error message makes a bit more sense (it was my suspicion
> but I didn't want make guesses).
>
>>
>>
>> Generating ChromosomeExplorer report...
>> Loading required package: Cairo
>> <simpleError in inDL(x, as.logical(local), as.logical(now), ...): unable
>> to load shared library
>> 'C:/Users/rmhkyji/R/win64-library/2.11/GLAD/libs/x64/GLAD.dll':
>>  LoadLibrary failure:  The specified module could not be found.
>>
>> And there  is a pop out window saying: The program can't start because
>> libgsl-0.dll I smissing from your computer. Try reinstalling the program
>> to fix this program.
>
> I can reproduce this on 64-bit Windows 7 - you get the same error if
> you try library("GLAD").  It is because we utilize part of the GLAD
> package, if and only if it is *installed*, and otherwise we turn to
> backup solutions.  What happens here is that *GLAD is installed but
> doesn't load*, which causes the error so that backup solutions doesn't
> kick in.   In the next release I'll try to make sure the backup
> solutions will also work when there is an error load GLAD.  In
> meanwhile, you can do this:
>
> WORKAROUND:
>
> 1. Uninstall the GLAD package (it doesn't work anyway):
>
>> remove.packages("GLAD")
> Removing package(s) from 'C:\Users\hb\R\win-library\2.12'
> (as 'lib' is unspecified)
>
>> library("GLAD")
> Error in library("GLAD") : there is no package called 'GLAD'
>
> That should do it.  Let me know if it works for you.
>
> TECHNICAL DETAILS: It happens because the GNU Scientific Library (GSL)
> is not installed on the system (hence the 'gsl' part of
> 'libgsl-0.dll'). There is a hard-to-find note that you need GSL in
> order to use the GLAD package, cf.
> http://bioconductor.org/packages/release/bioc/html/GLAD.html.  There
> exist 32-bit binaries of GSL at
> http://gnuwin32.sourceforge.net/packages/gsl.htm.  Unfortunately, it
> does not work for the 64-bit version of R on Windows 64-bit.  It works
> if you do tricks an run the 32-bit version of R, but that is a rather
> inconvenient workaround.
>
> /Henrik
>
>>
>>
>> Yan
>>
>> -----Original Message-----
>> From: [hidden email]
>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>> Sent: 23 November 2010 18:50
>> To: aroma-affymetrix
>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>
>> Hi.
>>
>> On Tue, Nov 23, 2010 at 10:05 AM, Yan Jiao <[hidden email]> wrote:
>>>
>>>
>>> Dear all,
>>>
>>> I'm trying to do DNA segmentation,
>>>
>>> This is what I'm doing:
>>>
>>> ds <- doCRMAv1("Fockens_1", chipType="Mapping50K_Hind240",
>> verbose=TRUE);
>>>
>>> ###this is done sucessfully
>>>
>>> # Segmentation
>>>
>>> cbs <- CbsModel(ds);
>>>
>>>
>>>
>>> I got error libgsl-0.dll is missing, I think it's using GLAD, but I'm
>> trying
>>> to use DNAcopy for segmentation.
>>
>> Is it really the case that you get that error when you do:
>>
>> cbs <- CbsModel(ds);
>>
>> or do you do anything else?  Is suspect you do something more.
>>
>> Also, after you got the error, could you cut'n'paste the verbose
>> output including any error messages you get and send it to us?   Also,
>> make sure to report what print(traceback()) gives immediate after
>> getting the error.
>>
>> /Henrik
>>
>> PS. The 'GLAD' package may indeed be used regardless of segmentation
>> method because it contains information about cytobands.
>>
>>>
>>> How to change it?
>>>
>>>
>>>
>>> Many thanks
>>>
>>>
>>>
>>> yan
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> **********************************************************************
>>>
>>> This email and any files transmitted with it are confidential and
>>>
>>> intended solely for the use of the individual or entity to whom they
>>>
>>> are addressed. If you have received this email in error please notify
>>>
>>> the system manager ([hidden email]).
>>>
>>> **********************************************************************
>>>
>>>
>>>
>>> --
>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>> latest
>>> version of the package, 2) to report the output of sessionInfo() and
>>> traceback(), and 3) to post a complete code example.
>>>
>>>
>>> You received this message because you are subscribed to the Google
>> Groups
>>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>>> To post to this group, send email to [hidden email]
>>> To unsubscribe and other options, go to
>> http://www.aroma-project.org/forum/
>>>
>>
>> --
>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>> latest version of the package, 2) to report the output of sessionInfo()
>> and traceback(), and 3) to post a complete code example.
>>
>>
>> You received this message because you are subscribed to the Google
>> Groups "aroma.affymetrix" group with website
>> http://www.aroma-project.org/.
>> To post to this group, send email to [hidden email]
>> To unsubscribe and other options, go to
>> http://www.aroma-project.org/forum/
>>
>> --
>> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
>>
>>
>> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> To post to this group, send email to [hidden email]
>> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>>
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to [hidden email]
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
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[aroma.affymetrix] Copy number segmentation result

Yan Jiao
Hi Henrik,

Another question about the result is : is there a way to map the copy number to the gene ID automatically? Also does aroma choose threshold for calling gain and loss?

Many thanks

yan

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
Sent: 24 November 2010 15:08
To: aroma-affymetrix
Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error

Hi,

great.  Contrary to error messages, warnings are alright to get.

/H

On Wed, Nov 24, 2010 at 2:51 AM, Yan Jiao <[hidden email]> wrote:

> Thank you Henrik,
> It works now, but I got some warning:
>
> process(ce, verbose=TRUE);
> Generating ChromosomeExplorer report...
> Loading required package: Cairo
> Generating ChromosomeExplorer report...done
> [1] TRUE
> Warning messages:
> 1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
>  there is no package called 'Cairo'
> 2: In method(static, ...) :
>  Ghostscript not found. Searched directories: C:/gs, C:\Program Files/gs, /gs, C:\Program Files\Common Files/gs
>
> Are those warning messages serious? Could I ignore them?
>
>
> Yan
>
> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
> Sent: 23 November 2010 21:53
> To: aroma-affymetrix
> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>
> Hi.
>
> On Tue, Nov 23, 2010 at 11:51 AM, Yan Jiao <[hidden email]> wrote:
>> Hi Henrik,
>>
>> Sorry, the error is after
>> cbs <- CbsModel(ds);
>> ce <- ChromosomeExplorer(cbs);
>> process(ce, verbose=TRUE);
>
> Ok, now the error message makes a bit more sense (it was my suspicion
> but I didn't want make guesses).
>
>>
>>
>> Generating ChromosomeExplorer report...
>> Loading required package: Cairo
>> <simpleError in inDL(x, as.logical(local), as.logical(now), ...): unable
>> to load shared library
>> 'C:/Users/rmhkyji/R/win64-library/2.11/GLAD/libs/x64/GLAD.dll':
>>  LoadLibrary failure:  The specified module could not be found.
>>
>> And there  is a pop out window saying: The program can't start because
>> libgsl-0.dll I smissing from your computer. Try reinstalling the program
>> to fix this program.
>
> I can reproduce this on 64-bit Windows 7 - you get the same error if
> you try library("GLAD").  It is because we utilize part of the GLAD
> package, if and only if it is *installed*, and otherwise we turn to
> backup solutions.  What happens here is that *GLAD is installed but
> doesn't load*, which causes the error so that backup solutions doesn't
> kick in.   In the next release I'll try to make sure the backup
> solutions will also work when there is an error load GLAD.  In
> meanwhile, you can do this:
>
> WORKAROUND:
>
> 1. Uninstall the GLAD package (it doesn't work anyway):
>
>> remove.packages("GLAD")
> Removing package(s) from 'C:\Users\hb\R\win-library\2.12'
> (as 'lib' is unspecified)
>
>> library("GLAD")
> Error in library("GLAD") : there is no package called 'GLAD'
>
> That should do it.  Let me know if it works for you.
>
> TECHNICAL DETAILS: It happens because the GNU Scientific Library (GSL)
> is not installed on the system (hence the 'gsl' part of
> 'libgsl-0.dll'). There is a hard-to-find note that you need GSL in
> order to use the GLAD package, cf.
> http://bioconductor.org/packages/release/bioc/html/GLAD.html.  There
> exist 32-bit binaries of GSL at
> http://gnuwin32.sourceforge.net/packages/gsl.htm.  Unfortunately, it
> does not work for the 64-bit version of R on Windows 64-bit.  It works
> if you do tricks an run the 32-bit version of R, but that is a rather
> inconvenient workaround.
>
> /Henrik
>
>>
>>
>> Yan
>>
>> -----Original Message-----
>> From: [hidden email]
>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>> Sent: 23 November 2010 18:50
>> To: aroma-affymetrix
>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>
>> Hi.
>>
>> On Tue, Nov 23, 2010 at 10:05 AM, Yan Jiao <[hidden email]> wrote:
>>>
>>>
>>> Dear all,
>>>
>>> I'm trying to do DNA segmentation,
>>>
>>> This is what I'm doing:
>>>
>>> ds <- doCRMAv1("Fockens_1", chipType="Mapping50K_Hind240",
>> verbose=TRUE);
>>>
>>> ###this is done sucessfully
>>>
>>> # Segmentation
>>>
>>> cbs <- CbsModel(ds);
>>>
>>>
>>>
>>> I got error libgsl-0.dll is missing, I think it's using GLAD, but I'm
>> trying
>>> to use DNAcopy for segmentation.
>>
>> Is it really the case that you get that error when you do:
>>
>> cbs <- CbsModel(ds);
>>
>> or do you do anything else?  Is suspect you do something more.
>>
>> Also, after you got the error, could you cut'n'paste the verbose
>> output including any error messages you get and send it to us?   Also,
>> make sure to report what print(traceback()) gives immediate after
>> getting the error.
>>
>> /Henrik
>>
>> PS. The 'GLAD' package may indeed be used regardless of segmentation
>> method because it contains information about cytobands.
>>
>>>
>>> How to change it?
>>>
>>>
>>>
>>> Many thanks
>>>
>>>
>>>
>>> yan
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> **********************************************************************
>>>
>>> This email and any files transmitted with it are confidential and
>>>
>>> intended solely for the use of the individual or entity to whom they
>>>
>>> are addressed. If you have received this email in error please notify
>>>
>>> the system manager ([hidden email]).
>>>
>>> **********************************************************************
>>>
>>>
>>>
>>> --
>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>> latest
>>> version of the package, 2) to report the output of sessionInfo() and
>>> traceback(), and 3) to post a complete code example.
>>>
>>>
>>> You received this message because you are subscribed to the Google
>> Groups
>>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>>> To post to this group, send email to [hidden email]
>>> To unsubscribe and other options, go to
>> http://www.aroma-project.org/forum/
>>>
>>
>> --
>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>> latest version of the package, 2) to report the output of sessionInfo()
>> and traceback(), and 3) to post a complete code example.
>>
>>
>> You received this message because you are subscribed to the Google
>> Groups "aroma.affymetrix" group with website
>> http://www.aroma-project.org/.
>> To post to this group, send email to [hidden email]
>> To unsubscribe and other options, go to
>> http://www.aroma-project.org/forum/
>>
>> --
>> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
>>
>>
>> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> To post to this group, send email to [hidden email]
>> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>>
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to [hidden email]
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to [hidden email]
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>

--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.


You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
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You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
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RE: [aroma.affymetrix] libgsl-0.dll missing error

Yan Jiao
In reply to this post by Henrik Bengtsson-4
Hi Henrik,

Another question, I was trying to only do segmentation on 3 chromosomes, how should I do it, I tried:
process(ce,chromosomes=c(1,8,17), verbose=TRUE);

but got error message:

Generating ChromosomeExplorer report...
Loading required package: Cairo
Error: package 'Cairo' is not installed for 'arch=x64'
Generating ChromosomeExplorer report...done


Many thanks

yan



-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
Sent: 24 November 2010 15:08
To: aroma-affymetrix
Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error

Hi,

great.  Contrary to error messages, warnings are alright to get.

/H

On Wed, Nov 24, 2010 at 2:51 AM, Yan Jiao <[hidden email]> wrote:

> Thank you Henrik,
> It works now, but I got some warning:
>
> process(ce, verbose=TRUE);
> Generating ChromosomeExplorer report...
> Loading required package: Cairo
> Generating ChromosomeExplorer report...done
> [1] TRUE
> Warning messages:
> 1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
>  there is no package called 'Cairo'
> 2: In method(static, ...) :
>  Ghostscript not found. Searched directories: C:/gs, C:\Program Files/gs, /gs, C:\Program Files\Common Files/gs
>
> Are those warning messages serious? Could I ignore them?
>
>
> Yan
>
> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
> Sent: 23 November 2010 21:53
> To: aroma-affymetrix
> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>
> Hi.
>
> On Tue, Nov 23, 2010 at 11:51 AM, Yan Jiao <[hidden email]> wrote:
>> Hi Henrik,
>>
>> Sorry, the error is after
>> cbs <- CbsModel(ds);
>> ce <- ChromosomeExplorer(cbs);
>> process(ce, verbose=TRUE);
>
> Ok, now the error message makes a bit more sense (it was my suspicion
> but I didn't want make guesses).
>
>>
>>
>> Generating ChromosomeExplorer report...
>> Loading required package: Cairo
>> <simpleError in inDL(x, as.logical(local), as.logical(now), ...): unable
>> to load shared library
>> 'C:/Users/rmhkyji/R/win64-library/2.11/GLAD/libs/x64/GLAD.dll':
>>  LoadLibrary failure:  The specified module could not be found.
>>
>> And there  is a pop out window saying: The program can't start because
>> libgsl-0.dll I smissing from your computer. Try reinstalling the program
>> to fix this program.
>
> I can reproduce this on 64-bit Windows 7 - you get the same error if
> you try library("GLAD").  It is because we utilize part of the GLAD
> package, if and only if it is *installed*, and otherwise we turn to
> backup solutions.  What happens here is that *GLAD is installed but
> doesn't load*, which causes the error so that backup solutions doesn't
> kick in.   In the next release I'll try to make sure the backup
> solutions will also work when there is an error load GLAD.  In
> meanwhile, you can do this:
>
> WORKAROUND:
>
> 1. Uninstall the GLAD package (it doesn't work anyway):
>
>> remove.packages("GLAD")
> Removing package(s) from 'C:\Users\hb\R\win-library\2.12'
> (as 'lib' is unspecified)
>
>> library("GLAD")
> Error in library("GLAD") : there is no package called 'GLAD'
>
> That should do it.  Let me know if it works for you.
>
> TECHNICAL DETAILS: It happens because the GNU Scientific Library (GSL)
> is not installed on the system (hence the 'gsl' part of
> 'libgsl-0.dll'). There is a hard-to-find note that you need GSL in
> order to use the GLAD package, cf.
> http://bioconductor.org/packages/release/bioc/html/GLAD.html.  There
> exist 32-bit binaries of GSL at
> http://gnuwin32.sourceforge.net/packages/gsl.htm.  Unfortunately, it
> does not work for the 64-bit version of R on Windows 64-bit.  It works
> if you do tricks an run the 32-bit version of R, but that is a rather
> inconvenient workaround.
>
> /Henrik
>
>>
>>
>> Yan
>>
>> -----Original Message-----
>> From: [hidden email]
>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>> Sent: 23 November 2010 18:50
>> To: aroma-affymetrix
>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>
>> Hi.
>>
>> On Tue, Nov 23, 2010 at 10:05 AM, Yan Jiao <[hidden email]> wrote:
>>>
>>>
>>> Dear all,
>>>
>>> I'm trying to do DNA segmentation,
>>>
>>> This is what I'm doing:
>>>
>>> ds <- doCRMAv1("Fockens_1", chipType="Mapping50K_Hind240",
>> verbose=TRUE);
>>>
>>> ###this is done sucessfully
>>>
>>> # Segmentation
>>>
>>> cbs <- CbsModel(ds);
>>>
>>>
>>>
>>> I got error libgsl-0.dll is missing, I think it's using GLAD, but I'm
>> trying
>>> to use DNAcopy for segmentation.
>>
>> Is it really the case that you get that error when you do:
>>
>> cbs <- CbsModel(ds);
>>
>> or do you do anything else?  Is suspect you do something more.
>>
>> Also, after you got the error, could you cut'n'paste the verbose
>> output including any error messages you get and send it to us?   Also,
>> make sure to report what print(traceback()) gives immediate after
>> getting the error.
>>
>> /Henrik
>>
>> PS. The 'GLAD' package may indeed be used regardless of segmentation
>> method because it contains information about cytobands.
>>
>>>
>>> How to change it?
>>>
>>>
>>>
>>> Many thanks
>>>
>>>
>>>
>>> yan
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> **********************************************************************
>>>
>>> This email and any files transmitted with it are confidential and
>>>
>>> intended solely for the use of the individual or entity to whom they
>>>
>>> are addressed. If you have received this email in error please notify
>>>
>>> the system manager ([hidden email]).
>>>
>>> **********************************************************************
>>>
>>>
>>>
>>> --
>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>> latest
>>> version of the package, 2) to report the output of sessionInfo() and
>>> traceback(), and 3) to post a complete code example.
>>>
>>>
>>> You received this message because you are subscribed to the Google
>> Groups
>>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>>> To post to this group, send email to [hidden email]
>>> To unsubscribe and other options, go to
>> http://www.aroma-project.org/forum/
>>>
>>
>> --
>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>> latest version of the package, 2) to report the output of sessionInfo()
>> and traceback(), and 3) to post a complete code example.
>>
>>
>> You received this message because you are subscribed to the Google
>> Groups "aroma.affymetrix" group with website
>> http://www.aroma-project.org/.
>> To post to this group, send email to [hidden email]
>> To unsubscribe and other options, go to
>> http://www.aroma-project.org/forum/
>>
>> --
>> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
>>
>>
>> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> To post to this group, send email to [hidden email]
>> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>>
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to [hidden email]
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to [hidden email]
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>

--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.


You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to [hidden email]
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When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.


You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
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Re: [aroma.affymetrix] libgsl-0.dll missing error

Henrik Bengtsson-4
Hi.

On Wed, Nov 24, 2010 at 8:10 AM, Yan Jiao <[hidden email]> wrote:

> Hi Henrik,
>
> Another question, I was trying to only do segmentation on 3 chromosomes, how should I do it, I tried:
> process(ce,chromosomes=c(1,8,17), verbose=TRUE);
>
> but got error message:
>
> Generating ChromosomeExplorer report...
> Loading required package: Cairo
> Error: package 'Cairo' is not installed for 'arch=x64'
> Generating ChromosomeExplorer report...done

Odd, because specifying a subset of chromosomes shouldn't be any
different from running all, as you did before.

So, there seem to be several packages that install on R 64-bit in
Windows, but when trying to use then fails.  The Cairo package is
actually "deprecated" (replaced with similar function builtin in R),
but we've kept support for backward compatibilities.  It seems like
you're facing these issues - and not that many people are running
64-bit Windows yet so you seem to be the one hitting the bumps.

What does traceback() give when you get the error?

What is your sessionInfo()?

Can you use process(ce,chromosomes=c(1,8,17), verbose=-10) in order to
narrow down where the error occurs.

/Henrik

>
>
> Many thanks
>
> yan
>
>
>
> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
> Sent: 24 November 2010 15:08
> To: aroma-affymetrix
> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>
> Hi,
>
> great.  Contrary to error messages, warnings are alright to get.
>
> /H
>
> On Wed, Nov 24, 2010 at 2:51 AM, Yan Jiao <[hidden email]> wrote:
>> Thank you Henrik,
>> It works now, but I got some warning:
>>
>> process(ce, verbose=TRUE);
>> Generating ChromosomeExplorer report...
>> Loading required package: Cairo
>> Generating ChromosomeExplorer report...done
>> [1] TRUE
>> Warning messages:
>> 1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
>>  there is no package called 'Cairo'
>> 2: In method(static, ...) :
>>  Ghostscript not found. Searched directories: C:/gs, C:\Program Files/gs, /gs, C:\Program Files\Common Files/gs
>>
>> Are those warning messages serious? Could I ignore them?
>>
>>
>> Yan
>>
>> -----Original Message-----
>> From: [hidden email] [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>> Sent: 23 November 2010 21:53
>> To: aroma-affymetrix
>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>
>> Hi.
>>
>> On Tue, Nov 23, 2010 at 11:51 AM, Yan Jiao <[hidden email]> wrote:
>>> Hi Henrik,
>>>
>>> Sorry, the error is after
>>> cbs <- CbsModel(ds);
>>> ce <- ChromosomeExplorer(cbs);
>>> process(ce, verbose=TRUE);
>>
>> Ok, now the error message makes a bit more sense (it was my suspicion
>> but I didn't want make guesses).
>>
>>>
>>>
>>> Generating ChromosomeExplorer report...
>>> Loading required package: Cairo
>>> <simpleError in inDL(x, as.logical(local), as.logical(now), ...): unable
>>> to load shared library
>>> 'C:/Users/rmhkyji/R/win64-library/2.11/GLAD/libs/x64/GLAD.dll':
>>>  LoadLibrary failure:  The specified module could not be found.
>>>
>>> And there  is a pop out window saying: The program can't start because
>>> libgsl-0.dll I smissing from your computer. Try reinstalling the program
>>> to fix this program.
>>
>> I can reproduce this on 64-bit Windows 7 - you get the same error if
>> you try library("GLAD").  It is because we utilize part of the GLAD
>> package, if and only if it is *installed*, and otherwise we turn to
>> backup solutions.  What happens here is that *GLAD is installed but
>> doesn't load*, which causes the error so that backup solutions doesn't
>> kick in.   In the next release I'll try to make sure the backup
>> solutions will also work when there is an error load GLAD.  In
>> meanwhile, you can do this:
>>
>> WORKAROUND:
>>
>> 1. Uninstall the GLAD package (it doesn't work anyway):
>>
>>> remove.packages("GLAD")
>> Removing package(s) from 'C:\Users\hb\R\win-library\2.12'
>> (as 'lib' is unspecified)
>>
>>> library("GLAD")
>> Error in library("GLAD") : there is no package called 'GLAD'
>>
>> That should do it.  Let me know if it works for you.
>>
>> TECHNICAL DETAILS: It happens because the GNU Scientific Library (GSL)
>> is not installed on the system (hence the 'gsl' part of
>> 'libgsl-0.dll'). There is a hard-to-find note that you need GSL in
>> order to use the GLAD package, cf.
>> http://bioconductor.org/packages/release/bioc/html/GLAD.html.  There
>> exist 32-bit binaries of GSL at
>> http://gnuwin32.sourceforge.net/packages/gsl.htm.  Unfortunately, it
>> does not work for the 64-bit version of R on Windows 64-bit.  It works
>> if you do tricks an run the 32-bit version of R, but that is a rather
>> inconvenient workaround.
>>
>> /Henrik
>>
>>>
>>>
>>> Yan
>>>
>>> -----Original Message-----
>>> From: [hidden email]
>>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>>> Sent: 23 November 2010 18:50
>>> To: aroma-affymetrix
>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>>
>>> Hi.
>>>
>>> On Tue, Nov 23, 2010 at 10:05 AM, Yan Jiao <[hidden email]> wrote:
>>>>
>>>>
>>>> Dear all,
>>>>
>>>> I'm trying to do DNA segmentation,
>>>>
>>>> This is what I'm doing:
>>>>
>>>> ds <- doCRMAv1("Fockens_1", chipType="Mapping50K_Hind240",
>>> verbose=TRUE);
>>>>
>>>> ###this is done sucessfully
>>>>
>>>> # Segmentation
>>>>
>>>> cbs <- CbsModel(ds);
>>>>
>>>>
>>>>
>>>> I got error libgsl-0.dll is missing, I think it's using GLAD, but I'm
>>> trying
>>>> to use DNAcopy for segmentation.
>>>
>>> Is it really the case that you get that error when you do:
>>>
>>> cbs <- CbsModel(ds);
>>>
>>> or do you do anything else?  Is suspect you do something more.
>>>
>>> Also, after you got the error, could you cut'n'paste the verbose
>>> output including any error messages you get and send it to us?   Also,
>>> make sure to report what print(traceback()) gives immediate after
>>> getting the error.
>>>
>>> /Henrik
>>>
>>> PS. The 'GLAD' package may indeed be used regardless of segmentation
>>> method because it contains information about cytobands.
>>>
>>>>
>>>> How to change it?
>>>>
>>>>
>>>>
>>>> Many thanks
>>>>
>>>>
>>>>
>>>> yan
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> **********************************************************************
>>>>
>>>> This email and any files transmitted with it are confidential and
>>>>
>>>> intended solely for the use of the individual or entity to whom they
>>>>
>>>> are addressed. If you have received this email in error please notify
>>>>
>>>> the system manager ([hidden email]).
>>>>
>>>> **********************************************************************
>>>>
>>>>
>>>>
>>>> --
>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>> latest
>>>> version of the package, 2) to report the output of sessionInfo() and
>>>> traceback(), and 3) to post a complete code example.
>>>>
>>>>
>>>> You received this message because you are subscribed to the Google
>>> Groups
>>>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>>>> To post to this group, send email to [hidden email]
>>>> To unsubscribe and other options, go to
>>> http://www.aroma-project.org/forum/
>>>>
>>>
>>> --
>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>> latest version of the package, 2) to report the output of sessionInfo()
>>> and traceback(), and 3) to post a complete code example.
>>>
>>>
>>> You received this message because you are subscribed to the Google
>>> Groups "aroma.affymetrix" group with website
>>> http://www.aroma-project.org/.
>>> To post to this group, send email to [hidden email]
>>> To unsubscribe and other options, go to
>>> http://www.aroma-project.org/forum/
>>>
>>> --
>>> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
>>>
>>>
>>> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
>>> To post to this group, send email to [hidden email]
>>> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>>>
>>
>> --
>> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
>>
>>
>> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> To post to this group, send email to [hidden email]
>> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>>
>> --
>> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
>>
>>
>> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> To post to this group, send email to [hidden email]
>> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>>
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to [hidden email]
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>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
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RE: [aroma.affymetrix] libgsl-0.dll missing error

Yan Jiao
RE: [aroma.affymetrix] libgsl-0.dll missing error

Hi Henrik,

I did what you suggested:



> traceback()

13: stop(gettextf("package '%s' is not installed for 'arch=%s'",

        pkgname, r_arch), call. = FALSE, domain = NA)

12: testRversion(pkgInfo, package, pkgpath)

11: library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,

        warn.conflicts = warn.conflicts, keep.source = keep.source)

10: base::require(...)

9: require("Cairo")

8: findPngDevice.default(transparent = FALSE)

7: findPngDevice(transparent = FALSE)

6: plot.CopyNumberSegmentationModel(model, path = path, imageFormat = "png",

       plotband = plotband, arrays = arrays, ...)

5: plot(model, path = path, imageFormat = "png", plotband = plotband,

       arrays = arrays, ...)

4: writeGraphs.ChromosomeExplorer(this, arrays = arrays, chromosomes = chromosomes,

       zooms = zooms, ..., verbose = less(verbose))

3: writeGraphs(this, arrays = arrays, chromosomes = chromosomes,

       zooms = zooms, ..., verbose = less(verbose))

2: process.ChromosomeExplorer(ce.all, verbose = TRUE)

1: process(ce.all, verbose = TRUE)


> sessionInfo()

R version 2.11.0 (2010-04-22)

x86_64-pc-mingw32

locale:

[1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United Kingdom.1252    LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C                          

[5] LC_TIME=English_United Kingdom.1252   

attached base packages:

[1] stats     graphics  grDevices utils     datasets  methods   base    

other attached packages:

 [1] RColorBrewer_1.0-2     DNAcopy_1.22.1         preprocessCore_1.10.0  sfit_0.1.9             aroma.affymetrix_1.7.0 aroma.apd_0.1.7        affxparser_1.20.0    

 [8] R.huge_0.2.0           aroma.core_1.7.0       aroma.light_1.16.1     matrixStats_0.2.2      R.rsp_0.4.0            R.cache_0.3.0          R.filesets_0.9.0     

[15] digest_0.4.2           R.utils_1.5.3          R.oo_1.7.4             R.methodsS3_1.2.1    

loaded via a namespace (and not attached):

[1] tools_2.11.0

>

process(ce,chromosomes=c(1,8,17), verbose=-10)

Generating ChromosomeExplorer report...

 Setting up ChromosomeExplorer report files...

  Copying template files...

   Source path: C:/Users/rmhkyji/R/win64-library/2.11/aroma.core/reports/includes

   Destination path: reports/includes

  Copying template files...done

 Setting up ChromosomeExplorer report files...done

 Explorer output version: 3

 Compiling ChromosomeExplorer.onLoad.js.rsp...

  Source: C:/Users/rmhkyji/R/win64-library/2.11/aroma.core/reports/templates/rsp/ChromosomeExplorer3/ChromosomeExplorer.onLoad.js.rsp

  Output path: reports/Fockens_1/ACC,-XY,RMA,+300,A+B,FLN,-XY

  Scanning directories for available chip types...

   Detected chip types: Mapping50K_Hind240

  Scanning directories for available chip types...done

  Scanning image files for available zooms...

   Detected (or default) zooms: 1, 2, 4, 8, 16, 32, 64

  Scanning image files for available zooms...done

  Scanning directory for subdirectories...

   Detected (or default) sets: cbs

  Scanning directory for subdirectories...done

  Compiling RSP...

           member data.class dimension objectSize

   1    chipTypes  character         1        120

   2    chrLayers  character         0         40

   3 sampleLabels  character         3        240

   4 sampleLayers  character         0         40

   5      samples  character         3        240

   6         sets  character         1         96

   7        zooms    numeric         7         72

   Sample names:

   [1] "GSM255038" "GSM255039" "GSM255040"

   Full sample names:

   [1] "GSM255038,total" "GSM255039,total" "GSM255040,total"

  Compiling RSP...done

 Compiling ChromosomeExplorer.onLoad.js.rsp...done

Loading required package: Cairo

Error: package 'Cairo' is not installed for 'arch=x64'

Generating ChromosomeExplorer report...done




-----Original Message-----
From: [hidden email] [[hidden email]] On Behalf Of Henrik Bengtsson
Sent: 24 November 2010 16:50
To: aroma-affymetrix
Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error

Hi.

On Wed, Nov 24, 2010 at 8:10 AM, Yan Jiao <[hidden email]> wrote:

> Hi Henrik,

>

> Another question, I was trying to only do segmentation on 3 chromosomes, how should I do it, I tried:

> process(ce,chromosomes=c(1,8,17), verbose=TRUE);

>

> but got error message:

>

> Generating ChromosomeExplorer report...

> Loading required package: Cairo

> Error: package 'Cairo' is not installed for 'arch=x64'

> Generating ChromosomeExplorer report...done

Odd, because specifying a subset of chromosomes shouldn't be any

different from running all, as you did before.

So, there seem to be several packages that install on R 64-bit in

Windows, but when trying to use then fails.  The Cairo package is

actually "deprecated" (replaced with similar function builtin in R),

but we've kept support for backward compatibilities.  It seems like

you're facing these issues - and not that many people are running

64-bit Windows yet so you seem to be the one hitting the bumps.

What does traceback() give when you get the error?

What is your sessionInfo()?

Can you use process(ce,chromosomes=c(1,8,17), verbose=-10) in order to

narrow down where the error occurs.

/Henrik

>

>

> Many thanks

>

> yan

>

>

>

> -----Original Message-----

> From: [hidden email] [[hidden email]] On Behalf Of Henrik Bengtsson

> Sent: 24 November 2010 15:08

> To: aroma-affymetrix

> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error

>

> Hi,

>

> great.  Contrary to error messages, warnings are alright to get.

>

> /H

>

> On Wed, Nov 24, 2010 at 2:51 AM, Yan Jiao <[hidden email]> wrote:

>> Thank you Henrik,

>> It works now, but I got some warning:

>>

>> process(ce, verbose=TRUE);

>> Generating ChromosomeExplorer report...

>> Loading required package: Cairo

>> Generating ChromosomeExplorer report...done

>> [1] TRUE

>> Warning messages:

>> 1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :

>>  there is no package called 'Cairo'

>> 2: In method(static, ...) :

>>  Ghostscript not found. Searched directories: C:/gs, C:\Program Files/gs, /gs, C:\Program Files\Common Files/gs

>>

>> Are those warning messages serious? Could I ignore them?

>>

>>

>> Yan

>>

>> -----Original Message-----

>> From: [hidden email] [[hidden email]] On Behalf Of Henrik Bengtsson

>> Sent: 23 November 2010 21:53

>> To: aroma-affymetrix

>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error

>>

>> Hi.

>>

>> On Tue, Nov 23, 2010 at 11:51 AM, Yan Jiao <[hidden email]> wrote:

>>> Hi Henrik,

>>>

>>> Sorry, the error is after

>>> cbs <- CbsModel(ds);

>>> ce <- ChromosomeExplorer(cbs);

>>> process(ce, verbose=TRUE);

>>

>> Ok, now the error message makes a bit more sense (it was my suspicion

>> but I didn't want make guesses).

>>

>>>

>>>

>>> Generating ChromosomeExplorer report...

>>> Loading required package: Cairo

>>> <simpleError in inDL(x, as.logical(local), as.logical(now), ...): unable

>>> to load shared library

>>> 'C:/Users/rmhkyji/R/win64-library/2.11/GLAD/libs/x64/GLAD.dll':

>>>  LoadLibrary failure:  The specified module could not be found.

>>>

>>> And there  is a pop out window saying: The program can't start because

>>> libgsl-0.dll I smissing from your computer. Try reinstalling the program

>>> to fix this program.

>>

>> I can reproduce this on 64-bit Windows 7 - you get the same error if

>> you try library("GLAD").  It is because we utilize part of the GLAD

>> package, if and only if it is *installed*, and otherwise we turn to

>> backup solutions.  What happens here is that *GLAD is installed but

>> doesn't load*, which causes the error so that backup solutions doesn't

>> kick in.   In the next release I'll try to make sure the backup

>> solutions will also work when there is an error load GLAD.  In

>> meanwhile, you can do this:

>>

>> WORKAROUND:

>>

>> 1. Uninstall the GLAD package (it doesn't work anyway):

>>

>>> remove.packages("GLAD")

>> Removing package(s) from 'C:\Users\hb\R\win-library\2.12'

>> (as 'lib' is unspecified)

>>

>>> library("GLAD")

>> Error in library("GLAD") : there is no package called 'GLAD'

>>

>> That should do it.  Let me know if it works for you.

>>

>> TECHNICAL DETAILS: It happens because the GNU Scientific Library (GSL)

>> is not installed on the system (hence the 'gsl' part of

>> 'libgsl-0.dll'). There is a hard-to-find note that you need GSL in

>> order to use the GLAD package, cf.

>> http://bioconductor.org/packages/release/bioc/html/GLAD.html.  There

>> exist 32-bit binaries of GSL at

>> http://gnuwin32.sourceforge.net/packages/gsl.htm.  Unfortunately, it

>> does not work for the 64-bit version of R on Windows 64-bit.  It works

>> if you do tricks an run the 32-bit version of R, but that is a rather

>> inconvenient workaround.

>>

>> /Henrik

>>

>>>

>>>

>>> Yan

>>>

>>> -----Original Message-----

>>> From: [hidden email]

>>> [[hidden email]] On Behalf Of Henrik Bengtsson

>>> Sent: 23 November 2010 18:50

>>> To: aroma-affymetrix

>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error

>>>

>>> Hi.

>>>

>>> On Tue, Nov 23, 2010 at 10:05 AM, Yan Jiao <[hidden email]> wrote:

>>>>

>>>>

>>>> Dear all,

>>>>

>>>> I'm trying to do DNA segmentation,

>>>>

>>>> This is what I'm doing:

>>>>

>>>> ds <- doCRMAv1("Fockens_1", chipType="Mapping50K_Hind240",

>>> verbose=TRUE);

>>>>

>>>> ###this is done sucessfully

>>>>

>>>> # Segmentation

>>>>

>>>> cbs <- CbsModel(ds);

>>>>

>>>>

>>>>

>>>> I got error libgsl-0.dll is missing, I think it's using GLAD, but I'm

>>> trying

>>>> to use DNAcopy for segmentation.

>>>

>>> Is it really the case that you get that error when you do:

>>>

>>> cbs <- CbsModel(ds);

>>>

>>> or do you do anything else?  Is suspect you do something more.

>>>

>>> Also, after you got the error, could you cut'n'paste the verbose

>>> output including any error messages you get and send it to us?   Also,

>>> make sure to report what print(traceback()) gives immediate after

>>> getting the error.

>>>

>>> /Henrik

>>>

>>> PS. The 'GLAD' package may indeed be used regardless of segmentation

>>> method because it contains information about cytobands.

>>>

>>>>

>>>> How to change it?

>>>>

>>>>

>>>>

>>>> Many thanks

>>>>

>>>>

>>>>

>>>> yan

>>>>

>>>>

>>>>

>>>>

>>>>

>>>>

>>>>

>>>> **********************************************************************

>>>>

>>>> This email and any files transmitted with it are confidential and

>>>>

>>>> intended solely for the use of the individual or entity to whom they

>>>>

>>>> are addressed. If you have received this email in error please notify

>>>>

>>>> the system manager ([hidden email]).

>>>>

>>>> **********************************************************************

>>>>

>>>>

>>>>

>>>> --

>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the

>>> latest

>>>> version of the package, 2) to report the output of sessionInfo() and

>>>> traceback(), and 3) to post a complete code example.

>>>>

>>>>

>>>> You received this message because you are subscribed to the Google

>>> Groups

>>>> "aroma.affymetrix" group with website http://www.aroma-project.org/.

>>>> To post to this group, send email to [hidden email]

>>>> To unsubscribe and other options, go to

>>> http://www.aroma-project.org/forum/

>>>>

>>>

>>> --

>>> When reporting problems on aroma.affymetrix, make sure 1) to run the

>>> latest version of the package, 2) to report the output of sessionInfo()

>>> and traceback(), and 3) to post a complete code example.

>>>

>>>

>>> You received this message because you are subscribed to the Google

>>> Groups "aroma.affymetrix" group with website

>>> http://www.aroma-project.org/.

>>> To post to this group, send email to aroma-affymetrix@googlegroups.com

>>> To unsubscribe and other options, go to

>>> http://www.aroma-project.org/forum/

>>>

>>> --

>>> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.

>>>

>>>

>>> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.

>>> To post to this group, send email to aroma-[hidden email]

>>> To unsubscribe and other options, go to http://www.aroma-project.org/forum/

>>>

>>

>> --

>> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.

>>

>>

>> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.

>> To post to this group, send email to [hidden email]

>> To unsubscribe and other options, go to http://www.aroma-project.org/forum/

>>

>> --

>> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.

>>

>>

>> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.

>> To post to this group, send email to [hidden email]

>> To unsubscribe and other options, go to http://www.aroma-project.org/forum/

>>

>

> --

> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.

>

>

> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.

> To post to this group, send email to [hidden email]

> To unsubscribe and other options, go to http://www.aroma-project.org/forum/

>

> --

> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.

>

>

> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.

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Re: [aroma.affymetrix] libgsl-0.dll missing error

Henrik Bengtsson-4
Ok, after seing your sessionInfo();

You need to update to R v2.12.0, especially since you're on Windows
64-bit.  Lots of work have been done by R core people to support
Windows 64-bit on R v2.12.0 and beyond.  There is no shortcut to this.

Update aroma.affymetrix to v1.8.0, cf. http://aroma-project.org/install

Also, the Cairo package is not available for the 64-bit version of R
on Windows.  If you try install.packages("Cairo") on your Windows
machine, CRAN should report that package is not available.   Either
you have installed it by other means or it incorrectly installed on R
v2.11.0.

/Henrik


On Wed, Nov 24, 2010 at 8:58 AM, Yan Jiao <[hidden email]> wrote:

> Hi Henrik,
>
> I did what you suggested:
>
>> traceback()
>
> 13: stop(gettextf("package '%s' is not installed for 'arch=%s'",
>
>         pkgname, r_arch), call. = FALSE, domain = NA)
>
> 12: testRversion(pkgInfo, package, pkgpath)
>
> 11: library(package, lib.loc = lib.loc, character.only = TRUE,
> logical.return = TRUE,
>
>         warn.conflicts = warn.conflicts, keep.source = keep.source)
>
> 10: base::require(...)
>
> 9: require("Cairo")
>
> 8: findPngDevice.default(transparent = FALSE)
>
> 7: findPngDevice(transparent = FALSE)
>
> 6: plot.CopyNumberSegmentationModel(model, path = path, imageFormat = "png",
>
>        plotband = plotband, arrays = arrays, ...)
>
> 5: plot(model, path = path, imageFormat = "png", plotband = plotband,
>
>        arrays = arrays, ...)
>
> 4: writeGraphs.ChromosomeExplorer(this, arrays = arrays, chromosomes =
> chromosomes,
>
>        zooms = zooms, ..., verbose = less(verbose))
>
> 3: writeGraphs(this, arrays = arrays, chromosomes = chromosomes,
>
>        zooms = zooms, ..., verbose = less(verbose))
>
> 2: process.ChromosomeExplorer(ce.all, verbose = TRUE)
>
> 1: process(ce.all, verbose = TRUE)
>
>> sessionInfo()
>
> R version 2.11.0 (2010-04-22)
>
> x86_64-pc-mingw32
>
> locale:
>
> [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United
> Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
> LC_NUMERIC=C
>
> [5] LC_TIME=English_United Kingdom.1252
>
> attached base packages:
>
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>
>  [1] RColorBrewer_1.0-2     DNAcopy_1.22.1         preprocessCore_1.10.0
> sfit_0.1.9             aroma.affymetrix_1.7.0 aroma.apd_0.1.7
> affxparser_1.20.0
>
>  [8] R.huge_0.2.0           aroma.core_1.7.0       aroma.light_1.16.1
> matrixStats_0.2.2      R.rsp_0.4.0            R.cache_0.3.0
> R.filesets_0.9.0
>
> [15] digest_0.4.2           R.utils_1.5.3          R.oo_1.7.4
> R.methodsS3_1.2.1
>
> loaded via a namespace (and not attached):
>
> [1] tools_2.11.0
>
>>
>
> process(ce,chromosomes=c(1,8,17), verbose=-10)
>
> Generating ChromosomeExplorer report...
>
>  Setting up ChromosomeExplorer report files...
>
>   Copying template files...
>
>    Source path:
> C:/Users/rmhkyji/R/win64-library/2.11/aroma.core/reports/includes
>
>    Destination path: reports/includes
>
>   Copying template files...done
>
>  Setting up ChromosomeExplorer report files...done
>
>  Explorer output version: 3
>
>  Compiling ChromosomeExplorer.onLoad.js.rsp...
>
>   Source:
> C:/Users/rmhkyji/R/win64-library/2.11/aroma.core/reports/templates/rsp/ChromosomeExplorer3/ChromosomeExplorer.onLoad.js.rsp
>
>   Output path: reports/Fockens_1/ACC,-XY,RMA,+300,A+B,FLN,-XY
>
>   Scanning directories for available chip types...
>
>    Detected chip types: Mapping50K_Hind240
>
>   Scanning directories for available chip types...done
>
>   Scanning image files for available zooms...
>
>    Detected (or default) zooms: 1, 2, 4, 8, 16, 32, 64
>
>   Scanning image files for available zooms...done
>
>   Scanning directory for subdirectories...
>
>    Detected (or default) sets: cbs
>
>   Scanning directory for subdirectories...done
>
>   Compiling RSP...
>
>            member data.class dimension objectSize
>
>    1    chipTypes  character         1        120
>
>    2    chrLayers  character         0         40
>
>    3 sampleLabels  character         3        240
>
>    4 sampleLayers  character         0         40
>
>    5      samples  character         3        240
>
>    6         sets  character         1         96
>
>    7        zooms    numeric         7         72
>
>    Sample names:
>
>    [1] "GSM255038" "GSM255039" "GSM255040"
>
>    Full sample names:
>
>    [1] "GSM255038,total" "GSM255039,total" "GSM255040,total"
>
>   Compiling RSP...done
>
>  Compiling ChromosomeExplorer.onLoad.js.rsp...done
>
> Loading required package: Cairo
>
> Error: package 'Cairo' is not installed for 'arch=x64'
>
> Generating ChromosomeExplorer report...done
>
>
> -----Original Message-----
> From: [hidden email]
> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
> Sent: 24 November 2010 16:50
> To: aroma-affymetrix
> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>
> Hi.
>
> On Wed, Nov 24, 2010 at 8:10 AM, Yan Jiao <[hidden email]> wrote:
>
>> Hi Henrik,
>
>>
>
>> Another question, I was trying to only do segmentation on 3 chromosomes,
>> how should I do it, I tried:
>
>> process(ce,chromosomes=c(1,8,17), verbose=TRUE);
>
>>
>
>> but got error message:
>
>>
>
>> Generating ChromosomeExplorer report...
>
>> Loading required package: Cairo
>
>> Error: package 'Cairo' is not installed for 'arch=x64'
>
>> Generating ChromosomeExplorer report...done
>
> Odd, because specifying a subset of chromosomes shouldn't be any
>
> different from running all, as you did before.
>
> So, there seem to be several packages that install on R 64-bit in
>
> Windows, but when trying to use then fails.  The Cairo package is
>
> actually "deprecated" (replaced with similar function builtin in R),
>
> but we've kept support for backward compatibilities.  It seems like
>
> you're facing these issues - and not that many people are running
>
> 64-bit Windows yet so you seem to be the one hitting the bumps.
>
> What does traceback() give when you get the error?
>
> What is your sessionInfo()?
>
> Can you use process(ce,chromosomes=c(1,8,17), verbose=-10) in order to
>
> narrow down where the error occurs.
>
> /Henrik
>
>>
>
>>
>
>> Many thanks
>
>>
>
>> yan
>
>>
>
>>
>
>>
>
>> -----Original Message-----
>
>> From: [hidden email]
>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>
>> Sent: 24 November 2010 15:08
>
>> To: aroma-affymetrix
>
>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>
>>
>
>> Hi,
>
>>
>
>> great.  Contrary to error messages, warnings are alright to get.
>
>>
>
>> /H
>
>>
>
>> On Wed, Nov 24, 2010 at 2:51 AM, Yan Jiao <[hidden email]> wrote:
>
>>> Thank you Henrik,
>
>>> It works now, but I got some warning:
>
>>>
>
>>> process(ce, verbose=TRUE);
>
>>> Generating ChromosomeExplorer report...
>
>>> Loading required package: Cairo
>
>>> Generating ChromosomeExplorer report...done
>
>>> [1] TRUE
>
>>> Warning messages:
>
>>> 1: In library(package, lib.loc = lib.loc, character.only = TRUE,
>>> logical.return = TRUE,  :
>
>>>  there is no package called 'Cairo'
>
>>> 2: In method(static, ...) :
>
>>>  Ghostscript not found. Searched directories: C:/gs, C:\Program Files/gs,
>>> /gs, C:\Program Files\Common Files/gs
>
>>>
>
>>> Are those warning messages serious? Could I ignore them?
>
>>>
>
>>>
>
>>> Yan
>
>>>
>
>>> -----Original Message-----
>
>>> From: [hidden email]
>>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>
>>> Sent: 23 November 2010 21:53
>
>>> To: aroma-affymetrix
>
>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>
>>>
>
>>> Hi.
>
>>>
>
>>> On Tue, Nov 23, 2010 at 11:51 AM, Yan Jiao <[hidden email]> wrote:
>
>>>> Hi Henrik,
>
>>>>
>
>>>> Sorry, the error is after
>
>>>> cbs <- CbsModel(ds);
>
>>>> ce <- ChromosomeExplorer(cbs);
>
>>>> process(ce, verbose=TRUE);
>
>>>
>
>>> Ok, now the error message makes a bit more sense (it was my suspicion
>
>>> but I didn't want make guesses).
>
>>>
>
>>>>
>
>>>>
>
>>>> Generating ChromosomeExplorer report...
>
>>>> Loading required package: Cairo
>
>>>> <simpleError in inDL(x, as.logical(local), as.logical(now), ...): unable
>
>>>> to load shared library
>
>>>> 'C:/Users/rmhkyji/R/win64-library/2.11/GLAD/libs/x64/GLAD.dll':
>
>>>>  LoadLibrary failure:  The specified module could not be found.
>
>>>>
>
>>>> And there  is a pop out window saying: The program can't start because
>
>>>> libgsl-0.dll I smissing from your computer. Try reinstalling the program
>
>>>> to fix this program.
>
>>>
>
>>> I can reproduce this on 64-bit Windows 7 - you get the same error if
>
>>> you try library("GLAD").  It is because we utilize part of the GLAD
>
>>> package, if and only if it is *installed*, and otherwise we turn to
>
>>> backup solutions.  What happens here is that *GLAD is installed but
>
>>> doesn't load*, which causes the error so that backup solutions doesn't
>
>>> kick in.   In the next release I'll try to make sure the backup
>
>>> solutions will also work when there is an error load GLAD.  In
>
>>> meanwhile, you can do this:
>
>>>
>
>>> WORKAROUND:
>
>>>
>
>>> 1. Uninstall the GLAD package (it doesn't work anyway):
>
>>>
>
>>>> remove.packages("GLAD")
>
>>> Removing package(s) from 'C:\Users\hb\R\win-library\2.12'
>
>>> (as 'lib' is unspecified)
>
>>>
>
>>>> library("GLAD")
>
>>> Error in library("GLAD") : there is no package called 'GLAD'
>
>>>
>
>>> That should do it.  Let me know if it works for you.
>
>>>
>
>>> TECHNICAL DETAILS: It happens because the GNU Scientific Library (GSL)
>
>>> is not installed on the system (hence the 'gsl' part of
>
>>> 'libgsl-0.dll'). There is a hard-to-find note that you need GSL in
>
>>> order to use the GLAD package, cf.
>
>>> http://bioconductor.org/packages/release/bioc/html/GLAD.html.  There
>
>>> exist 32-bit binaries of GSL at
>
>>> http://gnuwin32.sourceforge.net/packages/gsl.htm.  Unfortunately, it
>
>>> does not work for the 64-bit version of R on Windows 64-bit.  It works
>
>>> if you do tricks an run the 32-bit version of R, but that is a rather
>
>>> inconvenient workaround.
>
>>>
>
>>> /Henrik
>
>>>
>
>>>>
>
>>>>
>
>>>> Yan
>
>>>>
>
>>>> -----Original Message-----
>
>>>> From: [hidden email]
>
>>>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>
>>>> Sent: 23 November 2010 18:50
>
>>>> To: aroma-affymetrix
>
>>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>
>>>>
>
>>>> Hi.
>
>>>>
>
>>>> On Tue, Nov 23, 2010 at 10:05 AM, Yan Jiao <[hidden email]> wrote:
>
>>>>>
>
>>>>>
>
>>>>> Dear all,
>
>>>>>
>
>>>>> I'm trying to do DNA segmentation,
>
>>>>>
>
>>>>> This is what I'm doing:
>
>>>>>
>
>>>>> ds <- doCRMAv1("Fockens_1", chipType="Mapping50K_Hind240",
>
>>>> verbose=TRUE);
>
>>>>>
>
>>>>> ###this is done sucessfully
>
>>>>>
>
>>>>> # Segmentation
>
>>>>>
>
>>>>> cbs <- CbsModel(ds);
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>> I got error libgsl-0.dll is missing, I think it's using GLAD, but I'm
>
>>>> trying
>
>>>>> to use DNAcopy for segmentation.
>
>>>>
>
>>>> Is it really the case that you get that error when you do:
>
>>>>
>
>>>> cbs <- CbsModel(ds);
>
>>>>
>
>>>> or do you do anything else?  Is suspect you do something more.
>
>>>>
>
>>>> Also, after you got the error, could you cut'n'paste the verbose
>
>>>> output including any error messages you get and send it to us?   Also,
>
>>>> make sure to report what print(traceback()) gives immediate after
>
>>>> getting the error.
>
>>>>
>
>>>> /Henrik
>
>>>>
>
>>>> PS. The 'GLAD' package may indeed be used regardless of segmentation
>
>>>> method because it contains information about cytobands.
>
>>>>
>
>>>>>
>
>>>>> How to change it?
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>> Many thanks
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>> yan
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>> **********************************************************************
>
>>>>>
>
>>>>> This email and any files transmitted with it are confidential and
>
>>>>>
>
>>>>> intended solely for the use of the individual or entity to whom they
>
>>>>>
>
>>>>> are addressed. If you have received this email in error please notify
>
>>>>>
>
>>>>> the system manager ([hidden email]).
>
>>>>>
>
>>>>> **********************************************************************
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>> --
>
>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>
>>>> latest
>
>>>>> version of the package, 2) to report the output of sessionInfo() and
>
>>>>> traceback(), and 3) to post a complete code example.
>
>>>>>
>
>>>>>
>
>>>>> You received this message because you are subscribed to the Google
>
>>>> Groups
>
>>>>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>
>>>>> To post to this group, send email to [hidden email]
>
>>>>> To unsubscribe and other options, go to
>
>>>> http://www.aroma-project.org/forum/
>
>>>>>
>
>>>>
>
>>>> --
>
>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>
>>>> latest version of the package, 2) to report the output of sessionInfo()
>
>>>> and traceback(), and 3) to post a complete code example.
>
>>>>
>
>>>>
>
>>>> You received this message because you are subscribed to the Google
>
>>>> Groups "aroma.affymetrix" group with website
>
>>>> http://www.aroma-project.org/.
>
>>>> To post to this group, send email to [hidden email]
>
>>>> To unsubscribe and other options, go to
>
>>>> http://www.aroma-project.org/forum/
>
>>>>
>
>>>> --
>
>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>> latest version of the package, 2) to report the output of sessionInfo() and
>>>> traceback(), and 3) to post a complete code example.
>
>>>>
>
>>>>
>
>>>> You received this message because you are subscribed to the Google
>>>> Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
>
>>>> To post to this group, send email to [hidden email]
>
>>>> To unsubscribe and other options, go to
>>>> http://www.aroma-project.org/forum/
>
>>>>
>
>>>
>
>>> --
>
>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>> latest version of the package, 2) to report the output of sessionInfo() and
>>> traceback(), and 3) to post a complete code example.
>
>>>
>
>>>
>
>>> You received this message because you are subscribed to the Google Groups
>>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>
>>> To post to this group, send email to [hidden email]
>
>>> To unsubscribe and other options, go to
>>> http://www.aroma-project.org/forum/
>
>>>
>
>>> --
>
>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>> latest version of the package, 2) to report the output of sessionInfo() and
>>> traceback(), and 3) to post a complete code example.
>
>>>
>
>>>
>
>>> You received this message because you are subscribed to the Google Groups
>>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>
>>> To post to this group, send email to [hidden email]
>
>>> To unsubscribe and other options, go to
>>> http://www.aroma-project.org/forum/
>
>>>
>
>>
>
>> --
>
>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>> latest version of the package, 2) to report the output of sessionInfo() and
>> traceback(), and 3) to post a complete code example.
>
>>
>
>>
>
>> You received this message because you are subscribed to the Google Groups
>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>
>> To post to this group, send email to [hidden email]
>
>> To unsubscribe and other options, go to
>> http://www.aroma-project.org/forum/
>
>>
>
>> --
>
>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>> latest version of the package, 2) to report the output of sessionInfo() and
>> traceback(), and 3) to post a complete code example.
>
>>
>
>>
>
>> You received this message because you are subscribed to the Google Groups
>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>
>> To post to this group, send email to [hidden email]
>
>> To unsubscribe and other options, go to
>> http://www.aroma-project.org/forum/
>
>>
>
> --
>
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>
> To post to this group, send email to [hidden email]
>
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to [hidden email]
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>

--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.


You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
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[aroma.affymetrix] DNAcopy parameter

Yan Jiao
Thanks Henrik,
I will update my R and aroma package,
Another question is what kind of parameters of aroma use for copy number segmentation, if using DNAcopy as the algorithm?

Many thanks

yan

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
Sent: 24 November 2010 17:06
To: aroma-affymetrix
Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error

Ok, after seing your sessionInfo();

You need to update to R v2.12.0, especially since you're on Windows
64-bit.  Lots of work have been done by R core people to support
Windows 64-bit on R v2.12.0 and beyond.  There is no shortcut to this.

Update aroma.affymetrix to v1.8.0, cf. http://aroma-project.org/install

Also, the Cairo package is not available for the 64-bit version of R
on Windows.  If you try install.packages("Cairo") on your Windows
machine, CRAN should report that package is not available.   Either
you have installed it by other means or it incorrectly installed on R
v2.11.0.

/Henrik


On Wed, Nov 24, 2010 at 8:58 AM, Yan Jiao <[hidden email]> wrote:

> Hi Henrik,
>
> I did what you suggested:
>
>> traceback()
>
> 13: stop(gettextf("package '%s' is not installed for 'arch=%s'",
>
>         pkgname, r_arch), call. = FALSE, domain = NA)
>
> 12: testRversion(pkgInfo, package, pkgpath)
>
> 11: library(package, lib.loc = lib.loc, character.only = TRUE,
> logical.return = TRUE,
>
>         warn.conflicts = warn.conflicts, keep.source = keep.source)
>
> 10: base::require(...)
>
> 9: require("Cairo")
>
> 8: findPngDevice.default(transparent = FALSE)
>
> 7: findPngDevice(transparent = FALSE)
>
> 6: plot.CopyNumberSegmentationModel(model, path = path, imageFormat = "png",
>
>        plotband = plotband, arrays = arrays, ...)
>
> 5: plot(model, path = path, imageFormat = "png", plotband = plotband,
>
>        arrays = arrays, ...)
>
> 4: writeGraphs.ChromosomeExplorer(this, arrays = arrays, chromosomes =
> chromosomes,
>
>        zooms = zooms, ..., verbose = less(verbose))
>
> 3: writeGraphs(this, arrays = arrays, chromosomes = chromosomes,
>
>        zooms = zooms, ..., verbose = less(verbose))
>
> 2: process.ChromosomeExplorer(ce.all, verbose = TRUE)
>
> 1: process(ce.all, verbose = TRUE)
>
>> sessionInfo()
>
> R version 2.11.0 (2010-04-22)
>
> x86_64-pc-mingw32
>
> locale:
>
> [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United
> Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
> LC_NUMERIC=C
>
> [5] LC_TIME=English_United Kingdom.1252
>
> attached base packages:
>
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>
>  [1] RColorBrewer_1.0-2     DNAcopy_1.22.1         preprocessCore_1.10.0
> sfit_0.1.9             aroma.affymetrix_1.7.0 aroma.apd_0.1.7
> affxparser_1.20.0
>
>  [8] R.huge_0.2.0           aroma.core_1.7.0       aroma.light_1.16.1
> matrixStats_0.2.2      R.rsp_0.4.0            R.cache_0.3.0
> R.filesets_0.9.0
>
> [15] digest_0.4.2           R.utils_1.5.3          R.oo_1.7.4
> R.methodsS3_1.2.1
>
> loaded via a namespace (and not attached):
>
> [1] tools_2.11.0
>
>>
>
> process(ce,chromosomes=c(1,8,17), verbose=-10)
>
> Generating ChromosomeExplorer report...
>
>  Setting up ChromosomeExplorer report files...
>
>   Copying template files...
>
>    Source path:
> C:/Users/rmhkyji/R/win64-library/2.11/aroma.core/reports/includes
>
>    Destination path: reports/includes
>
>   Copying template files...done
>
>  Setting up ChromosomeExplorer report files...done
>
>  Explorer output version: 3
>
>  Compiling ChromosomeExplorer.onLoad.js.rsp...
>
>   Source:
> C:/Users/rmhkyji/R/win64-library/2.11/aroma.core/reports/templates/rsp/ChromosomeExplorer3/ChromosomeExplorer.onLoad.js.rsp
>
>   Output path: reports/Fockens_1/ACC,-XY,RMA,+300,A+B,FLN,-XY
>
>   Scanning directories for available chip types...
>
>    Detected chip types: Mapping50K_Hind240
>
>   Scanning directories for available chip types...done
>
>   Scanning image files for available zooms...
>
>    Detected (or default) zooms: 1, 2, 4, 8, 16, 32, 64
>
>   Scanning image files for available zooms...done
>
>   Scanning directory for subdirectories...
>
>    Detected (or default) sets: cbs
>
>   Scanning directory for subdirectories...done
>
>   Compiling RSP...
>
>            member data.class dimension objectSize
>
>    1    chipTypes  character         1        120
>
>    2    chrLayers  character         0         40
>
>    3 sampleLabels  character         3        240
>
>    4 sampleLayers  character         0         40
>
>    5      samples  character         3        240
>
>    6         sets  character         1         96
>
>    7        zooms    numeric         7         72
>
>    Sample names:
>
>    [1] "GSM255038" "GSM255039" "GSM255040"
>
>    Full sample names:
>
>    [1] "GSM255038,total" "GSM255039,total" "GSM255040,total"
>
>   Compiling RSP...done
>
>  Compiling ChromosomeExplorer.onLoad.js.rsp...done
>
> Loading required package: Cairo
>
> Error: package 'Cairo' is not installed for 'arch=x64'
>
> Generating ChromosomeExplorer report...done
>
>
> -----Original Message-----
> From: [hidden email]
> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
> Sent: 24 November 2010 16:50
> To: aroma-affymetrix
> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>
> Hi.
>
> On Wed, Nov 24, 2010 at 8:10 AM, Yan Jiao <[hidden email]> wrote:
>
>> Hi Henrik,
>
>>
>
>> Another question, I was trying to only do segmentation on 3 chromosomes,
>> how should I do it, I tried:
>
>> process(ce,chromosomes=c(1,8,17), verbose=TRUE);
>
>>
>
>> but got error message:
>
>>
>
>> Generating ChromosomeExplorer report...
>
>> Loading required package: Cairo
>
>> Error: package 'Cairo' is not installed for 'arch=x64'
>
>> Generating ChromosomeExplorer report...done
>
> Odd, because specifying a subset of chromosomes shouldn't be any
>
> different from running all, as you did before.
>
> So, there seem to be several packages that install on R 64-bit in
>
> Windows, but when trying to use then fails.  The Cairo package is
>
> actually "deprecated" (replaced with similar function builtin in R),
>
> but we've kept support for backward compatibilities.  It seems like
>
> you're facing these issues - and not that many people are running
>
> 64-bit Windows yet so you seem to be the one hitting the bumps.
>
> What does traceback() give when you get the error?
>
> What is your sessionInfo()?
>
> Can you use process(ce,chromosomes=c(1,8,17), verbose=-10) in order to
>
> narrow down where the error occurs.
>
> /Henrik
>
>>
>
>>
>
>> Many thanks
>
>>
>
>> yan
>
>>
>
>>
>
>>
>
>> -----Original Message-----
>
>> From: [hidden email]
>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>
>> Sent: 24 November 2010 15:08
>
>> To: aroma-affymetrix
>
>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>
>>
>
>> Hi,
>
>>
>
>> great.  Contrary to error messages, warnings are alright to get.
>
>>
>
>> /H
>
>>
>
>> On Wed, Nov 24, 2010 at 2:51 AM, Yan Jiao <[hidden email]> wrote:
>
>>> Thank you Henrik,
>
>>> It works now, but I got some warning:
>
>>>
>
>>> process(ce, verbose=TRUE);
>
>>> Generating ChromosomeExplorer report...
>
>>> Loading required package: Cairo
>
>>> Generating ChromosomeExplorer report...done
>
>>> [1] TRUE
>
>>> Warning messages:
>
>>> 1: In library(package, lib.loc = lib.loc, character.only = TRUE,
>>> logical.return = TRUE,  :
>
>>>  there is no package called 'Cairo'
>
>>> 2: In method(static, ...) :
>
>>>  Ghostscript not found. Searched directories: C:/gs, C:\Program Files/gs,
>>> /gs, C:\Program Files\Common Files/gs
>
>>>
>
>>> Are those warning messages serious? Could I ignore them?
>
>>>
>
>>>
>
>>> Yan
>
>>>
>
>>> -----Original Message-----
>
>>> From: [hidden email]
>>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>
>>> Sent: 23 November 2010 21:53
>
>>> To: aroma-affymetrix
>
>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>
>>>
>
>>> Hi.
>
>>>
>
>>> On Tue, Nov 23, 2010 at 11:51 AM, Yan Jiao <[hidden email]> wrote:
>
>>>> Hi Henrik,
>
>>>>
>
>>>> Sorry, the error is after
>
>>>> cbs <- CbsModel(ds);
>
>>>> ce <- ChromosomeExplorer(cbs);
>
>>>> process(ce, verbose=TRUE);
>
>>>
>
>>> Ok, now the error message makes a bit more sense (it was my suspicion
>
>>> but I didn't want make guesses).
>
>>>
>
>>>>
>
>>>>
>
>>>> Generating ChromosomeExplorer report...
>
>>>> Loading required package: Cairo
>
>>>> <simpleError in inDL(x, as.logical(local), as.logical(now), ...): unable
>
>>>> to load shared library
>
>>>> 'C:/Users/rmhkyji/R/win64-library/2.11/GLAD/libs/x64/GLAD.dll':
>
>>>>  LoadLibrary failure:  The specified module could not be found.
>
>>>>
>
>>>> And there  is a pop out window saying: The program can't start because
>
>>>> libgsl-0.dll I smissing from your computer. Try reinstalling the program
>
>>>> to fix this program.
>
>>>
>
>>> I can reproduce this on 64-bit Windows 7 - you get the same error if
>
>>> you try library("GLAD").  It is because we utilize part of the GLAD
>
>>> package, if and only if it is *installed*, and otherwise we turn to
>
>>> backup solutions.  What happens here is that *GLAD is installed but
>
>>> doesn't load*, which causes the error so that backup solutions doesn't
>
>>> kick in.   In the next release I'll try to make sure the backup
>
>>> solutions will also work when there is an error load GLAD.  In
>
>>> meanwhile, you can do this:
>
>>>
>
>>> WORKAROUND:
>
>>>
>
>>> 1. Uninstall the GLAD package (it doesn't work anyway):
>
>>>
>
>>>> remove.packages("GLAD")
>
>>> Removing package(s) from 'C:\Users\hb\R\win-library\2.12'
>
>>> (as 'lib' is unspecified)
>
>>>
>
>>>> library("GLAD")
>
>>> Error in library("GLAD") : there is no package called 'GLAD'
>
>>>
>
>>> That should do it.  Let me know if it works for you.
>
>>>
>
>>> TECHNICAL DETAILS: It happens because the GNU Scientific Library (GSL)
>
>>> is not installed on the system (hence the 'gsl' part of
>
>>> 'libgsl-0.dll'). There is a hard-to-find note that you need GSL in
>
>>> order to use the GLAD package, cf.
>
>>> http://bioconductor.org/packages/release/bioc/html/GLAD.html.  There
>
>>> exist 32-bit binaries of GSL at
>
>>> http://gnuwin32.sourceforge.net/packages/gsl.htm.  Unfortunately, it
>
>>> does not work for the 64-bit version of R on Windows 64-bit.  It works
>
>>> if you do tricks an run the 32-bit version of R, but that is a rather
>
>>> inconvenient workaround.
>
>>>
>
>>> /Henrik
>
>>>
>
>>>>
>
>>>>
>
>>>> Yan
>
>>>>
>
>>>> -----Original Message-----
>
>>>> From: [hidden email]
>
>>>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>
>>>> Sent: 23 November 2010 18:50
>
>>>> To: aroma-affymetrix
>
>>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>
>>>>
>
>>>> Hi.
>
>>>>
>
>>>> On Tue, Nov 23, 2010 at 10:05 AM, Yan Jiao <[hidden email]> wrote:
>
>>>>>
>
>>>>>
>
>>>>> Dear all,
>
>>>>>
>
>>>>> I'm trying to do DNA segmentation,
>
>>>>>
>
>>>>> This is what I'm doing:
>
>>>>>
>
>>>>> ds <- doCRMAv1("Fockens_1", chipType="Mapping50K_Hind240",
>
>>>> verbose=TRUE);
>
>>>>>
>
>>>>> ###this is done sucessfully
>
>>>>>
>
>>>>> # Segmentation
>
>>>>>
>
>>>>> cbs <- CbsModel(ds);
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>> I got error libgsl-0.dll is missing, I think it's using GLAD, but I'm
>
>>>> trying
>
>>>>> to use DNAcopy for segmentation.
>
>>>>
>
>>>> Is it really the case that you get that error when you do:
>
>>>>
>
>>>> cbs <- CbsModel(ds);
>
>>>>
>
>>>> or do you do anything else?  Is suspect you do something more.
>
>>>>
>
>>>> Also, after you got the error, could you cut'n'paste the verbose
>
>>>> output including any error messages you get and send it to us?   Also,
>
>>>> make sure to report what print(traceback()) gives immediate after
>
>>>> getting the error.
>
>>>>
>
>>>> /Henrik
>
>>>>
>
>>>> PS. The 'GLAD' package may indeed be used regardless of segmentation
>
>>>> method because it contains information about cytobands.
>
>>>>
>
>>>>>
>
>>>>> How to change it?
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>> Many thanks
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>> yan
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>> **********************************************************************
>
>>>>>
>
>>>>> This email and any files transmitted with it are confidential and
>
>>>>>
>
>>>>> intended solely for the use of the individual or entity to whom they
>
>>>>>
>
>>>>> are addressed. If you have received this email in error please notify
>
>>>>>
>
>>>>> the system manager ([hidden email]).
>
>>>>>
>
>>>>> **********************************************************************
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>> --
>
>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>
>>>> latest
>
>>>>> version of the package, 2) to report the output of sessionInfo() and
>
>>>>> traceback(), and 3) to post a complete code example.
>
>>>>>
>
>>>>>
>
>>>>> You received this message because you are subscribed to the Google
>
>>>> Groups
>
>>>>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>
>>>>> To post to this group, send email to [hidden email]
>
>>>>> To unsubscribe and other options, go to
>
>>>> http://www.aroma-project.org/forum/
>
>>>>>
>
>>>>
>
>>>> --
>
>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>
>>>> latest version of the package, 2) to report the output of sessionInfo()
>
>>>> and traceback(), and 3) to post a complete code example.
>
>>>>
>
>>>>
>
>>>> You received this message because you are subscribed to the Google
>
>>>> Groups "aroma.affymetrix" group with website
>
>>>> http://www.aroma-project.org/.
>
>>>> To post to this group, send email to [hidden email]
>
>>>> To unsubscribe and other options, go to
>
>>>> http://www.aroma-project.org/forum/
>
>>>>
>
>>>> --
>
>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>> latest version of the package, 2) to report the output of sessionInfo() and
>>>> traceback(), and 3) to post a complete code example.
>
>>>>
>
>>>>
>
>>>> You received this message because you are subscribed to the Google
>>>> Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
>
>>>> To post to this group, send email to [hidden email]
>
>>>> To unsubscribe and other options, go to
>>>> http://www.aroma-project.org/forum/
>
>>>>
>
>>>
>
>>> --
>
>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>> latest version of the package, 2) to report the output of sessionInfo() and
>>> traceback(), and 3) to post a complete code example.
>
>>>
>
>>>
>
>>> You received this message because you are subscribed to the Google Groups
>>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>
>>> To post to this group, send email to [hidden email]
>
>>> To unsubscribe and other options, go to
>>> http://www.aroma-project.org/forum/
>
>>>
>
>>> --
>
>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>> latest version of the package, 2) to report the output of sessionInfo() and
>>> traceback(), and 3) to post a complete code example.
>
>>>
>
>>>
>
>>> You received this message because you are subscribed to the Google Groups
>>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>
>>> To post to this group, send email to [hidden email]
>
>>> To unsubscribe and other options, go to
>>> http://www.aroma-project.org/forum/
>
>>>
>
>>
>
>> --
>
>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>> latest version of the package, 2) to report the output of sessionInfo() and
>> traceback(), and 3) to post a complete code example.
>
>>
>
>>
>
>> You received this message because you are subscribed to the Google Groups
>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>
>> To post to this group, send email to [hidden email]
>
>> To unsubscribe and other options, go to
>> http://www.aroma-project.org/forum/
>
>>
>
>> --
>
>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>> latest version of the package, 2) to report the output of sessionInfo() and
>> traceback(), and 3) to post a complete code example.
>
>>
>
>>
>
>> You received this message because you are subscribed to the Google Groups
>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>
>> To post to this group, send email to [hidden email]
>
>> To unsubscribe and other options, go to
>> http://www.aroma-project.org/forum/
>
>>
>
> --
>
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>
> To post to this group, send email to [hidden email]
>
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
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> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>

--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.


You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
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[aroma.affymetrix] subselect samples for segmentation

Yan Jiao
In reply to this post by Henrik Bengtsson-4
Now it works after I update my R.
Another question is can I pass the sample names as a parameter to sub select the samples for segmentation? instead of removing the unwanted ones from data folder?

Many thanks

yan

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
Sent: 24 November 2010 17:06
To: aroma-affymetrix
Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error

Ok, after seing your sessionInfo();

You need to update to R v2.12.0, especially since you're on Windows
64-bit.  Lots of work have been done by R core people to support
Windows 64-bit on R v2.12.0 and beyond.  There is no shortcut to this.

Update aroma.affymetrix to v1.8.0, cf. http://aroma-project.org/install

Also, the Cairo package is not available for the 64-bit version of R
on Windows.  If you try install.packages("Cairo") on your Windows
machine, CRAN should report that package is not available.   Either
you have installed it by other means or it incorrectly installed on R
v2.11.0.

/Henrik


On Wed, Nov 24, 2010 at 8:58 AM, Yan Jiao <[hidden email]> wrote:

> Hi Henrik,
>
> I did what you suggested:
>
>> traceback()
>
> 13: stop(gettextf("package '%s' is not installed for 'arch=%s'",
>
>         pkgname, r_arch), call. = FALSE, domain = NA)
>
> 12: testRversion(pkgInfo, package, pkgpath)
>
> 11: library(package, lib.loc = lib.loc, character.only = TRUE,
> logical.return = TRUE,
>
>         warn.conflicts = warn.conflicts, keep.source = keep.source)
>
> 10: base::require(...)
>
> 9: require("Cairo")
>
> 8: findPngDevice.default(transparent = FALSE)
>
> 7: findPngDevice(transparent = FALSE)
>
> 6: plot.CopyNumberSegmentationModel(model, path = path, imageFormat = "png",
>
>        plotband = plotband, arrays = arrays, ...)
>
> 5: plot(model, path = path, imageFormat = "png", plotband = plotband,
>
>        arrays = arrays, ...)
>
> 4: writeGraphs.ChromosomeExplorer(this, arrays = arrays, chromosomes =
> chromosomes,
>
>        zooms = zooms, ..., verbose = less(verbose))
>
> 3: writeGraphs(this, arrays = arrays, chromosomes = chromosomes,
>
>        zooms = zooms, ..., verbose = less(verbose))
>
> 2: process.ChromosomeExplorer(ce.all, verbose = TRUE)
>
> 1: process(ce.all, verbose = TRUE)
>
>> sessionInfo()
>
> R version 2.11.0 (2010-04-22)
>
> x86_64-pc-mingw32
>
> locale:
>
> [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United
> Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
> LC_NUMERIC=C
>
> [5] LC_TIME=English_United Kingdom.1252
>
> attached base packages:
>
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>
>  [1] RColorBrewer_1.0-2     DNAcopy_1.22.1         preprocessCore_1.10.0
> sfit_0.1.9             aroma.affymetrix_1.7.0 aroma.apd_0.1.7
> affxparser_1.20.0
>
>  [8] R.huge_0.2.0           aroma.core_1.7.0       aroma.light_1.16.1
> matrixStats_0.2.2      R.rsp_0.4.0            R.cache_0.3.0
> R.filesets_0.9.0
>
> [15] digest_0.4.2           R.utils_1.5.3          R.oo_1.7.4
> R.methodsS3_1.2.1
>
> loaded via a namespace (and not attached):
>
> [1] tools_2.11.0
>
>>
>
> process(ce,chromosomes=c(1,8,17), verbose=-10)
>
> Generating ChromosomeExplorer report...
>
>  Setting up ChromosomeExplorer report files...
>
>   Copying template files...
>
>    Source path:
> C:/Users/rmhkyji/R/win64-library/2.11/aroma.core/reports/includes
>
>    Destination path: reports/includes
>
>   Copying template files...done
>
>  Setting up ChromosomeExplorer report files...done
>
>  Explorer output version: 3
>
>  Compiling ChromosomeExplorer.onLoad.js.rsp...
>
>   Source:
> C:/Users/rmhkyji/R/win64-library/2.11/aroma.core/reports/templates/rsp/ChromosomeExplorer3/ChromosomeExplorer.onLoad.js.rsp
>
>   Output path: reports/Fockens_1/ACC,-XY,RMA,+300,A+B,FLN,-XY
>
>   Scanning directories for available chip types...
>
>    Detected chip types: Mapping50K_Hind240
>
>   Scanning directories for available chip types...done
>
>   Scanning image files for available zooms...
>
>    Detected (or default) zooms: 1, 2, 4, 8, 16, 32, 64
>
>   Scanning image files for available zooms...done
>
>   Scanning directory for subdirectories...
>
>    Detected (or default) sets: cbs
>
>   Scanning directory for subdirectories...done
>
>   Compiling RSP...
>
>            member data.class dimension objectSize
>
>    1    chipTypes  character         1        120
>
>    2    chrLayers  character         0         40
>
>    3 sampleLabels  character         3        240
>
>    4 sampleLayers  character         0         40
>
>    5      samples  character         3        240
>
>    6         sets  character         1         96
>
>    7        zooms    numeric         7         72
>
>    Sample names:
>
>    [1] "GSM255038" "GSM255039" "GSM255040"
>
>    Full sample names:
>
>    [1] "GSM255038,total" "GSM255039,total" "GSM255040,total"
>
>   Compiling RSP...done
>
>  Compiling ChromosomeExplorer.onLoad.js.rsp...done
>
> Loading required package: Cairo
>
> Error: package 'Cairo' is not installed for 'arch=x64'
>
> Generating ChromosomeExplorer report...done
>
>
> -----Original Message-----
> From: [hidden email]
> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
> Sent: 24 November 2010 16:50
> To: aroma-affymetrix
> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>
> Hi.
>
> On Wed, Nov 24, 2010 at 8:10 AM, Yan Jiao <[hidden email]> wrote:
>
>> Hi Henrik,
>
>>
>
>> Another question, I was trying to only do segmentation on 3 chromosomes,
>> how should I do it, I tried:
>
>> process(ce,chromosomes=c(1,8,17), verbose=TRUE);
>
>>
>
>> but got error message:
>
>>
>
>> Generating ChromosomeExplorer report...
>
>> Loading required package: Cairo
>
>> Error: package 'Cairo' is not installed for 'arch=x64'
>
>> Generating ChromosomeExplorer report...done
>
> Odd, because specifying a subset of chromosomes shouldn't be any
>
> different from running all, as you did before.
>
> So, there seem to be several packages that install on R 64-bit in
>
> Windows, but when trying to use then fails.  The Cairo package is
>
> actually "deprecated" (replaced with similar function builtin in R),
>
> but we've kept support for backward compatibilities.  It seems like
>
> you're facing these issues - and not that many people are running
>
> 64-bit Windows yet so you seem to be the one hitting the bumps.
>
> What does traceback() give when you get the error?
>
> What is your sessionInfo()?
>
> Can you use process(ce,chromosomes=c(1,8,17), verbose=-10) in order to
>
> narrow down where the error occurs.
>
> /Henrik
>
>>
>
>>
>
>> Many thanks
>
>>
>
>> yan
>
>>
>
>>
>
>>
>
>> -----Original Message-----
>
>> From: [hidden email]
>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>
>> Sent: 24 November 2010 15:08
>
>> To: aroma-affymetrix
>
>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>
>>
>
>> Hi,
>
>>
>
>> great.  Contrary to error messages, warnings are alright to get.
>
>>
>
>> /H
>
>>
>
>> On Wed, Nov 24, 2010 at 2:51 AM, Yan Jiao <[hidden email]> wrote:
>
>>> Thank you Henrik,
>
>>> It works now, but I got some warning:
>
>>>
>
>>> process(ce, verbose=TRUE);
>
>>> Generating ChromosomeExplorer report...
>
>>> Loading required package: Cairo
>
>>> Generating ChromosomeExplorer report...done
>
>>> [1] TRUE
>
>>> Warning messages:
>
>>> 1: In library(package, lib.loc = lib.loc, character.only = TRUE,
>>> logical.return = TRUE,  :
>
>>>  there is no package called 'Cairo'
>
>>> 2: In method(static, ...) :
>
>>>  Ghostscript not found. Searched directories: C:/gs, C:\Program Files/gs,
>>> /gs, C:\Program Files\Common Files/gs
>
>>>
>
>>> Are those warning messages serious? Could I ignore them?
>
>>>
>
>>>
>
>>> Yan
>
>>>
>
>>> -----Original Message-----
>
>>> From: [hidden email]
>>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>
>>> Sent: 23 November 2010 21:53
>
>>> To: aroma-affymetrix
>
>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>
>>>
>
>>> Hi.
>
>>>
>
>>> On Tue, Nov 23, 2010 at 11:51 AM, Yan Jiao <[hidden email]> wrote:
>
>>>> Hi Henrik,
>
>>>>
>
>>>> Sorry, the error is after
>
>>>> cbs <- CbsModel(ds);
>
>>>> ce <- ChromosomeExplorer(cbs);
>
>>>> process(ce, verbose=TRUE);
>
>>>
>
>>> Ok, now the error message makes a bit more sense (it was my suspicion
>
>>> but I didn't want make guesses).
>
>>>
>
>>>>
>
>>>>
>
>>>> Generating ChromosomeExplorer report...
>
>>>> Loading required package: Cairo
>
>>>> <simpleError in inDL(x, as.logical(local), as.logical(now), ...): unable
>
>>>> to load shared library
>
>>>> 'C:/Users/rmhkyji/R/win64-library/2.11/GLAD/libs/x64/GLAD.dll':
>
>>>>  LoadLibrary failure:  The specified module could not be found.
>
>>>>
>
>>>> And there  is a pop out window saying: The program can't start because
>
>>>> libgsl-0.dll I smissing from your computer. Try reinstalling the program
>
>>>> to fix this program.
>
>>>
>
>>> I can reproduce this on 64-bit Windows 7 - you get the same error if
>
>>> you try library("GLAD").  It is because we utilize part of the GLAD
>
>>> package, if and only if it is *installed*, and otherwise we turn to
>
>>> backup solutions.  What happens here is that *GLAD is installed but
>
>>> doesn't load*, which causes the error so that backup solutions doesn't
>
>>> kick in.   In the next release I'll try to make sure the backup
>
>>> solutions will also work when there is an error load GLAD.  In
>
>>> meanwhile, you can do this:
>
>>>
>
>>> WORKAROUND:
>
>>>
>
>>> 1. Uninstall the GLAD package (it doesn't work anyway):
>
>>>
>
>>>> remove.packages("GLAD")
>
>>> Removing package(s) from 'C:\Users\hb\R\win-library\2.12'
>
>>> (as 'lib' is unspecified)
>
>>>
>
>>>> library("GLAD")
>
>>> Error in library("GLAD") : there is no package called 'GLAD'
>
>>>
>
>>> That should do it.  Let me know if it works for you.
>
>>>
>
>>> TECHNICAL DETAILS: It happens because the GNU Scientific Library (GSL)
>
>>> is not installed on the system (hence the 'gsl' part of
>
>>> 'libgsl-0.dll'). There is a hard-to-find note that you need GSL in
>
>>> order to use the GLAD package, cf.
>
>>> http://bioconductor.org/packages/release/bioc/html/GLAD.html.  There
>
>>> exist 32-bit binaries of GSL at
>
>>> http://gnuwin32.sourceforge.net/packages/gsl.htm.  Unfortunately, it
>
>>> does not work for the 64-bit version of R on Windows 64-bit.  It works
>
>>> if you do tricks an run the 32-bit version of R, but that is a rather
>
>>> inconvenient workaround.
>
>>>
>
>>> /Henrik
>
>>>
>
>>>>
>
>>>>
>
>>>> Yan
>
>>>>
>
>>>> -----Original Message-----
>
>>>> From: [hidden email]
>
>>>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>
>>>> Sent: 23 November 2010 18:50
>
>>>> To: aroma-affymetrix
>
>>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>
>>>>
>
>>>> Hi.
>
>>>>
>
>>>> On Tue, Nov 23, 2010 at 10:05 AM, Yan Jiao <[hidden email]> wrote:
>
>>>>>
>
>>>>>
>
>>>>> Dear all,
>
>>>>>
>
>>>>> I'm trying to do DNA segmentation,
>
>>>>>
>
>>>>> This is what I'm doing:
>
>>>>>
>
>>>>> ds <- doCRMAv1("Fockens_1", chipType="Mapping50K_Hind240",
>
>>>> verbose=TRUE);
>
>>>>>
>
>>>>> ###this is done sucessfully
>
>>>>>
>
>>>>> # Segmentation
>
>>>>>
>
>>>>> cbs <- CbsModel(ds);
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>> I got error libgsl-0.dll is missing, I think it's using GLAD, but I'm
>
>>>> trying
>
>>>>> to use DNAcopy for segmentation.
>
>>>>
>
>>>> Is it really the case that you get that error when you do:
>
>>>>
>
>>>> cbs <- CbsModel(ds);
>
>>>>
>
>>>> or do you do anything else?  Is suspect you do something more.
>
>>>>
>
>>>> Also, after you got the error, could you cut'n'paste the verbose
>
>>>> output including any error messages you get and send it to us?   Also,
>
>>>> make sure to report what print(traceback()) gives immediate after
>
>>>> getting the error.
>
>>>>
>
>>>> /Henrik
>
>>>>
>
>>>> PS. The 'GLAD' package may indeed be used regardless of segmentation
>
>>>> method because it contains information about cytobands.
>
>>>>
>
>>>>>
>
>>>>> How to change it?
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>> Many thanks
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>> yan
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>> **********************************************************************
>
>>>>>
>
>>>>> This email and any files transmitted with it are confidential and
>
>>>>>
>
>>>>> intended solely for the use of the individual or entity to whom they
>
>>>>>
>
>>>>> are addressed. If you have received this email in error please notify
>
>>>>>
>
>>>>> the system manager ([hidden email]).
>
>>>>>
>
>>>>> **********************************************************************
>
>>>>>
>
>>>>>
>
>>>>>
>
>>>>> --
>
>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>
>>>> latest
>
>>>>> version of the package, 2) to report the output of sessionInfo() and
>
>>>>> traceback(), and 3) to post a complete code example.
>
>>>>>
>
>>>>>
>
>>>>> You received this message because you are subscribed to the Google
>
>>>> Groups
>
>>>>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>
>>>>> To post to this group, send email to [hidden email]
>
>>>>> To unsubscribe and other options, go to
>
>>>> http://www.aroma-project.org/forum/
>
>>>>>
>
>>>>
>
>>>> --
>
>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>
>>>> latest version of the package, 2) to report the output of sessionInfo()
>
>>>> and traceback(), and 3) to post a complete code example.
>
>>>>
>
>>>>
>
>>>> You received this message because you are subscribed to the Google
>
>>>> Groups "aroma.affymetrix" group with website
>
>>>> http://www.aroma-project.org/.
>
>>>> To post to this group, send email to [hidden email]
>
>>>> To unsubscribe and other options, go to
>
>>>> http://www.aroma-project.org/forum/
>
>>>>
>
>>>> --
>
>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>> latest version of the package, 2) to report the output of sessionInfo() and
>>>> traceback(), and 3) to post a complete code example.
>
>>>>
>
>>>>
>
>>>> You received this message because you are subscribed to the Google
>>>> Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
>
>>>> To post to this group, send email to [hidden email]
>
>>>> To unsubscribe and other options, go to
>>>> http://www.aroma-project.org/forum/
>
>>>>
>
>>>
>
>>> --
>
>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>> latest version of the package, 2) to report the output of sessionInfo() and
>>> traceback(), and 3) to post a complete code example.
>
>>>
>
>>>
>
>>> You received this message because you are subscribed to the Google Groups
>>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>
>>> To post to this group, send email to [hidden email]
>
>>> To unsubscribe and other options, go to
>>> http://www.aroma-project.org/forum/
>
>>>
>
>>> --
>
>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>> latest version of the package, 2) to report the output of sessionInfo() and
>>> traceback(), and 3) to post a complete code example.
>
>>>
>
>>>
>
>>> You received this message because you are subscribed to the Google Groups
>>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>
>>> To post to this group, send email to [hidden email]
>
>>> To unsubscribe and other options, go to
>>> http://www.aroma-project.org/forum/
>
>>>
>
>>
>
>> --
>
>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>> latest version of the package, 2) to report the output of sessionInfo() and
>> traceback(), and 3) to post a complete code example.
>
>>
>
>>
>
>> You received this message because you are subscribed to the Google Groups
>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>
>> To post to this group, send email to [hidden email]
>
>> To unsubscribe and other options, go to
>> http://www.aroma-project.org/forum/
>
>>
>
>> --
>
>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>> latest version of the package, 2) to report the output of sessionInfo() and
>> traceback(), and 3) to post a complete code example.
>
>>
>
>>
>
>> You received this message because you are subscribed to the Google Groups
>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>
>> To post to this group, send email to [hidden email]
>
>> To unsubscribe and other options, go to
>> http://www.aroma-project.org/forum/
>
>>
>
> --
>
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>
> To post to this group, send email to [hidden email]
>
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
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>

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When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.


You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
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Re: [aroma.affymetrix] subselect samples for segmentation

Pierre Neuvial
Hi Yan,

You're right: removing files manually from data folders generated by
aroma.* is not a good idea.  This is can be done directly within R
using the methods provided by the package.

In your case, I think you were doing :

cbs <- CbsModel(ds);
ce <- ChromosomeExplorer(cbs);
process(ce, chromosomes=c(1,8,17), verbose=TRUE);

To run the segmentation on the first two samples, you can do

process(ce, arrays=c(1,2), chromosomes=c(1,8,17), verbose=TRUE);

If you want to specify the *names* of samples to be segmented, you can use

idxs <- indexOf(ce, sampleNames);
process(ce, arrays=idxs, chromosomes=c(1,8,17), verbose=TRUE);

where 'sampleNames' is a vector of sample names.

More generally, one can use the 'extract' method on any set of data files, e.g.

ds <- doCRMAv1("Fockens_1", chipType="Mapping50K_Hind240", verbose=TRUE);
idxs <- indexOf(ce, sampleNames);
dsSub <- extract(ds, idxs);

Hope this helps.

Pierre



On Thu, Nov 25, 2010 at 3:35 PM, Yan Jiao <[hidden email]> wrote:

> Now it works after I update my R.
> Another question is can I pass the sample names as a parameter to sub select the samples for segmentation? instead of removing the unwanted ones from data folder?
>
> Many thanks
>
> yan
>
> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
> Sent: 24 November 2010 17:06
> To: aroma-affymetrix
> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>
> Ok, after seing your sessionInfo();
>
> You need to update to R v2.12.0, especially since you're on Windows
> 64-bit.  Lots of work have been done by R core people to support
> Windows 64-bit on R v2.12.0 and beyond.  There is no shortcut to this.
>
> Update aroma.affymetrix to v1.8.0, cf. http://aroma-project.org/install
>
> Also, the Cairo package is not available for the 64-bit version of R
> on Windows.  If you try install.packages("Cairo") on your Windows
> machine, CRAN should report that package is not available.   Either
> you have installed it by other means or it incorrectly installed on R
> v2.11.0.
>
> /Henrik
>
>
> On Wed, Nov 24, 2010 at 8:58 AM, Yan Jiao <[hidden email]> wrote:
>> Hi Henrik,
>>
>> I did what you suggested:
>>
>>> traceback()
>>
>> 13: stop(gettextf("package '%s' is not installed for 'arch=%s'",
>>
>>         pkgname, r_arch), call. = FALSE, domain = NA)
>>
>> 12: testRversion(pkgInfo, package, pkgpath)
>>
>> 11: library(package, lib.loc = lib.loc, character.only = TRUE,
>> logical.return = TRUE,
>>
>>         warn.conflicts = warn.conflicts, keep.source = keep.source)
>>
>> 10: base::require(...)
>>
>> 9: require("Cairo")
>>
>> 8: findPngDevice.default(transparent = FALSE)
>>
>> 7: findPngDevice(transparent = FALSE)
>>
>> 6: plot.CopyNumberSegmentationModel(model, path = path, imageFormat = "png",
>>
>>        plotband = plotband, arrays = arrays, ...)
>>
>> 5: plot(model, path = path, imageFormat = "png", plotband = plotband,
>>
>>        arrays = arrays, ...)
>>
>> 4: writeGraphs.ChromosomeExplorer(this, arrays = arrays, chromosomes =
>> chromosomes,
>>
>>        zooms = zooms, ..., verbose = less(verbose))
>>
>> 3: writeGraphs(this, arrays = arrays, chromosomes = chromosomes,
>>
>>        zooms = zooms, ..., verbose = less(verbose))
>>
>> 2: process.ChromosomeExplorer(ce.all, verbose = TRUE)
>>
>> 1: process(ce.all, verbose = TRUE)
>>
>>> sessionInfo()
>>
>> R version 2.11.0 (2010-04-22)
>>
>> x86_64-pc-mingw32
>>
>> locale:
>>
>> [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United
>> Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
>> LC_NUMERIC=C
>>
>> [5] LC_TIME=English_United Kingdom.1252
>>
>> attached base packages:
>>
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>>
>>  [1] RColorBrewer_1.0-2     DNAcopy_1.22.1         preprocessCore_1.10.0
>> sfit_0.1.9             aroma.affymetrix_1.7.0 aroma.apd_0.1.7
>> affxparser_1.20.0
>>
>>  [8] R.huge_0.2.0           aroma.core_1.7.0       aroma.light_1.16.1
>> matrixStats_0.2.2      R.rsp_0.4.0            R.cache_0.3.0
>> R.filesets_0.9.0
>>
>> [15] digest_0.4.2           R.utils_1.5.3          R.oo_1.7.4
>> R.methodsS3_1.2.1
>>
>> loaded via a namespace (and not attached):
>>
>> [1] tools_2.11.0
>>
>>>
>>
>> process(ce,chromosomes=c(1,8,17), verbose=-10)
>>
>> Generating ChromosomeExplorer report...
>>
>>  Setting up ChromosomeExplorer report files...
>>
>>   Copying template files...
>>
>>    Source path:
>> C:/Users/rmhkyji/R/win64-library/2.11/aroma.core/reports/includes
>>
>>    Destination path: reports/includes
>>
>>   Copying template files...done
>>
>>  Setting up ChromosomeExplorer report files...done
>>
>>  Explorer output version: 3
>>
>>  Compiling ChromosomeExplorer.onLoad.js.rsp...
>>
>>   Source:
>> C:/Users/rmhkyji/R/win64-library/2.11/aroma.core/reports/templates/rsp/ChromosomeExplorer3/ChromosomeExplorer.onLoad.js.rsp
>>
>>   Output path: reports/Fockens_1/ACC,-XY,RMA,+300,A+B,FLN,-XY
>>
>>   Scanning directories for available chip types...
>>
>>    Detected chip types: Mapping50K_Hind240
>>
>>   Scanning directories for available chip types...done
>>
>>   Scanning image files for available zooms...
>>
>>    Detected (or default) zooms: 1, 2, 4, 8, 16, 32, 64
>>
>>   Scanning image files for available zooms...done
>>
>>   Scanning directory for subdirectories...
>>
>>    Detected (or default) sets: cbs
>>
>>   Scanning directory for subdirectories...done
>>
>>   Compiling RSP...
>>
>>            member data.class dimension objectSize
>>
>>    1    chipTypes  character         1        120
>>
>>    2    chrLayers  character         0         40
>>
>>    3 sampleLabels  character         3        240
>>
>>    4 sampleLayers  character         0         40
>>
>>    5      samples  character         3        240
>>
>>    6         sets  character         1         96
>>
>>    7        zooms    numeric         7         72
>>
>>    Sample names:
>>
>>    [1] "GSM255038" "GSM255039" "GSM255040"
>>
>>    Full sample names:
>>
>>    [1] "GSM255038,total" "GSM255039,total" "GSM255040,total"
>>
>>   Compiling RSP...done
>>
>>  Compiling ChromosomeExplorer.onLoad.js.rsp...done
>>
>> Loading required package: Cairo
>>
>> Error: package 'Cairo' is not installed for 'arch=x64'
>>
>> Generating ChromosomeExplorer report...done
>>
>>
>> -----Original Message-----
>> From: [hidden email]
>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>> Sent: 24 November 2010 16:50
>> To: aroma-affymetrix
>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>
>> Hi.
>>
>> On Wed, Nov 24, 2010 at 8:10 AM, Yan Jiao <[hidden email]> wrote:
>>
>>> Hi Henrik,
>>
>>>
>>
>>> Another question, I was trying to only do segmentation on 3 chromosomes,
>>> how should I do it, I tried:
>>
>>> process(ce,chromosomes=c(1,8,17), verbose=TRUE);
>>
>>>
>>
>>> but got error message:
>>
>>>
>>
>>> Generating ChromosomeExplorer report...
>>
>>> Loading required package: Cairo
>>
>>> Error: package 'Cairo' is not installed for 'arch=x64'
>>
>>> Generating ChromosomeExplorer report...done
>>
>> Odd, because specifying a subset of chromosomes shouldn't be any
>>
>> different from running all, as you did before.
>>
>> So, there seem to be several packages that install on R 64-bit in
>>
>> Windows, but when trying to use then fails.  The Cairo package is
>>
>> actually "deprecated" (replaced with similar function builtin in R),
>>
>> but we've kept support for backward compatibilities.  It seems like
>>
>> you're facing these issues - and not that many people are running
>>
>> 64-bit Windows yet so you seem to be the one hitting the bumps.
>>
>> What does traceback() give when you get the error?
>>
>> What is your sessionInfo()?
>>
>> Can you use process(ce,chromosomes=c(1,8,17), verbose=-10) in order to
>>
>> narrow down where the error occurs.
>>
>> /Henrik
>>
>>>
>>
>>>
>>
>>> Many thanks
>>
>>>
>>
>>> yan
>>
>>>
>>
>>>
>>
>>>
>>
>>> -----Original Message-----
>>
>>> From: [hidden email]
>>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>>
>>> Sent: 24 November 2010 15:08
>>
>>> To: aroma-affymetrix
>>
>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>
>>>
>>
>>> Hi,
>>
>>>
>>
>>> great.  Contrary to error messages, warnings are alright to get.
>>
>>>
>>
>>> /H
>>
>>>
>>
>>> On Wed, Nov 24, 2010 at 2:51 AM, Yan Jiao <[hidden email]> wrote:
>>
>>>> Thank you Henrik,
>>
>>>> It works now, but I got some warning:
>>
>>>>
>>
>>>> process(ce, verbose=TRUE);
>>
>>>> Generating ChromosomeExplorer report...
>>
>>>> Loading required package: Cairo
>>
>>>> Generating ChromosomeExplorer report...done
>>
>>>> [1] TRUE
>>
>>>> Warning messages:
>>
>>>> 1: In library(package, lib.loc = lib.loc, character.only = TRUE,
>>>> logical.return = TRUE,  :
>>
>>>>  there is no package called 'Cairo'
>>
>>>> 2: In method(static, ...) :
>>
>>>>  Ghostscript not found. Searched directories: C:/gs, C:\Program Files/gs,
>>>> /gs, C:\Program Files\Common Files/gs
>>
>>>>
>>
>>>> Are those warning messages serious? Could I ignore them?
>>
>>>>
>>
>>>>
>>
>>>> Yan
>>
>>>>
>>
>>>> -----Original Message-----
>>
>>>> From: [hidden email]
>>>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>>
>>>> Sent: 23 November 2010 21:53
>>
>>>> To: aroma-affymetrix
>>
>>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>
>>>>
>>
>>>> Hi.
>>
>>>>
>>
>>>> On Tue, Nov 23, 2010 at 11:51 AM, Yan Jiao <[hidden email]> wrote:
>>
>>>>> Hi Henrik,
>>
>>>>>
>>
>>>>> Sorry, the error is after
>>
>>>>> cbs <- CbsModel(ds);
>>
>>>>> ce <- ChromosomeExplorer(cbs);
>>
>>>>> process(ce, verbose=TRUE);
>>
>>>>
>>
>>>> Ok, now the error message makes a bit more sense (it was my suspicion
>>
>>>> but I didn't want make guesses).
>>
>>>>
>>
>>>>>
>>
>>>>>
>>
>>>>> Generating ChromosomeExplorer report...
>>
>>>>> Loading required package: Cairo
>>
>>>>> <simpleError in inDL(x, as.logical(local), as.logical(now), ...): unable
>>
>>>>> to load shared library
>>
>>>>> 'C:/Users/rmhkyji/R/win64-library/2.11/GLAD/libs/x64/GLAD.dll':
>>
>>>>>  LoadLibrary failure:  The specified module could not be found.
>>
>>>>>
>>
>>>>> And there  is a pop out window saying: The program can't start because
>>
>>>>> libgsl-0.dll I smissing from your computer. Try reinstalling the program
>>
>>>>> to fix this program.
>>
>>>>
>>
>>>> I can reproduce this on 64-bit Windows 7 - you get the same error if
>>
>>>> you try library("GLAD").  It is because we utilize part of the GLAD
>>
>>>> package, if and only if it is *installed*, and otherwise we turn to
>>
>>>> backup solutions.  What happens here is that *GLAD is installed but
>>
>>>> doesn't load*, which causes the error so that backup solutions doesn't
>>
>>>> kick in.   In the next release I'll try to make sure the backup
>>
>>>> solutions will also work when there is an error load GLAD.  In
>>
>>>> meanwhile, you can do this:
>>
>>>>
>>
>>>> WORKAROUND:
>>
>>>>
>>
>>>> 1. Uninstall the GLAD package (it doesn't work anyway):
>>
>>>>
>>
>>>>> remove.packages("GLAD")
>>
>>>> Removing package(s) from 'C:\Users\hb\R\win-library\2.12'
>>
>>>> (as 'lib' is unspecified)
>>
>>>>
>>
>>>>> library("GLAD")
>>
>>>> Error in library("GLAD") : there is no package called 'GLAD'
>>
>>>>
>>
>>>> That should do it.  Let me know if it works for you.
>>
>>>>
>>
>>>> TECHNICAL DETAILS: It happens because the GNU Scientific Library (GSL)
>>
>>>> is not installed on the system (hence the 'gsl' part of
>>
>>>> 'libgsl-0.dll'). There is a hard-to-find note that you need GSL in
>>
>>>> order to use the GLAD package, cf.
>>
>>>> http://bioconductor.org/packages/release/bioc/html/GLAD.html.  There
>>
>>>> exist 32-bit binaries of GSL at
>>
>>>> http://gnuwin32.sourceforge.net/packages/gsl.htm.  Unfortunately, it
>>
>>>> does not work for the 64-bit version of R on Windows 64-bit.  It works
>>
>>>> if you do tricks an run the 32-bit version of R, but that is a rather
>>
>>>> inconvenient workaround.
>>
>>>>
>>
>>>> /Henrik
>>
>>>>
>>
>>>>>
>>
>>>>>
>>
>>>>> Yan
>>
>>>>>
>>
>>>>> -----Original Message-----
>>
>>>>> From: [hidden email]
>>
>>>>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>>
>>>>> Sent: 23 November 2010 18:50
>>
>>>>> To: aroma-affymetrix
>>
>>>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>
>>>>>
>>
>>>>> Hi.
>>
>>>>>
>>
>>>>> On Tue, Nov 23, 2010 at 10:05 AM, Yan Jiao <[hidden email]> wrote:
>>
>>>>>>
>>
>>>>>>
>>
>>>>>> Dear all,
>>
>>>>>>
>>
>>>>>> I'm trying to do DNA segmentation,
>>
>>>>>>
>>
>>>>>> This is what I'm doing:
>>
>>>>>>
>>
>>>>>> ds <- doCRMAv1("Fockens_1", chipType="Mapping50K_Hind240",
>>
>>>>> verbose=TRUE);
>>
>>>>>>
>>
>>>>>> ###this is done sucessfully
>>
>>>>>>
>>
>>>>>> # Segmentation
>>
>>>>>>
>>
>>>>>> cbs <- CbsModel(ds);
>>
>>>>>>
>>
>>>>>>
>>
>>>>>>
>>
>>>>>> I got error libgsl-0.dll is missing, I think it's using GLAD, but I'm
>>
>>>>> trying
>>
>>>>>> to use DNAcopy for segmentation.
>>
>>>>>
>>
>>>>> Is it really the case that you get that error when you do:
>>
>>>>>
>>
>>>>> cbs <- CbsModel(ds);
>>
>>>>>
>>
>>>>> or do you do anything else?  Is suspect you do something more.
>>
>>>>>
>>
>>>>> Also, after you got the error, could you cut'n'paste the verbose
>>
>>>>> output including any error messages you get and send it to us?   Also,
>>
>>>>> make sure to report what print(traceback()) gives immediate after
>>
>>>>> getting the error.
>>
>>>>>
>>
>>>>> /Henrik
>>
>>>>>
>>
>>>>> PS. The 'GLAD' package may indeed be used regardless of segmentation
>>
>>>>> method because it contains information about cytobands.
>>
>>>>>
>>
>>>>>>
>>
>>>>>> How to change it?
>>
>>>>>>
>>
>>>>>>
>>
>>>>>>
>>
>>>>>> Many thanks
>>
>>>>>>
>>
>>>>>>
>>
>>>>>>
>>
>>>>>> yan
>>
>>>>>>
>>
>>>>>>
>>
>>>>>>
>>
>>>>>>
>>
>>>>>>
>>
>>>>>>
>>
>>>>>>
>>
>>>>>> **********************************************************************
>>
>>>>>>
>>
>>>>>> This email and any files transmitted with it are confidential and
>>
>>>>>>
>>
>>>>>> intended solely for the use of the individual or entity to whom they
>>
>>>>>>
>>
>>>>>> are addressed. If you have received this email in error please notify
>>
>>>>>>
>>
>>>>>> the system manager ([hidden email]).
>>
>>>>>>
>>
>>>>>> **********************************************************************
>>
>>>>>>
>>
>>>>>>
>>
>>>>>>
>>
>>>>>> --
>>
>>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>
>>>>> latest
>>
>>>>>> version of the package, 2) to report the output of sessionInfo() and
>>
>>>>>> traceback(), and 3) to post a complete code example.
>>
>>>>>>
>>
>>>>>>
>>
>>>>>> You received this message because you are subscribed to the Google
>>
>>>>> Groups
>>
>>>>>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>>
>>>>>> To post to this group, send email to [hidden email]
>>
>>>>>> To unsubscribe and other options, go to
>>
>>>>> http://www.aroma-project.org/forum/
>>
>>>>>>
>>
>>>>>
>>
>>>>> --
>>
>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>
>>>>> latest version of the package, 2) to report the output of sessionInfo()
>>
>>>>> and traceback(), and 3) to post a complete code example.
>>
>>>>>
>>
>>>>>
>>
>>>>> You received this message because you are subscribed to the Google
>>
>>>>> Groups "aroma.affymetrix" group with website
>>
>>>>> http://www.aroma-project.org/.
>>
>>>>> To post to this group, send email to [hidden email]
>>
>>>>> To unsubscribe and other options, go to
>>
>>>>> http://www.aroma-project.org/forum/
>>
>>>>>
>>
>>>>> --
>>
>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>>> latest version of the package, 2) to report the output of sessionInfo() and
>>>>> traceback(), and 3) to post a complete code example.
>>
>>>>>
>>
>>>>>
>>
>>>>> You received this message because you are subscribed to the Google
>>>>> Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
>>
>>>>> To post to this group, send email to [hidden email]
>>
>>>>> To unsubscribe and other options, go to
>>>>> http://www.aroma-project.org/forum/
>>
>>>>>
>>
>>>>
>>
>>>> --
>>
>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>> latest version of the package, 2) to report the output of sessionInfo() and
>>>> traceback(), and 3) to post a complete code example.
>>
>>>>
>>
>>>>
>>
>>>> You received this message because you are subscribed to the Google Groups
>>>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>>
>>>> To post to this group, send email to [hidden email]
>>
>>>> To unsubscribe and other options, go to
>>>> http://www.aroma-project.org/forum/
>>
>>>>
>>
>>>> --
>>
>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>> latest version of the package, 2) to report the output of sessionInfo() and
>>>> traceback(), and 3) to post a complete code example.
>>
>>>>
>>
>>>>
>>
>>>> You received this message because you are subscribed to the Google Groups
>>>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>>
>>>> To post to this group, send email to [hidden email]
>>
>>>> To unsubscribe and other options, go to
>>>> http://www.aroma-project.org/forum/
>>
>>>>
>>
>>>
>>
>>> --
>>
>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>> latest version of the package, 2) to report the output of sessionInfo() and
>>> traceback(), and 3) to post a complete code example.
>>
>>>
>>
>>>
>>
>>> You received this message because you are subscribed to the Google Groups
>>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>>
>>> To post to this group, send email to [hidden email]
>>
>>> To unsubscribe and other options, go to
>>> http://www.aroma-project.org/forum/
>>
>>>
>>
>>> --
>>
>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>> latest version of the package, 2) to report the output of sessionInfo() and
>>> traceback(), and 3) to post a complete code example.
>>
>>>
>>
>>>
>>
>>> You received this message because you are subscribed to the Google Groups
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>>
>>> To post to this group, send email to [hidden email]
>>
>>> To unsubscribe and other options, go to
>>> http://www.aroma-project.org/forum/
>>
>>>
>>
>> --
>>
>> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
>> version of the package, 2) to report the output of sessionInfo() and
>> traceback(), and 3) to post a complete code example.
>>
>> You received this message because you are subscribed to the Google Groups
>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>>
>> To post to this group, send email to [hidden email]
>>
>> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>>
>> --
>> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
>> version of the package, 2) to report the output of sessionInfo() and
>> traceback(), and 3) to post a complete code example.
>>
>>
>> You received this message because you are subscribed to the Google Groups
>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> To post to this group, send email to [hidden email]
>> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>>
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to [hidden email]
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
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Re: [aroma.affymetrix] DNAcopy parameter

Pierre Neuvial
In reply to this post by Yan Jiao
Hi,

The parameters used are the default parameters of the 'segment'
function of the DNAcopy package.  If you search for 'DNAcopy
parameters' on the "Search forum" box at http://aroma-project.org, you
will find this recent thread which gives an example of how these
parameters can be changed:

http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/aa9db6ac7835d828/b6ab6b1c9786d9ff

Hope this helps.

Pierre

On Wed, Nov 24, 2010 at 7:31 PM, Yan Jiao <[hidden email]> wrote:

> Thanks Henrik,
> I will update my R and aroma package,
> Another question is what kind of parameters of aroma use for copy number segmentation, if using DNAcopy as the algorithm?
>
> Many thanks
>
> yan
>
> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
> Sent: 24 November 2010 17:06
> To: aroma-affymetrix
> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>
> Ok, after seing your sessionInfo();
>
> You need to update to R v2.12.0, especially since you're on Windows
> 64-bit.  Lots of work have been done by R core people to support
> Windows 64-bit on R v2.12.0 and beyond.  There is no shortcut to this.
>
> Update aroma.affymetrix to v1.8.0, cf. http://aroma-project.org/install
>
> Also, the Cairo package is not available for the 64-bit version of R
> on Windows.  If you try install.packages("Cairo") on your Windows
> machine, CRAN should report that package is not available.   Either
> you have installed it by other means or it incorrectly installed on R
> v2.11.0.
>
> /Henrik
>
>
> On Wed, Nov 24, 2010 at 8:58 AM, Yan Jiao <[hidden email]> wrote:
>> Hi Henrik,
>>
>> I did what you suggested:
>>
>>> traceback()
>>
>> 13: stop(gettextf("package '%s' is not installed for 'arch=%s'",
>>
>>         pkgname, r_arch), call. = FALSE, domain = NA)
>>
>> 12: testRversion(pkgInfo, package, pkgpath)
>>
>> 11: library(package, lib.loc = lib.loc, character.only = TRUE,
>> logical.return = TRUE,
>>
>>         warn.conflicts = warn.conflicts, keep.source = keep.source)
>>
>> 10: base::require(...)
>>
>> 9: require("Cairo")
>>
>> 8: findPngDevice.default(transparent = FALSE)
>>
>> 7: findPngDevice(transparent = FALSE)
>>
>> 6: plot.CopyNumberSegmentationModel(model, path = path, imageFormat = "png",
>>
>>        plotband = plotband, arrays = arrays, ...)
>>
>> 5: plot(model, path = path, imageFormat = "png", plotband = plotband,
>>
>>        arrays = arrays, ...)
>>
>> 4: writeGraphs.ChromosomeExplorer(this, arrays = arrays, chromosomes =
>> chromosomes,
>>
>>        zooms = zooms, ..., verbose = less(verbose))
>>
>> 3: writeGraphs(this, arrays = arrays, chromosomes = chromosomes,
>>
>>        zooms = zooms, ..., verbose = less(verbose))
>>
>> 2: process.ChromosomeExplorer(ce.all, verbose = TRUE)
>>
>> 1: process(ce.all, verbose = TRUE)
>>
>>> sessionInfo()
>>
>> R version 2.11.0 (2010-04-22)
>>
>> x86_64-pc-mingw32
>>
>> locale:
>>
>> [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United
>> Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
>> LC_NUMERIC=C
>>
>> [5] LC_TIME=English_United Kingdom.1252
>>
>> attached base packages:
>>
>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> other attached packages:
>>
>>  [1] RColorBrewer_1.0-2     DNAcopy_1.22.1         preprocessCore_1.10.0
>> sfit_0.1.9             aroma.affymetrix_1.7.0 aroma.apd_0.1.7
>> affxparser_1.20.0
>>
>>  [8] R.huge_0.2.0           aroma.core_1.7.0       aroma.light_1.16.1
>> matrixStats_0.2.2      R.rsp_0.4.0            R.cache_0.3.0
>> R.filesets_0.9.0
>>
>> [15] digest_0.4.2           R.utils_1.5.3          R.oo_1.7.4
>> R.methodsS3_1.2.1
>>
>> loaded via a namespace (and not attached):
>>
>> [1] tools_2.11.0
>>
>>>
>>
>> process(ce,chromosomes=c(1,8,17), verbose=-10)
>>
>> Generating ChromosomeExplorer report...
>>
>>  Setting up ChromosomeExplorer report files...
>>
>>   Copying template files...
>>
>>    Source path:
>> C:/Users/rmhkyji/R/win64-library/2.11/aroma.core/reports/includes
>>
>>    Destination path: reports/includes
>>
>>   Copying template files...done
>>
>>  Setting up ChromosomeExplorer report files...done
>>
>>  Explorer output version: 3
>>
>>  Compiling ChromosomeExplorer.onLoad.js.rsp...
>>
>>   Source:
>> C:/Users/rmhkyji/R/win64-library/2.11/aroma.core/reports/templates/rsp/ChromosomeExplorer3/ChromosomeExplorer.onLoad.js.rsp
>>
>>   Output path: reports/Fockens_1/ACC,-XY,RMA,+300,A+B,FLN,-XY
>>
>>   Scanning directories for available chip types...
>>
>>    Detected chip types: Mapping50K_Hind240
>>
>>   Scanning directories for available chip types...done
>>
>>   Scanning image files for available zooms...
>>
>>    Detected (or default) zooms: 1, 2, 4, 8, 16, 32, 64
>>
>>   Scanning image files for available zooms...done
>>
>>   Scanning directory for subdirectories...
>>
>>    Detected (or default) sets: cbs
>>
>>   Scanning directory for subdirectories...done
>>
>>   Compiling RSP...
>>
>>            member data.class dimension objectSize
>>
>>    1    chipTypes  character         1        120
>>
>>    2    chrLayers  character         0         40
>>
>>    3 sampleLabels  character         3        240
>>
>>    4 sampleLayers  character         0         40
>>
>>    5      samples  character         3        240
>>
>>    6         sets  character         1         96
>>
>>    7        zooms    numeric         7         72
>>
>>    Sample names:
>>
>>    [1] "GSM255038" "GSM255039" "GSM255040"
>>
>>    Full sample names:
>>
>>    [1] "GSM255038,total" "GSM255039,total" "GSM255040,total"
>>
>>   Compiling RSP...done
>>
>>  Compiling ChromosomeExplorer.onLoad.js.rsp...done
>>
>> Loading required package: Cairo
>>
>> Error: package 'Cairo' is not installed for 'arch=x64'
>>
>> Generating ChromosomeExplorer report...done
>>
>>
>> -----Original Message-----
>> From: [hidden email]
>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>> Sent: 24 November 2010 16:50
>> To: aroma-affymetrix
>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>
>> Hi.
>>
>> On Wed, Nov 24, 2010 at 8:10 AM, Yan Jiao <[hidden email]> wrote:
>>
>>> Hi Henrik,
>>
>>>
>>
>>> Another question, I was trying to only do segmentation on 3 chromosomes,
>>> how should I do it, I tried:
>>
>>> process(ce,chromosomes=c(1,8,17), verbose=TRUE);
>>
>>>
>>
>>> but got error message:
>>
>>>
>>
>>> Generating ChromosomeExplorer report...
>>
>>> Loading required package: Cairo
>>
>>> Error: package 'Cairo' is not installed for 'arch=x64'
>>
>>> Generating ChromosomeExplorer report...done
>>
>> Odd, because specifying a subset of chromosomes shouldn't be any
>>
>> different from running all, as you did before.
>>
>> So, there seem to be several packages that install on R 64-bit in
>>
>> Windows, but when trying to use then fails.  The Cairo package is
>>
>> actually "deprecated" (replaced with similar function builtin in R),
>>
>> but we've kept support for backward compatibilities.  It seems like
>>
>> you're facing these issues - and not that many people are running
>>
>> 64-bit Windows yet so you seem to be the one hitting the bumps.
>>
>> What does traceback() give when you get the error?
>>
>> What is your sessionInfo()?
>>
>> Can you use process(ce,chromosomes=c(1,8,17), verbose=-10) in order to
>>
>> narrow down where the error occurs.
>>
>> /Henrik
>>
>>>
>>
>>>
>>
>>> Many thanks
>>
>>>
>>
>>> yan
>>
>>>
>>
>>>
>>
>>>
>>
>>> -----Original Message-----
>>
>>> From: [hidden email]
>>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>>
>>> Sent: 24 November 2010 15:08
>>
>>> To: aroma-affymetrix
>>
>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>
>>>
>>
>>> Hi,
>>
>>>
>>
>>> great.  Contrary to error messages, warnings are alright to get.
>>
>>>
>>
>>> /H
>>
>>>
>>
>>> On Wed, Nov 24, 2010 at 2:51 AM, Yan Jiao <[hidden email]> wrote:
>>
>>>> Thank you Henrik,
>>
>>>> It works now, but I got some warning:
>>
>>>>
>>
>>>> process(ce, verbose=TRUE);
>>
>>>> Generating ChromosomeExplorer report...
>>
>>>> Loading required package: Cairo
>>
>>>> Generating ChromosomeExplorer report...done
>>
>>>> [1] TRUE
>>
>>>> Warning messages:
>>
>>>> 1: In library(package, lib.loc = lib.loc, character.only = TRUE,
>>>> logical.return = TRUE,  :
>>
>>>>  there is no package called 'Cairo'
>>
>>>> 2: In method(static, ...) :
>>
>>>>  Ghostscript not found. Searched directories: C:/gs, C:\Program Files/gs,
>>>> /gs, C:\Program Files\Common Files/gs
>>
>>>>
>>
>>>> Are those warning messages serious? Could I ignore them?
>>
>>>>
>>
>>>>
>>
>>>> Yan
>>
>>>>
>>
>>>> -----Original Message-----
>>
>>>> From: [hidden email]
>>>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>>
>>>> Sent: 23 November 2010 21:53
>>
>>>> To: aroma-affymetrix
>>
>>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>
>>>>
>>
>>>> Hi.
>>
>>>>
>>
>>>> On Tue, Nov 23, 2010 at 11:51 AM, Yan Jiao <[hidden email]> wrote:
>>
>>>>> Hi Henrik,
>>
>>>>>
>>
>>>>> Sorry, the error is after
>>
>>>>> cbs <- CbsModel(ds);
>>
>>>>> ce <- ChromosomeExplorer(cbs);
>>
>>>>> process(ce, verbose=TRUE);
>>
>>>>
>>
>>>> Ok, now the error message makes a bit more sense (it was my suspicion
>>
>>>> but I didn't want make guesses).
>>
>>>>
>>
>>>>>
>>
>>>>>
>>
>>>>> Generating ChromosomeExplorer report...
>>
>>>>> Loading required package: Cairo
>>
>>>>> <simpleError in inDL(x, as.logical(local), as.logical(now), ...): unable
>>
>>>>> to load shared library
>>
>>>>> 'C:/Users/rmhkyji/R/win64-library/2.11/GLAD/libs/x64/GLAD.dll':
>>
>>>>>  LoadLibrary failure:  The specified module could not be found.
>>
>>>>>
>>
>>>>> And there  is a pop out window saying: The program can't start because
>>
>>>>> libgsl-0.dll I smissing from your computer. Try reinstalling the program
>>
>>>>> to fix this program.
>>
>>>>
>>
>>>> I can reproduce this on 64-bit Windows 7 - you get the same error if
>>
>>>> you try library("GLAD").  It is because we utilize part of the GLAD
>>
>>>> package, if and only if it is *installed*, and otherwise we turn to
>>
>>>> backup solutions.  What happens here is that *GLAD is installed but
>>
>>>> doesn't load*, which causes the error so that backup solutions doesn't
>>
>>>> kick in.   In the next release I'll try to make sure the backup
>>
>>>> solutions will also work when there is an error load GLAD.  In
>>
>>>> meanwhile, you can do this:
>>
>>>>
>>
>>>> WORKAROUND:
>>
>>>>
>>
>>>> 1. Uninstall the GLAD package (it doesn't work anyway):
>>
>>>>
>>
>>>>> remove.packages("GLAD")
>>
>>>> Removing package(s) from 'C:\Users\hb\R\win-library\2.12'
>>
>>>> (as 'lib' is unspecified)
>>
>>>>
>>
>>>>> library("GLAD")
>>
>>>> Error in library("GLAD") : there is no package called 'GLAD'
>>
>>>>
>>
>>>> That should do it.  Let me know if it works for you.
>>
>>>>
>>
>>>> TECHNICAL DETAILS: It happens because the GNU Scientific Library (GSL)
>>
>>>> is not installed on the system (hence the 'gsl' part of
>>
>>>> 'libgsl-0.dll'). There is a hard-to-find note that you need GSL in
>>
>>>> order to use the GLAD package, cf.
>>
>>>> http://bioconductor.org/packages/release/bioc/html/GLAD.html.  There
>>
>>>> exist 32-bit binaries of GSL at
>>
>>>> http://gnuwin32.sourceforge.net/packages/gsl.htm.  Unfortunately, it
>>
>>>> does not work for the 64-bit version of R on Windows 64-bit.  It works
>>
>>>> if you do tricks an run the 32-bit version of R, but that is a rather
>>
>>>> inconvenient workaround.
>>
>>>>
>>
>>>> /Henrik
>>
>>>>
>>
>>>>>
>>
>>>>>
>>
>>>>> Yan
>>
>>>>>
>>
>>>>> -----Original Message-----
>>
>>>>> From: [hidden email]
>>
>>>>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>>
>>>>> Sent: 23 November 2010 18:50
>>
>>>>> To: aroma-affymetrix
>>
>>>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>
>>>>>
>>
>>>>> Hi.
>>
>>>>>
>>
>>>>> On Tue, Nov 23, 2010 at 10:05 AM, Yan Jiao <[hidden email]> wrote:
>>
>>>>>>
>>
>>>>>>
>>
>>>>>> Dear all,
>>
>>>>>>
>>
>>>>>> I'm trying to do DNA segmentation,
>>
>>>>>>
>>
>>>>>> This is what I'm doing:
>>
>>>>>>
>>
>>>>>> ds <- doCRMAv1("Fockens_1", chipType="Mapping50K_Hind240",
>>
>>>>> verbose=TRUE);
>>
>>>>>>
>>
>>>>>> ###this is done sucessfully
>>
>>>>>>
>>
>>>>>> # Segmentation
>>
>>>>>>
>>
>>>>>> cbs <- CbsModel(ds);
>>
>>>>>>
>>
>>>>>>
>>
>>>>>>
>>
>>>>>> I got error libgsl-0.dll is missing, I think it's using GLAD, but I'm
>>
>>>>> trying
>>
>>>>>> to use DNAcopy for segmentation.
>>
>>>>>
>>
>>>>> Is it really the case that you get that error when you do:
>>
>>>>>
>>
>>>>> cbs <- CbsModel(ds);
>>
>>>>>
>>
>>>>> or do you do anything else?  Is suspect you do something more.
>>
>>>>>
>>
>>>>> Also, after you got the error, could you cut'n'paste the verbose
>>
>>>>> output including any error messages you get and send it to us?   Also,
>>
>>>>> make sure to report what print(traceback()) gives immediate after
>>
>>>>> getting the error.
>>
>>>>>
>>
>>>>> /Henrik
>>
>>>>>
>>
>>>>> PS. The 'GLAD' package may indeed be used regardless of segmentation
>>
>>>>> method because it contains information about cytobands.
>>
>>>>>
>>
>>>>>>
>>
>>>>>> How to change it?
>>
>>>>>>
>>
>>>>>>
>>
>>>>>>
>>
>>>>>> Many thanks
>>
>>>>>>
>>
>>>>>>
>>
>>>>>>
>>
>>>>>> yan
>>
>>>>>>
>>
>>>>>>
>>
>>>>>>
>>
>>>>>>
>>
>>>>>>
>>
>>>>>>
>>
>>>>>>
>>
>>>>>> **********************************************************************
>>
>>>>>>
>>
>>>>>> This email and any files transmitted with it are confidential and
>>
>>>>>>
>>
>>>>>> intended solely for the use of the individual or entity to whom they
>>
>>>>>>
>>
>>>>>> are addressed. If you have received this email in error please notify
>>
>>>>>>
>>
>>>>>> the system manager ([hidden email]).
>>
>>>>>>
>>
>>>>>> **********************************************************************
>>
>>>>>>
>>
>>>>>>
>>
>>>>>>
>>
>>>>>> --
>>
>>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>
>>>>> latest
>>
>>>>>> version of the package, 2) to report the output of sessionInfo() and
>>
>>>>>> traceback(), and 3) to post a complete code example.
>>
>>>>>>
>>
>>>>>>
>>
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>>
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>>>>>>
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>>>>>
>>
>>>>> --
>>
>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>
>>>>> latest version of the package, 2) to report the output of sessionInfo()
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>>>>>
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>>>>> --
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>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>>> latest version of the package, 2) to report the output of sessionInfo() and
>>>>> traceback(), and 3) to post a complete code example.
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>>>>>
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>>>>>
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>>>>>
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>>>>
>>
>>>> --
>>
>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>> latest version of the package, 2) to report the output of sessionInfo() and
>>>> traceback(), and 3) to post a complete code example.
>>
>>>>
>>
>>>>
>>
>>>> You received this message because you are subscribed to the Google Groups
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>>
>>>> To post to this group, send email to [hidden email]
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>>>>
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>>>> --
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>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>> latest version of the package, 2) to report the output of sessionInfo() and
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>>>>
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>>>> You received this message because you are subscribed to the Google Groups
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>>>>
>>
>>>
>>
>>> --
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>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>> latest version of the package, 2) to report the output of sessionInfo() and
>>> traceback(), and 3) to post a complete code example.
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>>>
>>
>>>
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>>
>>> To post to this group, send email to [hidden email]
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>>> --
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>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>> latest version of the package, 2) to report the output of sessionInfo() and
>>> traceback(), and 3) to post a complete code example.
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>>>
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>>>
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>>> You received this message because you are subscribed to the Google Groups
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>> --
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>> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
>> version of the package, 2) to report the output of sessionInfo() and
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>> You received this message because you are subscribed to the Google Groups
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>> --
>> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
>> version of the package, 2) to report the output of sessionInfo() and
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>>
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>> You received this message because you are subscribed to the Google Groups
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>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
>
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> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to [hidden email]
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> --
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Re: [aroma.affymetrix] Copy number segmentation result

Pierre Neuvial
In reply to this post by Yan Jiao
Hi,

On Wed, Nov 24, 2010 at 4:17 PM, Yan Jiao <[hidden email]> wrote:
> Hi Henrik,
>
> Another question about the result is : is there a way to map the copy number to the gene ID automatically?

You mean retrieving a list of genes contained in each DNAcopy segment
?  No, this is not implemented in aroma.*
You can use (for example) the biomaRt package to do this.

> Also does aroma choose threshold for calling gain and loss?

No, aroma.* just calls the DNAcopy::segment function for you, and this
function just performs segmentation, and gives you the mean copy
number in each segment.  It does not call gains or losses.

Cheers,

Pierre

>
> Many thanks
>
> yan
>
> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
> Sent: 24 November 2010 15:08
> To: aroma-affymetrix
> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>
> Hi,
>
> great.  Contrary to error messages, warnings are alright to get.
>
> /H
>
> On Wed, Nov 24, 2010 at 2:51 AM, Yan Jiao <[hidden email]> wrote:
>> Thank you Henrik,
>> It works now, but I got some warning:
>>
>> process(ce, verbose=TRUE);
>> Generating ChromosomeExplorer report...
>> Loading required package: Cairo
>> Generating ChromosomeExplorer report...done
>> [1] TRUE
>> Warning messages:
>> 1: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
>>  there is no package called 'Cairo'
>> 2: In method(static, ...) :
>>  Ghostscript not found. Searched directories: C:/gs, C:\Program Files/gs, /gs, C:\Program Files\Common Files/gs
>>
>> Are those warning messages serious? Could I ignore them?
>>
>>
>> Yan
>>
>> -----Original Message-----
>> From: [hidden email] [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>> Sent: 23 November 2010 21:53
>> To: aroma-affymetrix
>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>
>> Hi.
>>
>> On Tue, Nov 23, 2010 at 11:51 AM, Yan Jiao <[hidden email]> wrote:
>>> Hi Henrik,
>>>
>>> Sorry, the error is after
>>> cbs <- CbsModel(ds);
>>> ce <- ChromosomeExplorer(cbs);
>>> process(ce, verbose=TRUE);
>>
>> Ok, now the error message makes a bit more sense (it was my suspicion
>> but I didn't want make guesses).
>>
>>>
>>>
>>> Generating ChromosomeExplorer report...
>>> Loading required package: Cairo
>>> <simpleError in inDL(x, as.logical(local), as.logical(now), ...): unable
>>> to load shared library
>>> 'C:/Users/rmhkyji/R/win64-library/2.11/GLAD/libs/x64/GLAD.dll':
>>>  LoadLibrary failure:  The specified module could not be found.
>>>
>>> And there  is a pop out window saying: The program can't start because
>>> libgsl-0.dll I smissing from your computer. Try reinstalling the program
>>> to fix this program.
>>
>> I can reproduce this on 64-bit Windows 7 - you get the same error if
>> you try library("GLAD").  It is because we utilize part of the GLAD
>> package, if and only if it is *installed*, and otherwise we turn to
>> backup solutions.  What happens here is that *GLAD is installed but
>> doesn't load*, which causes the error so that backup solutions doesn't
>> kick in.   In the next release I'll try to make sure the backup
>> solutions will also work when there is an error load GLAD.  In
>> meanwhile, you can do this:
>>
>> WORKAROUND:
>>
>> 1. Uninstall the GLAD package (it doesn't work anyway):
>>
>>> remove.packages("GLAD")
>> Removing package(s) from 'C:\Users\hb\R\win-library\2.12'
>> (as 'lib' is unspecified)
>>
>>> library("GLAD")
>> Error in library("GLAD") : there is no package called 'GLAD'
>>
>> That should do it.  Let me know if it works for you.
>>
>> TECHNICAL DETAILS: It happens because the GNU Scientific Library (GSL)
>> is not installed on the system (hence the 'gsl' part of
>> 'libgsl-0.dll'). There is a hard-to-find note that you need GSL in
>> order to use the GLAD package, cf.
>> http://bioconductor.org/packages/release/bioc/html/GLAD.html.  There
>> exist 32-bit binaries of GSL at
>> http://gnuwin32.sourceforge.net/packages/gsl.htm.  Unfortunately, it
>> does not work for the 64-bit version of R on Windows 64-bit.  It works
>> if you do tricks an run the 32-bit version of R, but that is a rather
>> inconvenient workaround.
>>
>> /Henrik
>>
>>>
>>>
>>> Yan
>>>
>>> -----Original Message-----
>>> From: [hidden email]
>>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>>> Sent: 23 November 2010 18:50
>>> To: aroma-affymetrix
>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>>
>>> Hi.
>>>
>>> On Tue, Nov 23, 2010 at 10:05 AM, Yan Jiao <[hidden email]> wrote:
>>>>
>>>>
>>>> Dear all,
>>>>
>>>> I'm trying to do DNA segmentation,
>>>>
>>>> This is what I'm doing:
>>>>
>>>> ds <- doCRMAv1("Fockens_1", chipType="Mapping50K_Hind240",
>>> verbose=TRUE);
>>>>
>>>> ###this is done sucessfully
>>>>
>>>> # Segmentation
>>>>
>>>> cbs <- CbsModel(ds);
>>>>
>>>>
>>>>
>>>> I got error libgsl-0.dll is missing, I think it's using GLAD, but I'm
>>> trying
>>>> to use DNAcopy for segmentation.
>>>
>>> Is it really the case that you get that error when you do:
>>>
>>> cbs <- CbsModel(ds);
>>>
>>> or do you do anything else?  Is suspect you do something more.
>>>
>>> Also, after you got the error, could you cut'n'paste the verbose
>>> output including any error messages you get and send it to us?   Also,
>>> make sure to report what print(traceback()) gives immediate after
>>> getting the error.
>>>
>>> /Henrik
>>>
>>> PS. The 'GLAD' package may indeed be used regardless of segmentation
>>> method because it contains information about cytobands.
>>>
>>>>
>>>> How to change it?
>>>>
>>>>
>>>>
>>>> Many thanks
>>>>
>>>>
>>>>
>>>> yan
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>>>> **********************************************************************
>>>>
>>>> This email and any files transmitted with it are confidential and
>>>>
>>>> intended solely for the use of the individual or entity to whom they
>>>>
>>>> are addressed. If you have received this email in error please notify
>>>>
>>>> the system manager ([hidden email]).
>>>>
>>>> **********************************************************************
>>>>
>>>>
>>>>
>>>> --
>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>> latest
>>>> version of the package, 2) to report the output of sessionInfo() and
>>>> traceback(), and 3) to post a complete code example.
>>>>
>>>>
>>>> You received this message because you are subscribed to the Google
>>> Groups
>>>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>>>> To post to this group, send email to [hidden email]
>>>> To unsubscribe and other options, go to
>>> http://www.aroma-project.org/forum/
>>>>
>>>
>>> --
>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>> latest version of the package, 2) to report the output of sessionInfo()
>>> and traceback(), and 3) to post a complete code example.
>>>
>>>
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>>> --
>>> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
>>>
>>>
>>> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
>>> To post to this group, send email to [hidden email]
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>>>
>>
>> --
>> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
>>
>>
>> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> To post to this group, send email to [hidden email]
>> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>>
>> --
>> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
>>
>>
>> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
>> To post to this group, send email to [hidden email]
>> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>>
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to [hidden email]
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>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
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Re: [aroma.affymetrix] DNAcopy parameter

Henrik Bengtsson-4
In reply to this post by Pierre Neuvial
On Sun, Nov 28, 2010 at 6:01 AM, Pierre Neuvial
<[hidden email]> wrote:
> Hi,
>
> The parameters used are the default parameters of the 'segment'
> function of the DNAcopy package.  If you search for 'DNAcopy
> parameters' on the "Search forum" box at http://aroma-project.org, you
> will find this recent thread which gives an example of how these
> parameters can be changed:
>
> http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/aa9db6ac7835d828/b6ab6b1c9786d9ff

Note that I just posted a follow up on that thread clarified that it
is now possible to specify optional arguments specific to
DNAcopy::segment() as:

seg <- CbsModel(ds, min.width=5);

In order to find out which they are and what they do, see the specific
segmentation method, i.e. help("segment", package="DNAcopy").

/Henrik

>
> Hope this helps.
>
> Pierre
>
> On Wed, Nov 24, 2010 at 7:31 PM, Yan Jiao <[hidden email]> wrote:
>> Thanks Henrik,
>> I will update my R and aroma package,
>> Another question is what kind of parameters of aroma use for copy number
>> segmentation, if using DNAcopy as the algorithm?
>>
>> Many thanks
>>
>> yan
>>
>> -----Original Message-----
>> From: [hidden email]
>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>> Sent: 24 November 2010 17:06
>> To: aroma-affymetrix
>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>
>> Ok, after seing your sessionInfo();
>>
>> You need to update to R v2.12.0, especially since you're on Windows
>> 64-bit.  Lots of work have been done by R core people to support
>> Windows 64-bit on R v2.12.0 and beyond.  There is no shortcut to this.
>>
>> Update aroma.affymetrix to v1.8.0, cf. http://aroma-project.org/install
>>
>> Also, the Cairo package is not available for the 64-bit version of R
>> on Windows.  If you try install.packages("Cairo") on your Windows
>> machine, CRAN should report that package is not available.   Either
>> you have installed it by other means or it incorrectly installed on R
>> v2.11.0.
>>
>> /Henrik
>>
>>
>> On Wed, Nov 24, 2010 at 8:58 AM, Yan Jiao <[hidden email]> wrote:
>>> Hi Henrik,
>>>
>>> I did what you suggested:
>>>
>>>> traceback()
>>>
>>> 13: stop(gettextf("package '%s' is not installed for 'arch=%s'",
>>>
>>>         pkgname, r_arch), call. = FALSE, domain = NA)
>>>
>>> 12: testRversion(pkgInfo, package, pkgpath)
>>>
>>> 11: library(package, lib.loc = lib.loc, character.only = TRUE,
>>> logical.return = TRUE,
>>>
>>>         warn.conflicts = warn.conflicts, keep.source = keep.source)
>>>
>>> 10: base::require(...)
>>>
>>> 9: require("Cairo")
>>>
>>> 8: findPngDevice.default(transparent = FALSE)
>>>
>>> 7: findPngDevice(transparent = FALSE)
>>>
>>> 6: plot.CopyNumberSegmentationModel(model, path = path, imageFormat =
>>> "png",
>>>
>>>        plotband = plotband, arrays = arrays, ...)
>>>
>>> 5: plot(model, path = path, imageFormat = "png", plotband = plotband,
>>>
>>>        arrays = arrays, ...)
>>>
>>> 4: writeGraphs.ChromosomeExplorer(this, arrays = arrays, chromosomes =
>>> chromosomes,
>>>
>>>        zooms = zooms, ..., verbose = less(verbose))
>>>
>>> 3: writeGraphs(this, arrays = arrays, chromosomes = chromosomes,
>>>
>>>        zooms = zooms, ..., verbose = less(verbose))
>>>
>>> 2: process.ChromosomeExplorer(ce.all, verbose = TRUE)
>>>
>>> 1: process(ce.all, verbose = TRUE)
>>>
>>>> sessionInfo()
>>>
>>> R version 2.11.0 (2010-04-22)
>>>
>>> x86_64-pc-mingw32
>>>
>>> locale:
>>>
>>> [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United
>>> Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
>>> LC_NUMERIC=C
>>>
>>> [5] LC_TIME=English_United Kingdom.1252
>>>
>>> attached base packages:
>>>
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> other attached packages:
>>>
>>>  [1] RColorBrewer_1.0-2     DNAcopy_1.22.1         preprocessCore_1.10.0
>>> sfit_0.1.9             aroma.affymetrix_1.7.0 aroma.apd_0.1.7
>>> affxparser_1.20.0
>>>
>>>  [8] R.huge_0.2.0           aroma.core_1.7.0       aroma.light_1.16.1
>>> matrixStats_0.2.2      R.rsp_0.4.0            R.cache_0.3.0
>>> R.filesets_0.9.0
>>>
>>> [15] digest_0.4.2           R.utils_1.5.3          R.oo_1.7.4
>>> R.methodsS3_1.2.1
>>>
>>> loaded via a namespace (and not attached):
>>>
>>> [1] tools_2.11.0
>>>
>>>>
>>>
>>> process(ce,chromosomes=c(1,8,17), verbose=-10)
>>>
>>> Generating ChromosomeExplorer report...
>>>
>>>  Setting up ChromosomeExplorer report files...
>>>
>>>   Copying template files...
>>>
>>>    Source path:
>>> C:/Users/rmhkyji/R/win64-library/2.11/aroma.core/reports/includes
>>>
>>>    Destination path: reports/includes
>>>
>>>   Copying template files...done
>>>
>>>  Setting up ChromosomeExplorer report files...done
>>>
>>>  Explorer output version: 3
>>>
>>>  Compiling ChromosomeExplorer.onLoad.js.rsp...
>>>
>>>   Source:
>>>
>>> C:/Users/rmhkyji/R/win64-library/2.11/aroma.core/reports/templates/rsp/ChromosomeExplorer3/ChromosomeExplorer.onLoad.js.rsp
>>>
>>>   Output path: reports/Fockens_1/ACC,-XY,RMA,+300,A+B,FLN,-XY
>>>
>>>   Scanning directories for available chip types...
>>>
>>>    Detected chip types: Mapping50K_Hind240
>>>
>>>   Scanning directories for available chip types...done
>>>
>>>   Scanning image files for available zooms...
>>>
>>>    Detected (or default) zooms: 1, 2, 4, 8, 16, 32, 64
>>>
>>>   Scanning image files for available zooms...done
>>>
>>>   Scanning directory for subdirectories...
>>>
>>>    Detected (or default) sets: cbs
>>>
>>>   Scanning directory for subdirectories...done
>>>
>>>   Compiling RSP...
>>>
>>>            member data.class dimension objectSize
>>>
>>>    1    chipTypes  character         1        120
>>>
>>>    2    chrLayers  character         0         40
>>>
>>>    3 sampleLabels  character         3        240
>>>
>>>    4 sampleLayers  character         0         40
>>>
>>>    5      samples  character         3        240
>>>
>>>    6         sets  character         1         96
>>>
>>>    7        zooms    numeric         7         72
>>>
>>>    Sample names:
>>>
>>>    [1] "GSM255038" "GSM255039" "GSM255040"
>>>
>>>    Full sample names:
>>>
>>>    [1] "GSM255038,total" "GSM255039,total" "GSM255040,total"
>>>
>>>   Compiling RSP...done
>>>
>>>  Compiling ChromosomeExplorer.onLoad.js.rsp...done
>>>
>>> Loading required package: Cairo
>>>
>>> Error: package 'Cairo' is not installed for 'arch=x64'
>>>
>>> Generating ChromosomeExplorer report...done
>>>
>>>
>>> -----Original Message-----
>>> From: [hidden email]
>>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>>> Sent: 24 November 2010 16:50
>>> To: aroma-affymetrix
>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>>
>>> Hi.
>>>
>>> On Wed, Nov 24, 2010 at 8:10 AM, Yan Jiao <[hidden email]> wrote:
>>>
>>>> Hi Henrik,
>>>
>>>>
>>>
>>>> Another question, I was trying to only do segmentation on 3 chromosomes,
>>>> how should I do it, I tried:
>>>
>>>> process(ce,chromosomes=c(1,8,17), verbose=TRUE);
>>>
>>>>
>>>
>>>> but got error message:
>>>
>>>>
>>>
>>>> Generating ChromosomeExplorer report...
>>>
>>>> Loading required package: Cairo
>>>
>>>> Error: package 'Cairo' is not installed for 'arch=x64'
>>>
>>>> Generating ChromosomeExplorer report...done
>>>
>>> Odd, because specifying a subset of chromosomes shouldn't be any
>>>
>>> different from running all, as you did before.
>>>
>>> So, there seem to be several packages that install on R 64-bit in
>>>
>>> Windows, but when trying to use then fails.  The Cairo package is
>>>
>>> actually "deprecated" (replaced with similar function builtin in R),
>>>
>>> but we've kept support for backward compatibilities.  It seems like
>>>
>>> you're facing these issues - and not that many people are running
>>>
>>> 64-bit Windows yet so you seem to be the one hitting the bumps.
>>>
>>> What does traceback() give when you get the error?
>>>
>>> What is your sessionInfo()?
>>>
>>> Can you use process(ce,chromosomes=c(1,8,17), verbose=-10) in order to
>>>
>>> narrow down where the error occurs.
>>>
>>> /Henrik
>>>
>>>>
>>>
>>>>
>>>
>>>> Many thanks
>>>
>>>>
>>>
>>>> yan
>>>
>>>>
>>>
>>>>
>>>
>>>>
>>>
>>>> -----Original Message-----
>>>
>>>> From: [hidden email]
>>>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>>>
>>>> Sent: 24 November 2010 15:08
>>>
>>>> To: aroma-affymetrix
>>>
>>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>>
>>>>
>>>
>>>> Hi,
>>>
>>>>
>>>
>>>> great.  Contrary to error messages, warnings are alright to get.
>>>
>>>>
>>>
>>>> /H
>>>
>>>>
>>>
>>>> On Wed, Nov 24, 2010 at 2:51 AM, Yan Jiao <[hidden email]> wrote:
>>>
>>>>> Thank you Henrik,
>>>
>>>>> It works now, but I got some warning:
>>>
>>>>>
>>>
>>>>> process(ce, verbose=TRUE);
>>>
>>>>> Generating ChromosomeExplorer report...
>>>
>>>>> Loading required package: Cairo
>>>
>>>>> Generating ChromosomeExplorer report...done
>>>
>>>>> [1] TRUE
>>>
>>>>> Warning messages:
>>>
>>>>> 1: In library(package, lib.loc = lib.loc, character.only = TRUE,
>>>>> logical.return = TRUE,  :
>>>
>>>>>  there is no package called 'Cairo'
>>>
>>>>> 2: In method(static, ...) :
>>>
>>>>>  Ghostscript not found. Searched directories: C:/gs, C:\Program
>>>>> Files/gs,
>>>>> /gs, C:\Program Files\Common Files/gs
>>>
>>>>>
>>>
>>>>> Are those warning messages serious? Could I ignore them?
>>>
>>>>>
>>>
>>>>>
>>>
>>>>> Yan
>>>
>>>>>
>>>
>>>>> -----Original Message-----
>>>
>>>>> From: [hidden email]
>>>>> [mailto:[hidden email]] On Behalf Of Henrik
>>>>> Bengtsson
>>>
>>>>> Sent: 23 November 2010 21:53
>>>
>>>>> To: aroma-affymetrix
>>>
>>>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>>
>>>>>
>>>
>>>>> Hi.
>>>
>>>>>
>>>
>>>>> On Tue, Nov 23, 2010 at 11:51 AM, Yan Jiao <[hidden email]> wrote:
>>>
>>>>>> Hi Henrik,
>>>
>>>>>>
>>>
>>>>>> Sorry, the error is after
>>>
>>>>>> cbs <- CbsModel(ds);
>>>
>>>>>> ce <- ChromosomeExplorer(cbs);
>>>
>>>>>> process(ce, verbose=TRUE);
>>>
>>>>>
>>>
>>>>> Ok, now the error message makes a bit more sense (it was my suspicion
>>>
>>>>> but I didn't want make guesses).
>>>
>>>>>
>>>
>>>>>>
>>>
>>>>>>
>>>
>>>>>> Generating ChromosomeExplorer report...
>>>
>>>>>> Loading required package: Cairo
>>>
>>>>>> <simpleError in inDL(x, as.logical(local), as.logical(now), ...):
>>>>>> unable
>>>
>>>>>> to load shared library
>>>
>>>>>> 'C:/Users/rmhkyji/R/win64-library/2.11/GLAD/libs/x64/GLAD.dll':
>>>
>>>>>>  LoadLibrary failure:  The specified module could not be found.
>>>
>>>>>>
>>>
>>>>>> And there  is a pop out window saying: The program can't start because
>>>
>>>>>> libgsl-0.dll I smissing from your computer. Try reinstalling the
>>>>>> program
>>>
>>>>>> to fix this program.
>>>
>>>>>
>>>
>>>>> I can reproduce this on 64-bit Windows 7 - you get the same error if
>>>
>>>>> you try library("GLAD").  It is because we utilize part of the GLAD
>>>
>>>>> package, if and only if it is *installed*, and otherwise we turn to
>>>
>>>>> backup solutions.  What happens here is that *GLAD is installed but
>>>
>>>>> doesn't load*, which causes the error so that backup solutions doesn't
>>>
>>>>> kick in.   In the next release I'll try to make sure the backup
>>>
>>>>> solutions will also work when there is an error load GLAD.  In
>>>
>>>>> meanwhile, you can do this:
>>>
>>>>>
>>>
>>>>> WORKAROUND:
>>>
>>>>>
>>>
>>>>> 1. Uninstall the GLAD package (it doesn't work anyway):
>>>
>>>>>
>>>
>>>>>> remove.packages("GLAD")
>>>
>>>>> Removing package(s) from 'C:\Users\hb\R\win-library\2.12'
>>>
>>>>> (as 'lib' is unspecified)
>>>
>>>>>
>>>
>>>>>> library("GLAD")
>>>
>>>>> Error in library("GLAD") : there is no package called 'GLAD'
>>>
>>>>>
>>>
>>>>> That should do it.  Let me know if it works for you.
>>>
>>>>>
>>>
>>>>> TECHNICAL DETAILS: It happens because the GNU Scientific Library (GSL)
>>>
>>>>> is not installed on the system (hence the 'gsl' part of
>>>
>>>>> 'libgsl-0.dll'). There is a hard-to-find note that you need GSL in
>>>
>>>>> order to use the GLAD package, cf.
>>>
>>>>> http://bioconductor.org/packages/release/bioc/html/GLAD.html.  There
>>>
>>>>> exist 32-bit binaries of GSL at
>>>
>>>>> http://gnuwin32.sourceforge.net/packages/gsl.htm.  Unfortunately, it
>>>
>>>>> does not work for the 64-bit version of R on Windows 64-bit.  It works
>>>
>>>>> if you do tricks an run the 32-bit version of R, but that is a rather
>>>
>>>>> inconvenient workaround.
>>>
>>>>>
>>>
>>>>> /Henrik
>>>
>>>>>
>>>
>>>>>>
>>>
>>>>>>
>>>
>>>>>> Yan
>>>
>>>>>>
>>>
>>>>>> -----Original Message-----
>>>
>>>>>> From: [hidden email]
>>>
>>>>>> [mailto:[hidden email]] On Behalf Of Henrik
>>>>>> Bengtsson
>>>
>>>>>> Sent: 23 November 2010 18:50
>>>
>>>>>> To: aroma-affymetrix
>>>
>>>>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>>
>>>>>>
>>>
>>>>>> Hi.
>>>
>>>>>>
>>>
>>>>>> On Tue, Nov 23, 2010 at 10:05 AM, Yan Jiao <[hidden email]> wrote:
>>>
>>>>>>>
>>>
>>>>>>>
>>>
>>>>>>> Dear all,
>>>
>>>>>>>
>>>
>>>>>>> I'm trying to do DNA segmentation,
>>>
>>>>>>>
>>>
>>>>>>> This is what I'm doing:
>>>
>>>>>>>
>>>
>>>>>>> ds <- doCRMAv1("Fockens_1", chipType="Mapping50K_Hind240",
>>>
>>>>>> verbose=TRUE);
>>>
>>>>>>>
>>>
>>>>>>> ###this is done sucessfully
>>>
>>>>>>>
>>>
>>>>>>> # Segmentation
>>>
>>>>>>>
>>>
>>>>>>> cbs <- CbsModel(ds);
>>>
>>>>>>>
>>>
>>>>>>>
>>>
>>>>>>>
>>>
>>>>>>> I got error libgsl-0.dll is missing, I think it's using GLAD, but I'm
>>>
>>>>>> trying
>>>
>>>>>>> to use DNAcopy for segmentation.
>>>
>>>>>>
>>>
>>>>>> Is it really the case that you get that error when you do:
>>>
>>>>>>
>>>
>>>>>> cbs <- CbsModel(ds);
>>>
>>>>>>
>>>
>>>>>> or do you do anything else?  Is suspect you do something more.
>>>
>>>>>>
>>>
>>>>>> Also, after you got the error, could you cut'n'paste the verbose
>>>
>>>>>> output including any error messages you get and send it to us?   Also,
>>>
>>>>>> make sure to report what print(traceback()) gives immediate after
>>>
>>>>>> getting the error.
>>>
>>>>>>
>>>
>>>>>> /Henrik
>>>
>>>>>>
>>>
>>>>>> PS. The 'GLAD' package may indeed be used regardless of segmentation
>>>
>>>>>> method because it contains information about cytobands.
>>>
>>>>>>
>>>
>>>>>>>
>>>
>>>>>>> How to change it?
>>>
>>>>>>>
>>>
>>>>>>>
>>>
>>>>>>>
>>>
>>>>>>> Many thanks
>>>
>>>>>>>
>>>
>>>>>>>
>>>
>>>>>>>
>>>
>>>>>>> yan
>>>
>>>>>>>
>>>
>>>>>>>
>>>
>>>>>>>
>>>
>>>>>>>
>>>
>>>>>>>
>>>
>>>>>>>
>>>
>>>>>>>
>>>
>>>>>>>
>>>>>>> **********************************************************************
>>>
>>>>>>>
>>>
>>>>>>> This email and any files transmitted with it are confidential and
>>>
>>>>>>>
>>>
>>>>>>> intended solely for the use of the individual or entity to whom they
>>>
>>>>>>>
>>>
>>>>>>> are addressed. If you have received this email in error please notify
>>>
>>>>>>>
>>>
>>>>>>> the system manager ([hidden email]).
>>>
>>>>>>>
>>>
>>>>>>>
>>>>>>> **********************************************************************
>>>
>>>>>>>
>>>
>>>>>>>
>>>
>>>>>>>
>>>
>>>>>>> --
>>>
>>>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>
>>>>>> latest
>>>
>>>>>>> version of the package, 2) to report the output of sessionInfo() and
>>>
>>>>>>> traceback(), and 3) to post a complete code example.
>>>
>>>>>>>
>>>
>>>>>>>
>>>
>>>>>>> You received this message because you are subscribed to the Google
>>>
>>>>>> Groups
>>>
>>>>>>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>>>
>>>>>>> To post to this group, send email to
>>>>>>> [hidden email]
>>>
>>>>>>> To unsubscribe and other options, go to
>>>
>>>>>> http://www.aroma-project.org/forum/
>>>
>>>>>>>
>>>
>>>>>>
>>>
>>>>>> --
>>>
>>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>
>>>>>> latest version of the package, 2) to report the output of
>>>>>> sessionInfo()
>>>
>>>>>> and traceback(), and 3) to post a complete code example.
>>>
>>>>>>
>>>
>>>>>>
>>>
>>>>>> You received this message because you are subscribed to the Google
>>>
>>>>>> Groups "aroma.affymetrix" group with website
>>>
>>>>>> http://www.aroma-project.org/.
>>>
>>>>>> To post to this group, send email to [hidden email]
>>>
>>>>>> To unsubscribe and other options, go to
>>>
>>>>>> http://www.aroma-project.org/forum/
>>>
>>>>>>
>>>
>>>>>> --
>>>
>>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>>>> latest version of the package, 2) to report the output of
>>>>>> sessionInfo() and
>>>>>> traceback(), and 3) to post a complete code example.
>>>
>>>>>>
>>>
>>>>>>
>>>
>>>>>> You received this message because you are subscribed to the Google
>>>>>> Groups "aroma.affymetrix" group with website
>>>>>> http://www.aroma-project.org/.
>>>
>>>>>> To post to this group, send email to [hidden email]
>>>
>>>>>> To unsubscribe and other options, go to
>>>>>> http://www.aroma-project.org/forum/
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>>>>>>
>>>
>>>>>
>>>
>>>>> --
>>>
>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>>> latest version of the package, 2) to report the output of sessionInfo()
>>>>> and
>>>>> traceback(), and 3) to post a complete code example.
>>>
>>>>>
>>>
>>>>>
>>>
>>>>> You received this message because you are subscribed to the Google
>>>>> Groups
>>>>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>>>
>>>>> To post to this group, send email to [hidden email]
>>>
>>>>> To unsubscribe and other options, go to
>>>>> http://www.aroma-project.org/forum/
>>>
>>>>>
>>>
>>>>> --
>>>
>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>>> latest version of the package, 2) to report the output of sessionInfo()
>>>>> and
>>>>> traceback(), and 3) to post a complete code example.
>>>
>>>>>
>>>
>>>>>
>>>
>>>>> You received this message because you are subscribed to the Google
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>>>
>>>>> To post to this group, send email to [hidden email]
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>>>>> To unsubscribe and other options, go to
>>>>> http://www.aroma-project.org/forum/
>>>
>>>>>
>>>
>>>>
>>>
>>>> --
>>>
>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>> latest version of the package, 2) to report the output of sessionInfo()
>>>> and
>>>> traceback(), and 3) to post a complete code example.
>>>
>>>>
>>>
>>>>
>>>
>>>> You received this message because you are subscribed to the Google
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>>>
>>>> To post to this group, send email to [hidden email]
>>>
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>>>>
>>>
>>>> --
>>>
>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>> latest version of the package, 2) to report the output of sessionInfo()
>>>> and
>>>> traceback(), and 3) to post a complete code example.
>>>
>>>>
>>>
>>>>
>>>
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>>>
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>>>>
>>>
>>> --
>>>
>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>> latest
>>> version of the package, 2) to report the output of sessionInfo() and
>>> traceback(), and 3) to post a complete code example.
>>>
>>> You received this message because you are subscribed to the Google Groups
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>>>
>>> To post to this group, send email to [hidden email]
>>>
>>> To unsubscribe and other options, go to
>>> http://www.aroma-project.org/forum/
>>>
>>> --
>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>> latest
>>> version of the package, 2) to report the output of sessionInfo() and
>>> traceback(), and 3) to post a complete code example.
>>>
>>>
>>> You received this message because you are subscribed to the Google Groups
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>>> To post to this group, send email to [hidden email]
>>> To unsubscribe and other options, go to
>>> http://www.aroma-project.org/forum/
>>>
>>
>> --
>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>> latest version of the package, 2) to report the output of sessionInfo() and
>> traceback(), and 3) to post a complete code example.
>>
>>
>> You received this message because you are subscribed to the Google Groups
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>> To post to this group, send email to [hidden email]
>> To unsubscribe and other options, go to
>> http://www.aroma-project.org/forum/
>>
>> --
>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>> latest version of the package, 2) to report the output of sessionInfo() and
>> traceback(), and 3) to post a complete code example.
>>
>>
>> You received this message because you are subscribed to the Google Groups
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>> To unsubscribe and other options, go to
>> http://www.aroma-project.org/forum/
>>
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
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[aroma.affymetrix] DNA segmentation result

Yan Jiao
Hi,

Sorry to bother you again

If I don't need the chromosome Explorer as result, I just need that excel file with copy number in (regions.xls, in CBS folder), how should I set the parameter, I guess it will speed up the procedure as well, right?

Many thanks

yan

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
Sent: 28 November 2010 22:57
To: aroma-affymetrix
Subject: Re: [aroma.affymetrix] DNAcopy parameter

On Sun, Nov 28, 2010 at 6:01 AM, Pierre Neuvial
<[hidden email]> wrote:
> Hi,
>
> The parameters used are the default parameters of the 'segment'
> function of the DNAcopy package.  If you search for 'DNAcopy
> parameters' on the "Search forum" box at http://aroma-project.org, you
> will find this recent thread which gives an example of how these
> parameters can be changed:
>
> http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/aa9db6ac7835d828/b6ab6b1c9786d9ff

Note that I just posted a follow up on that thread clarified that it
is now possible to specify optional arguments specific to
DNAcopy::segment() as:

seg <- CbsModel(ds, min.width=5);

In order to find out which they are and what they do, see the specific
segmentation method, i.e. help("segment", package="DNAcopy").

/Henrik

>
> Hope this helps.
>
> Pierre
>
> On Wed, Nov 24, 2010 at 7:31 PM, Yan Jiao <[hidden email]> wrote:
>> Thanks Henrik,
>> I will update my R and aroma package,
>> Another question is what kind of parameters of aroma use for copy number
>> segmentation, if using DNAcopy as the algorithm?
>>
>> Many thanks
>>
>> yan
>>
>> -----Original Message-----
>> From: [hidden email]
>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>> Sent: 24 November 2010 17:06
>> To: aroma-affymetrix
>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>
>> Ok, after seing your sessionInfo();
>>
>> You need to update to R v2.12.0, especially since you're on Windows
>> 64-bit.  Lots of work have been done by R core people to support
>> Windows 64-bit on R v2.12.0 and beyond.  There is no shortcut to this.
>>
>> Update aroma.affymetrix to v1.8.0, cf. http://aroma-project.org/install
>>
>> Also, the Cairo package is not available for the 64-bit version of R
>> on Windows.  If you try install.packages("Cairo") on your Windows
>> machine, CRAN should report that package is not available.   Either
>> you have installed it by other means or it incorrectly installed on R
>> v2.11.0.
>>
>> /Henrik
>>
>>
>> On Wed, Nov 24, 2010 at 8:58 AM, Yan Jiao <[hidden email]> wrote:
>>> Hi Henrik,
>>>
>>> I did what you suggested:
>>>
>>>> traceback()
>>>
>>> 13: stop(gettextf("package '%s' is not installed for 'arch=%s'",
>>>
>>>         pkgname, r_arch), call. = FALSE, domain = NA)
>>>
>>> 12: testRversion(pkgInfo, package, pkgpath)
>>>
>>> 11: library(package, lib.loc = lib.loc, character.only = TRUE,
>>> logical.return = TRUE,
>>>
>>>         warn.conflicts = warn.conflicts, keep.source = keep.source)
>>>
>>> 10: base::require(...)
>>>
>>> 9: require("Cairo")
>>>
>>> 8: findPngDevice.default(transparent = FALSE)
>>>
>>> 7: findPngDevice(transparent = FALSE)
>>>
>>> 6: plot.CopyNumberSegmentationModel(model, path = path, imageFormat =
>>> "png",
>>>
>>>        plotband = plotband, arrays = arrays, ...)
>>>
>>> 5: plot(model, path = path, imageFormat = "png", plotband = plotband,
>>>
>>>        arrays = arrays, ...)
>>>
>>> 4: writeGraphs.ChromosomeExplorer(this, arrays = arrays, chromosomes =
>>> chromosomes,
>>>
>>>        zooms = zooms, ..., verbose = less(verbose))
>>>
>>> 3: writeGraphs(this, arrays = arrays, chromosomes = chromosomes,
>>>
>>>        zooms = zooms, ..., verbose = less(verbose))
>>>
>>> 2: process.ChromosomeExplorer(ce.all, verbose = TRUE)
>>>
>>> 1: process(ce.all, verbose = TRUE)
>>>
>>>> sessionInfo()
>>>
>>> R version 2.11.0 (2010-04-22)
>>>
>>> x86_64-pc-mingw32
>>>
>>> locale:
>>>
>>> [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United
>>> Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
>>> LC_NUMERIC=C
>>>
>>> [5] LC_TIME=English_United Kingdom.1252
>>>
>>> attached base packages:
>>>
>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>
>>> other attached packages:
>>>
>>>  [1] RColorBrewer_1.0-2     DNAcopy_1.22.1         preprocessCore_1.10.0
>>> sfit_0.1.9             aroma.affymetrix_1.7.0 aroma.apd_0.1.7
>>> affxparser_1.20.0
>>>
>>>  [8] R.huge_0.2.0           aroma.core_1.7.0       aroma.light_1.16.1
>>> matrixStats_0.2.2      R.rsp_0.4.0            R.cache_0.3.0
>>> R.filesets_0.9.0
>>>
>>> [15] digest_0.4.2           R.utils_1.5.3          R.oo_1.7.4
>>> R.methodsS3_1.2.1
>>>
>>> loaded via a namespace (and not attached):
>>>
>>> [1] tools_2.11.0
>>>
>>>>
>>>
>>> process(ce,chromosomes=c(1,8,17), verbose=-10)
>>>
>>> Generating ChromosomeExplorer report...
>>>
>>>  Setting up ChromosomeExplorer report files...
>>>
>>>   Copying template files...
>>>
>>>    Source path:
>>> C:/Users/rmhkyji/R/win64-library/2.11/aroma.core/reports/includes
>>>
>>>    Destination path: reports/includes
>>>
>>>   Copying template files...done
>>>
>>>  Setting up ChromosomeExplorer report files...done
>>>
>>>  Explorer output version: 3
>>>
>>>  Compiling ChromosomeExplorer.onLoad.js.rsp...
>>>
>>>   Source:
>>>
>>> C:/Users/rmhkyji/R/win64-library/2.11/aroma.core/reports/templates/rsp/ChromosomeExplorer3/ChromosomeExplorer.onLoad.js.rsp
>>>
>>>   Output path: reports/Fockens_1/ACC,-XY,RMA,+300,A+B,FLN,-XY
>>>
>>>   Scanning directories for available chip types...
>>>
>>>    Detected chip types: Mapping50K_Hind240
>>>
>>>   Scanning directories for available chip types...done
>>>
>>>   Scanning image files for available zooms...
>>>
>>>    Detected (or default) zooms: 1, 2, 4, 8, 16, 32, 64
>>>
>>>   Scanning image files for available zooms...done
>>>
>>>   Scanning directory for subdirectories...
>>>
>>>    Detected (or default) sets: cbs
>>>
>>>   Scanning directory for subdirectories...done
>>>
>>>   Compiling RSP...
>>>
>>>            member data.class dimension objectSize
>>>
>>>    1    chipTypes  character         1        120
>>>
>>>    2    chrLayers  character         0         40
>>>
>>>    3 sampleLabels  character         3        240
>>>
>>>    4 sampleLayers  character         0         40
>>>
>>>    5      samples  character         3        240
>>>
>>>    6         sets  character         1         96
>>>
>>>    7        zooms    numeric         7         72
>>>
>>>    Sample names:
>>>
>>>    [1] "GSM255038" "GSM255039" "GSM255040"
>>>
>>>    Full sample names:
>>>
>>>    [1] "GSM255038,total" "GSM255039,total" "GSM255040,total"
>>>
>>>   Compiling RSP...done
>>>
>>>  Compiling ChromosomeExplorer.onLoad.js.rsp...done
>>>
>>> Loading required package: Cairo
>>>
>>> Error: package 'Cairo' is not installed for 'arch=x64'
>>>
>>> Generating ChromosomeExplorer report...done
>>>
>>>
>>> -----Original Message-----
>>> From: [hidden email]
>>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>>> Sent: 24 November 2010 16:50
>>> To: aroma-affymetrix
>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>>
>>> Hi.
>>>
>>> On Wed, Nov 24, 2010 at 8:10 AM, Yan Jiao <[hidden email]> wrote:
>>>
>>>> Hi Henrik,
>>>
>>>>
>>>
>>>> Another question, I was trying to only do segmentation on 3 chromosomes,
>>>> how should I do it, I tried:
>>>
>>>> process(ce,chromosomes=c(1,8,17), verbose=TRUE);
>>>
>>>>
>>>
>>>> but got error message:
>>>
>>>>
>>>
>>>> Generating ChromosomeExplorer report...
>>>
>>>> Loading required package: Cairo
>>>
>>>> Error: package 'Cairo' is not installed for 'arch=x64'
>>>
>>>> Generating ChromosomeExplorer report...done
>>>
>>> Odd, because specifying a subset of chromosomes shouldn't be any
>>>
>>> different from running all, as you did before.
>>>
>>> So, there seem to be several packages that install on R 64-bit in
>>>
>>> Windows, but when trying to use then fails.  The Cairo package is
>>>
>>> actually "deprecated" (replaced with similar function builtin in R),
>>>
>>> but we've kept support for backward compatibilities.  It seems like
>>>
>>> you're facing these issues - and not that many people are running
>>>
>>> 64-bit Windows yet so you seem to be the one hitting the bumps.
>>>
>>> What does traceback() give when you get the error?
>>>
>>> What is your sessionInfo()?
>>>
>>> Can you use process(ce,chromosomes=c(1,8,17), verbose=-10) in order to
>>>
>>> narrow down where the error occurs.
>>>
>>> /Henrik
>>>
>>>>
>>>
>>>>
>>>
>>>> Many thanks
>>>
>>>>
>>>
>>>> yan
>>>
>>>>
>>>
>>>>
>>>
>>>>
>>>
>>>> -----Original Message-----
>>>
>>>> From: [hidden email]
>>>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>>>
>>>> Sent: 24 November 2010 15:08
>>>
>>>> To: aroma-affymetrix
>>>
>>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>>
>>>>
>>>
>>>> Hi,
>>>
>>>>
>>>
>>>> great.  Contrary to error messages, warnings are alright to get.
>>>
>>>>
>>>
>>>> /H
>>>
>>>>
>>>
>>>> On Wed, Nov 24, 2010 at 2:51 AM, Yan Jiao <[hidden email]> wrote:
>>>
>>>>> Thank you Henrik,
>>>
>>>>> It works now, but I got some warning:
>>>
>>>>>
>>>
>>>>> process(ce, verbose=TRUE);
>>>
>>>>> Generating ChromosomeExplorer report...
>>>
>>>>> Loading required package: Cairo
>>>
>>>>> Generating ChromosomeExplorer report...done
>>>
>>>>> [1] TRUE
>>>
>>>>> Warning messages:
>>>
>>>>> 1: In library(package, lib.loc = lib.loc, character.only = TRUE,
>>>>> logical.return = TRUE,  :
>>>
>>>>>  there is no package called 'Cairo'
>>>
>>>>> 2: In method(static, ...) :
>>>
>>>>>  Ghostscript not found. Searched directories: C:/gs, C:\Program
>>>>> Files/gs,
>>>>> /gs, C:\Program Files\Common Files/gs
>>>
>>>>>
>>>
>>>>> Are those warning messages serious? Could I ignore them?
>>>
>>>>>
>>>
>>>>>
>>>
>>>>> Yan
>>>
>>>>>
>>>
>>>>> -----Original Message-----
>>>
>>>>> From: [hidden email]
>>>>> [mailto:[hidden email]] On Behalf Of Henrik
>>>>> Bengtsson
>>>
>>>>> Sent: 23 November 2010 21:53
>>>
>>>>> To: aroma-affymetrix
>>>
>>>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>>
>>>>>
>>>
>>>>> Hi.
>>>
>>>>>
>>>
>>>>> On Tue, Nov 23, 2010 at 11:51 AM, Yan Jiao <[hidden email]> wrote:
>>>
>>>>>> Hi Henrik,
>>>
>>>>>>
>>>
>>>>>> Sorry, the error is after
>>>
>>>>>> cbs <- CbsModel(ds);
>>>
>>>>>> ce <- ChromosomeExplorer(cbs);
>>>
>>>>>> process(ce, verbose=TRUE);
>>>
>>>>>
>>>
>>>>> Ok, now the error message makes a bit more sense (it was my suspicion
>>>
>>>>> but I didn't want make guesses).
>>>
>>>>>
>>>
>>>>>>
>>>
>>>>>>
>>>
>>>>>> Generating ChromosomeExplorer report...
>>>
>>>>>> Loading required package: Cairo
>>>
>>>>>> <simpleError in inDL(x, as.logical(local), as.logical(now), ...):
>>>>>> unable
>>>
>>>>>> to load shared library
>>>
>>>>>> 'C:/Users/rmhkyji/R/win64-library/2.11/GLAD/libs/x64/GLAD.dll':
>>>
>>>>>>  LoadLibrary failure:  The specified module could not be found.
>>>
>>>>>>
>>>
>>>>>> And there  is a pop out window saying: The program can't start because
>>>
>>>>>> libgsl-0.dll I smissing from your computer. Try reinstalling the
>>>>>> program
>>>
>>>>>> to fix this program.
>>>
>>>>>
>>>
>>>>> I can reproduce this on 64-bit Windows 7 - you get the same error if
>>>
>>>>> you try library("GLAD").  It is because we utilize part of the GLAD
>>>
>>>>> package, if and only if it is *installed*, and otherwise we turn to
>>>
>>>>> backup solutions.  What happens here is that *GLAD is installed but
>>>
>>>>> doesn't load*, which causes the error so that backup solutions doesn't
>>>
>>>>> kick in.   In the next release I'll try to make sure the backup
>>>
>>>>> solutions will also work when there is an error load GLAD.  In
>>>
>>>>> meanwhile, you can do this:
>>>
>>>>>
>>>
>>>>> WORKAROUND:
>>>
>>>>>
>>>
>>>>> 1. Uninstall the GLAD package (it doesn't work anyway):
>>>
>>>>>
>>>
>>>>>> remove.packages("GLAD")
>>>
>>>>> Removing package(s) from 'C:\Users\hb\R\win-library\2.12'
>>>
>>>>> (as 'lib' is unspecified)
>>>
>>>>>
>>>
>>>>>> library("GLAD")
>>>
>>>>> Error in library("GLAD") : there is no package called 'GLAD'
>>>
>>>>>
>>>
>>>>> That should do it.  Let me know if it works for you.
>>>
>>>>>
>>>
>>>>> TECHNICAL DETAILS: It happens because the GNU Scientific Library (GSL)
>>>
>>>>> is not installed on the system (hence the 'gsl' part of
>>>
>>>>> 'libgsl-0.dll'). There is a hard-to-find note that you need GSL in
>>>
>>>>> order to use the GLAD package, cf.
>>>
>>>>> http://bioconductor.org/packages/release/bioc/html/GLAD.html.  There
>>>
>>>>> exist 32-bit binaries of GSL at
>>>
>>>>> http://gnuwin32.sourceforge.net/packages/gsl.htm.  Unfortunately, it
>>>
>>>>> does not work for the 64-bit version of R on Windows 64-bit.  It works
>>>
>>>>> if you do tricks an run the 32-bit version of R, but that is a rather
>>>
>>>>> inconvenient workaround.
>>>
>>>>>
>>>
>>>>> /Henrik
>>>
>>>>>
>>>
>>>>>>
>>>
>>>>>>
>>>
>>>>>> Yan
>>>
>>>>>>
>>>
>>>>>> -----Original Message-----
>>>
>>>>>> From: [hidden email]
>>>
>>>>>> [mailto:[hidden email]] On Behalf Of Henrik
>>>>>> Bengtsson
>>>
>>>>>> Sent: 23 November 2010 18:50
>>>
>>>>>> To: aroma-affymetrix
>>>
>>>>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>>
>>>>>>
>>>
>>>>>> Hi.
>>>
>>>>>>
>>>
>>>>>> On Tue, Nov 23, 2010 at 10:05 AM, Yan Jiao <[hidden email]> wrote:
>>>
>>>>>>>
>>>
>>>>>>>
>>>
>>>>>>> Dear all,
>>>
>>>>>>>
>>>
>>>>>>> I'm trying to do DNA segmentation,
>>>
>>>>>>>
>>>
>>>>>>> This is what I'm doing:
>>>
>>>>>>>
>>>
>>>>>>> ds <- doCRMAv1("Fockens_1", chipType="Mapping50K_Hind240",
>>>
>>>>>> verbose=TRUE);
>>>
>>>>>>>
>>>
>>>>>>> ###this is done sucessfully
>>>
>>>>>>>
>>>
>>>>>>> # Segmentation
>>>
>>>>>>>
>>>
>>>>>>> cbs <- CbsModel(ds);
>>>
>>>>>>>
>>>
>>>>>>>
>>>
>>>>>>>
>>>
>>>>>>> I got error libgsl-0.dll is missing, I think it's using GLAD, but I'm
>>>
>>>>>> trying
>>>
>>>>>>> to use DNAcopy for segmentation.
>>>
>>>>>>
>>>
>>>>>> Is it really the case that you get that error when you do:
>>>
>>>>>>
>>>
>>>>>> cbs <- CbsModel(ds);
>>>
>>>>>>
>>>
>>>>>> or do you do anything else?  Is suspect you do something more.
>>>
>>>>>>
>>>
>>>>>> Also, after you got the error, could you cut'n'paste the verbose
>>>
>>>>>> output including any error messages you get and send it to us?   Also,
>>>
>>>>>> make sure to report what print(traceback()) gives immediate after
>>>
>>>>>> getting the error.
>>>
>>>>>>
>>>
>>>>>> /Henrik
>>>
>>>>>>
>>>
>>>>>> PS. The 'GLAD' package may indeed be used regardless of segmentation
>>>
>>>>>> method because it contains information about cytobands.
>>>
>>>>>>
>>>
>>>>>>>
>>>
>>>>>>> How to change it?
>>>
>>>>>>>
>>>
>>>>>>>
>>>
>>>>>>>
>>>
>>>>>>> Many thanks
>>>
>>>>>>>
>>>
>>>>>>>
>>>
>>>>>>>
>>>
>>>>>>> yan
>>>
>>>>>>>
>>>
>>>>>>>
>>>
>>>>>>>
>>>
>>>>>>>
>>>
>>>>>>>
>>>
>>>>>>>
>>>
>>>>>>>
>>>
>>>>>>>
>>>>>>> **********************************************************************
>>>
>>>>>>>
>>>
>>>>>>> This email and any files transmitted with it are confidential and
>>>
>>>>>>>
>>>
>>>>>>> intended solely for the use of the individual or entity to whom they
>>>
>>>>>>>
>>>
>>>>>>> are addressed. If you have received this email in error please notify
>>>
>>>>>>>
>>>
>>>>>>> the system manager ([hidden email]).
>>>
>>>>>>>
>>>
>>>>>>>
>>>>>>> **********************************************************************
>>>
>>>>>>>
>>>
>>>>>>>
>>>
>>>>>>>
>>>
>>>>>>> --
>>>
>>>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>
>>>>>> latest
>>>
>>>>>>> version of the package, 2) to report the output of sessionInfo() and
>>>
>>>>>>> traceback(), and 3) to post a complete code example.
>>>
>>>>>>>
>>>
>>>>>>>
>>>
>>>>>>> You received this message because you are subscribed to the Google
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>>>
>>>>>>> To post to this group, send email to
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>>>>>>
>>>
>>>>>> --
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>>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>
>>>>>> latest version of the package, 2) to report the output of
>>>>>> sessionInfo()
>>>
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>>>>>>
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>>>>>> Groups "aroma.affymetrix" group with website
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>>>
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>>>
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>>>>>>
>>>
>>>>>> --
>>>
>>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>>>> latest version of the package, 2) to report the output of
>>>>>> sessionInfo() and
>>>>>> traceback(), and 3) to post a complete code example.
>>>
>>>>>>
>>>
>>>>>>
>>>
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>>>>>>
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>>>>>
>>>
>>>>> --
>>>
>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>>> latest version of the package, 2) to report the output of sessionInfo()
>>>>> and
>>>>> traceback(), and 3) to post a complete code example.
>>>
>>>>>
>>>
>>>>>
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>>>>> You received this message because you are subscribed to the Google
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>>>>>
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>>>>> --
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>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>>> latest version of the package, 2) to report the output of sessionInfo()
>>>>> and
>>>>> traceback(), and 3) to post a complete code example.
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>>>>> You received this message because you are subscribed to the Google
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>>>>>
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>>>>
>>>
>>>> --
>>>
>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>> latest version of the package, 2) to report the output of sessionInfo()
>>>> and
>>>> traceback(), and 3) to post a complete code example.
>>>
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>>>> latest version of the package, 2) to report the output of sessionInfo()
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>>> --
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>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>> latest
>>> version of the package, 2) to report the output of sessionInfo() and
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>>> You received this message because you are subscribed to the Google Groups
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>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>> latest
>>> version of the package, 2) to report the output of sessionInfo() and
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>> --
>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>> latest version of the package, 2) to report the output of sessionInfo() and
>> traceback(), and 3) to post a complete code example.
>>
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>> latest version of the package, 2) to report the output of sessionInfo() and
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>
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Re: [aroma.affymetrix] DNA segmentation result

Pierre Neuvial
Hi,

Sure, it will be quicker.

In this case, you only have to setup the CBS segmentation model, and
fit it.  For example:

## define the segmentation model
## (and its parameters)
seg <- CbsModel(ds, min.width=5);

## perform the segmentation
## (possibly for a subset of arrays and chromosomes)
fit(seg, array=2, chromosome=5, verbose=TRUE);

There are other examples on the aroma project website, e.g.
http://aroma-project.org/vignettes/pairedTotalCopyNumberAnalysis

Best,

Pierre

On Mon, Nov 29, 2010 at 7:33 PM, Yan Jiao <[hidden email]> wrote:

> Hi,
>
> Sorry to bother you again
>
> If I don't need the chromosome Explorer as result, I just need that excel file with copy number in (regions.xls, in CBS folder), how should I set the parameter, I guess it will speed up the procedure as well, right?
>
> Many thanks
>
> yan
>
> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
> Sent: 28 November 2010 22:57
> To: aroma-affymetrix
> Subject: Re: [aroma.affymetrix] DNAcopy parameter
>
> On Sun, Nov 28, 2010 at 6:01 AM, Pierre Neuvial
> <[hidden email]> wrote:
>> Hi,
>>
>> The parameters used are the default parameters of the 'segment'
>> function of the DNAcopy package.  If you search for 'DNAcopy
>> parameters' on the "Search forum" box at http://aroma-project.org, you
>> will find this recent thread which gives an example of how these
>> parameters can be changed:
>>
>> http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/aa9db6ac7835d828/b6ab6b1c9786d9ff
>
> Note that I just posted a follow up on that thread clarified that it
> is now possible to specify optional arguments specific to
> DNAcopy::segment() as:
>
> seg <- CbsModel(ds, min.width=5);
>
> In order to find out which they are and what they do, see the specific
> segmentation method, i.e. help("segment", package="DNAcopy").
>
> /Henrik
>
>>
>> Hope this helps.
>>
>> Pierre
>>
>> On Wed, Nov 24, 2010 at 7:31 PM, Yan Jiao <[hidden email]> wrote:
>>> Thanks Henrik,
>>> I will update my R and aroma package,
>>> Another question is what kind of parameters of aroma use for copy number
>>> segmentation, if using DNAcopy as the algorithm?
>>>
>>> Many thanks
>>>
>>> yan
>>>
>>> -----Original Message-----
>>> From: [hidden email]
>>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>>> Sent: 24 November 2010 17:06
>>> To: aroma-affymetrix
>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>>
>>> Ok, after seing your sessionInfo();
>>>
>>> You need to update to R v2.12.0, especially since you're on Windows
>>> 64-bit.  Lots of work have been done by R core people to support
>>> Windows 64-bit on R v2.12.0 and beyond.  There is no shortcut to this.
>>>
>>> Update aroma.affymetrix to v1.8.0, cf. http://aroma-project.org/install
>>>
>>> Also, the Cairo package is not available for the 64-bit version of R
>>> on Windows.  If you try install.packages("Cairo") on your Windows
>>> machine, CRAN should report that package is not available.   Either
>>> you have installed it by other means or it incorrectly installed on R
>>> v2.11.0.
>>>
>>> /Henrik
>>>
>>>
>>> On Wed, Nov 24, 2010 at 8:58 AM, Yan Jiao <[hidden email]> wrote:
>>>> Hi Henrik,
>>>>
>>>> I did what you suggested:
>>>>
>>>>> traceback()
>>>>
>>>> 13: stop(gettextf("package '%s' is not installed for 'arch=%s'",
>>>>
>>>>         pkgname, r_arch), call. = FALSE, domain = NA)
>>>>
>>>> 12: testRversion(pkgInfo, package, pkgpath)
>>>>
>>>> 11: library(package, lib.loc = lib.loc, character.only = TRUE,
>>>> logical.return = TRUE,
>>>>
>>>>         warn.conflicts = warn.conflicts, keep.source = keep.source)
>>>>
>>>> 10: base::require(...)
>>>>
>>>> 9: require("Cairo")
>>>>
>>>> 8: findPngDevice.default(transparent = FALSE)
>>>>
>>>> 7: findPngDevice(transparent = FALSE)
>>>>
>>>> 6: plot.CopyNumberSegmentationModel(model, path = path, imageFormat =
>>>> "png",
>>>>
>>>>        plotband = plotband, arrays = arrays, ...)
>>>>
>>>> 5: plot(model, path = path, imageFormat = "png", plotband = plotband,
>>>>
>>>>        arrays = arrays, ...)
>>>>
>>>> 4: writeGraphs.ChromosomeExplorer(this, arrays = arrays, chromosomes =
>>>> chromosomes,
>>>>
>>>>        zooms = zooms, ..., verbose = less(verbose))
>>>>
>>>> 3: writeGraphs(this, arrays = arrays, chromosomes = chromosomes,
>>>>
>>>>        zooms = zooms, ..., verbose = less(verbose))
>>>>
>>>> 2: process.ChromosomeExplorer(ce.all, verbose = TRUE)
>>>>
>>>> 1: process(ce.all, verbose = TRUE)
>>>>
>>>>> sessionInfo()
>>>>
>>>> R version 2.11.0 (2010-04-22)
>>>>
>>>> x86_64-pc-mingw32
>>>>
>>>> locale:
>>>>
>>>> [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United
>>>> Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
>>>> LC_NUMERIC=C
>>>>
>>>> [5] LC_TIME=English_United Kingdom.1252
>>>>
>>>> attached base packages:
>>>>
>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>
>>>> other attached packages:
>>>>
>>>>  [1] RColorBrewer_1.0-2     DNAcopy_1.22.1         preprocessCore_1.10.0
>>>> sfit_0.1.9             aroma.affymetrix_1.7.0 aroma.apd_0.1.7
>>>> affxparser_1.20.0
>>>>
>>>>  [8] R.huge_0.2.0           aroma.core_1.7.0       aroma.light_1.16.1
>>>> matrixStats_0.2.2      R.rsp_0.4.0            R.cache_0.3.0
>>>> R.filesets_0.9.0
>>>>
>>>> [15] digest_0.4.2           R.utils_1.5.3          R.oo_1.7.4
>>>> R.methodsS3_1.2.1
>>>>
>>>> loaded via a namespace (and not attached):
>>>>
>>>> [1] tools_2.11.0
>>>>
>>>>>
>>>>
>>>> process(ce,chromosomes=c(1,8,17), verbose=-10)
>>>>
>>>> Generating ChromosomeExplorer report...
>>>>
>>>>  Setting up ChromosomeExplorer report files...
>>>>
>>>>   Copying template files...
>>>>
>>>>    Source path:
>>>> C:/Users/rmhkyji/R/win64-library/2.11/aroma.core/reports/includes
>>>>
>>>>    Destination path: reports/includes
>>>>
>>>>   Copying template files...done
>>>>
>>>>  Setting up ChromosomeExplorer report files...done
>>>>
>>>>  Explorer output version: 3
>>>>
>>>>  Compiling ChromosomeExplorer.onLoad.js.rsp...
>>>>
>>>>   Source:
>>>>
>>>> C:/Users/rmhkyji/R/win64-library/2.11/aroma.core/reports/templates/rsp/ChromosomeExplorer3/ChromosomeExplorer.onLoad.js.rsp
>>>>
>>>>   Output path: reports/Fockens_1/ACC,-XY,RMA,+300,A+B,FLN,-XY
>>>>
>>>>   Scanning directories for available chip types...
>>>>
>>>>    Detected chip types: Mapping50K_Hind240
>>>>
>>>>   Scanning directories for available chip types...done
>>>>
>>>>   Scanning image files for available zooms...
>>>>
>>>>    Detected (or default) zooms: 1, 2, 4, 8, 16, 32, 64
>>>>
>>>>   Scanning image files for available zooms...done
>>>>
>>>>   Scanning directory for subdirectories...
>>>>
>>>>    Detected (or default) sets: cbs
>>>>
>>>>   Scanning directory for subdirectories...done
>>>>
>>>>   Compiling RSP...
>>>>
>>>>            member data.class dimension objectSize
>>>>
>>>>    1    chipTypes  character         1        120
>>>>
>>>>    2    chrLayers  character         0         40
>>>>
>>>>    3 sampleLabels  character         3        240
>>>>
>>>>    4 sampleLayers  character         0         40
>>>>
>>>>    5      samples  character         3        240
>>>>
>>>>    6         sets  character         1         96
>>>>
>>>>    7        zooms    numeric         7         72
>>>>
>>>>    Sample names:
>>>>
>>>>    [1] "GSM255038" "GSM255039" "GSM255040"
>>>>
>>>>    Full sample names:
>>>>
>>>>    [1] "GSM255038,total" "GSM255039,total" "GSM255040,total"
>>>>
>>>>   Compiling RSP...done
>>>>
>>>>  Compiling ChromosomeExplorer.onLoad.js.rsp...done
>>>>
>>>> Loading required package: Cairo
>>>>
>>>> Error: package 'Cairo' is not installed for 'arch=x64'
>>>>
>>>> Generating ChromosomeExplorer report...done
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: [hidden email]
>>>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>>>> Sent: 24 November 2010 16:50
>>>> To: aroma-affymetrix
>>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>>>
>>>> Hi.
>>>>
>>>> On Wed, Nov 24, 2010 at 8:10 AM, Yan Jiao <[hidden email]> wrote:
>>>>
>>>>> Hi Henrik,
>>>>
>>>>>
>>>>
>>>>> Another question, I was trying to only do segmentation on 3 chromosomes,
>>>>> how should I do it, I tried:
>>>>
>>>>> process(ce,chromosomes=c(1,8,17), verbose=TRUE);
>>>>
>>>>>
>>>>
>>>>> but got error message:
>>>>
>>>>>
>>>>
>>>>> Generating ChromosomeExplorer report...
>>>>
>>>>> Loading required package: Cairo
>>>>
>>>>> Error: package 'Cairo' is not installed for 'arch=x64'
>>>>
>>>>> Generating ChromosomeExplorer report...done
>>>>
>>>> Odd, because specifying a subset of chromosomes shouldn't be any
>>>>
>>>> different from running all, as you did before.
>>>>
>>>> So, there seem to be several packages that install on R 64-bit in
>>>>
>>>> Windows, but when trying to use then fails.  The Cairo package is
>>>>
>>>> actually "deprecated" (replaced with similar function builtin in R),
>>>>
>>>> but we've kept support for backward compatibilities.  It seems like
>>>>
>>>> you're facing these issues - and not that many people are running
>>>>
>>>> 64-bit Windows yet so you seem to be the one hitting the bumps.
>>>>
>>>> What does traceback() give when you get the error?
>>>>
>>>> What is your sessionInfo()?
>>>>
>>>> Can you use process(ce,chromosomes=c(1,8,17), verbose=-10) in order to
>>>>
>>>> narrow down where the error occurs.
>>>>
>>>> /Henrik
>>>>
>>>>>
>>>>
>>>>>
>>>>
>>>>> Many thanks
>>>>
>>>>>
>>>>
>>>>> yan
>>>>
>>>>>
>>>>
>>>>>
>>>>
>>>>>
>>>>
>>>>> -----Original Message-----
>>>>
>>>>> From: [hidden email]
>>>>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>>>>
>>>>> Sent: 24 November 2010 15:08
>>>>
>>>>> To: aroma-affymetrix
>>>>
>>>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>>>
>>>>>
>>>>
>>>>> Hi,
>>>>
>>>>>
>>>>
>>>>> great.  Contrary to error messages, warnings are alright to get.
>>>>
>>>>>
>>>>
>>>>> /H
>>>>
>>>>>
>>>>
>>>>> On Wed, Nov 24, 2010 at 2:51 AM, Yan Jiao <[hidden email]> wrote:
>>>>
>>>>>> Thank you Henrik,
>>>>
>>>>>> It works now, but I got some warning:
>>>>
>>>>>>
>>>>
>>>>>> process(ce, verbose=TRUE);
>>>>
>>>>>> Generating ChromosomeExplorer report...
>>>>
>>>>>> Loading required package: Cairo
>>>>
>>>>>> Generating ChromosomeExplorer report...done
>>>>
>>>>>> [1] TRUE
>>>>
>>>>>> Warning messages:
>>>>
>>>>>> 1: In library(package, lib.loc = lib.loc, character.only = TRUE,
>>>>>> logical.return = TRUE,  :
>>>>
>>>>>>  there is no package called 'Cairo'
>>>>
>>>>>> 2: In method(static, ...) :
>>>>
>>>>>>  Ghostscript not found. Searched directories: C:/gs, C:\Program
>>>>>> Files/gs,
>>>>>> /gs, C:\Program Files\Common Files/gs
>>>>
>>>>>>
>>>>
>>>>>> Are those warning messages serious? Could I ignore them?
>>>>
>>>>>>
>>>>
>>>>>>
>>>>
>>>>>> Yan
>>>>
>>>>>>
>>>>
>>>>>> -----Original Message-----
>>>>
>>>>>> From: [hidden email]
>>>>>> [mailto:[hidden email]] On Behalf Of Henrik
>>>>>> Bengtsson
>>>>
>>>>>> Sent: 23 November 2010 21:53
>>>>
>>>>>> To: aroma-affymetrix
>>>>
>>>>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>>>
>>>>>>
>>>>
>>>>>> Hi.
>>>>
>>>>>>
>>>>
>>>>>> On Tue, Nov 23, 2010 at 11:51 AM, Yan Jiao <[hidden email]> wrote:
>>>>
>>>>>>> Hi Henrik,
>>>>
>>>>>>>
>>>>
>>>>>>> Sorry, the error is after
>>>>
>>>>>>> cbs <- CbsModel(ds);
>>>>
>>>>>>> ce <- ChromosomeExplorer(cbs);
>>>>
>>>>>>> process(ce, verbose=TRUE);
>>>>
>>>>>>
>>>>
>>>>>> Ok, now the error message makes a bit more sense (it was my suspicion
>>>>
>>>>>> but I didn't want make guesses).
>>>>
>>>>>>
>>>>
>>>>>>>
>>>>
>>>>>>>
>>>>
>>>>>>> Generating ChromosomeExplorer report...
>>>>
>>>>>>> Loading required package: Cairo
>>>>
>>>>>>> <simpleError in inDL(x, as.logical(local), as.logical(now), ...):
>>>>>>> unable
>>>>
>>>>>>> to load shared library
>>>>
>>>>>>> 'C:/Users/rmhkyji/R/win64-library/2.11/GLAD/libs/x64/GLAD.dll':
>>>>
>>>>>>>  LoadLibrary failure:  The specified module could not be found.
>>>>
>>>>>>>
>>>>
>>>>>>> And there  is a pop out window saying: The program can't start because
>>>>
>>>>>>> libgsl-0.dll I smissing from your computer. Try reinstalling the
>>>>>>> program
>>>>
>>>>>>> to fix this program.
>>>>
>>>>>>
>>>>
>>>>>> I can reproduce this on 64-bit Windows 7 - you get the same error if
>>>>
>>>>>> you try library("GLAD").  It is because we utilize part of the GLAD
>>>>
>>>>>> package, if and only if it is *installed*, and otherwise we turn to
>>>>
>>>>>> backup solutions.  What happens here is that *GLAD is installed but
>>>>
>>>>>> doesn't load*, which causes the error so that backup solutions doesn't
>>>>
>>>>>> kick in.   In the next release I'll try to make sure the backup
>>>>
>>>>>> solutions will also work when there is an error load GLAD.  In
>>>>
>>>>>> meanwhile, you can do this:
>>>>
>>>>>>
>>>>
>>>>>> WORKAROUND:
>>>>
>>>>>>
>>>>
>>>>>> 1. Uninstall the GLAD package (it doesn't work anyway):
>>>>
>>>>>>
>>>>
>>>>>>> remove.packages("GLAD")
>>>>
>>>>>> Removing package(s) from 'C:\Users\hb\R\win-library\2.12'
>>>>
>>>>>> (as 'lib' is unspecified)
>>>>
>>>>>>
>>>>
>>>>>>> library("GLAD")
>>>>
>>>>>> Error in library("GLAD") : there is no package called 'GLAD'
>>>>
>>>>>>
>>>>
>>>>>> That should do it.  Let me know if it works for you.
>>>>
>>>>>>
>>>>
>>>>>> TECHNICAL DETAILS: It happens because the GNU Scientific Library (GSL)
>>>>
>>>>>> is not installed on the system (hence the 'gsl' part of
>>>>
>>>>>> 'libgsl-0.dll'). There is a hard-to-find note that you need GSL in
>>>>
>>>>>> order to use the GLAD package, cf.
>>>>
>>>>>> http://bioconductor.org/packages/release/bioc/html/GLAD.html.  There
>>>>
>>>>>> exist 32-bit binaries of GSL at
>>>>
>>>>>> http://gnuwin32.sourceforge.net/packages/gsl.htm.  Unfortunately, it
>>>>
>>>>>> does not work for the 64-bit version of R on Windows 64-bit.  It works
>>>>
>>>>>> if you do tricks an run the 32-bit version of R, but that is a rather
>>>>
>>>>>> inconvenient workaround.
>>>>
>>>>>>
>>>>
>>>>>> /Henrik
>>>>
>>>>>>
>>>>
>>>>>>>
>>>>
>>>>>>>
>>>>
>>>>>>> Yan
>>>>
>>>>>>>
>>>>
>>>>>>> -----Original Message-----
>>>>
>>>>>>> From: [hidden email]
>>>>
>>>>>>> [mailto:[hidden email]] On Behalf Of Henrik
>>>>>>> Bengtsson
>>>>
>>>>>>> Sent: 23 November 2010 18:50
>>>>
>>>>>>> To: aroma-affymetrix
>>>>
>>>>>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>>>
>>>>>>>
>>>>
>>>>>>> Hi.
>>>>
>>>>>>>
>>>>
>>>>>>> On Tue, Nov 23, 2010 at 10:05 AM, Yan Jiao <[hidden email]> wrote:
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>> Dear all,
>>>>
>>>>>>>>
>>>>
>>>>>>>> I'm trying to do DNA segmentation,
>>>>
>>>>>>>>
>>>>
>>>>>>>> This is what I'm doing:
>>>>
>>>>>>>>
>>>>
>>>>>>>> ds <- doCRMAv1("Fockens_1", chipType="Mapping50K_Hind240",
>>>>
>>>>>>> verbose=TRUE);
>>>>
>>>>>>>>
>>>>
>>>>>>>> ###this is done sucessfully
>>>>
>>>>>>>>
>>>>
>>>>>>>> # Segmentation
>>>>
>>>>>>>>
>>>>
>>>>>>>> cbs <- CbsModel(ds);
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>> I got error libgsl-0.dll is missing, I think it's using GLAD, but I'm
>>>>
>>>>>>> trying
>>>>
>>>>>>>> to use DNAcopy for segmentation.
>>>>
>>>>>>>
>>>>
>>>>>>> Is it really the case that you get that error when you do:
>>>>
>>>>>>>
>>>>
>>>>>>> cbs <- CbsModel(ds);
>>>>
>>>>>>>
>>>>
>>>>>>> or do you do anything else?  Is suspect you do something more.
>>>>
>>>>>>>
>>>>
>>>>>>> Also, after you got the error, could you cut'n'paste the verbose
>>>>
>>>>>>> output including any error messages you get and send it to us?   Also,
>>>>
>>>>>>> make sure to report what print(traceback()) gives immediate after
>>>>
>>>>>>> getting the error.
>>>>
>>>>>>>
>>>>
>>>>>>> /Henrik
>>>>
>>>>>>>
>>>>
>>>>>>> PS. The 'GLAD' package may indeed be used regardless of segmentation
>>>>
>>>>>>> method because it contains information about cytobands.
>>>>
>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>> How to change it?
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>> Many thanks
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>> yan
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>>>>> **********************************************************************
>>>>
>>>>>>>>
>>>>
>>>>>>>> This email and any files transmitted with it are confidential and
>>>>
>>>>>>>>
>>>>
>>>>>>>> intended solely for the use of the individual or entity to whom they
>>>>
>>>>>>>>
>>>>
>>>>>>>> are addressed. If you have received this email in error please notify
>>>>
>>>>>>>>
>>>>
>>>>>>>> the system manager ([hidden email]).
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>>>>> **********************************************************************
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>> --
>>>>
>>>>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>>
>>>>>>> latest
>>>>
>>>>>>>> version of the package, 2) to report the output of sessionInfo() and
>>>>
>>>>>>>> traceback(), and 3) to post a complete code example.
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>> You received this message because you are subscribed to the Google
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>>>>
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>>>>>>>>
>>>>
>>>>>>>
>>>>
>>>>>>> --
>>>>
>>>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>>
>>>>>>> latest version of the package, 2) to report the output of
>>>>>>> sessionInfo()
>>>>
>>>>>>> and traceback(), and 3) to post a complete code example.
>>>>
>>>>>>>
>>>>
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>>>>
>>>>>>> You received this message because you are subscribed to the Google
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>>>>>>> Groups "aroma.affymetrix" group with website
>>>>
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>>>>>>> To post to this group, send email to [hidden email]
>>>>
>>>>>>> To unsubscribe and other options, go to
>>>>
>>>>>>> http://www.aroma-project.org/forum/
>>>>
>>>>>>>
>>>>
>>>>>>> --
>>>>
>>>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>>>>> latest version of the package, 2) to report the output of
>>>>>>> sessionInfo() and
>>>>>>> traceback(), and 3) to post a complete code example.
>>>>
>>>>>>>
>>>>
>>>>>>>
>>>>
>>>>>>> You received this message because you are subscribed to the Google
>>>>>>> Groups "aroma.affymetrix" group with website
>>>>>>> http://www.aroma-project.org/.
>>>>
>>>>>>> To post to this group, send email to [hidden email]
>>>>
>>>>>>> To unsubscribe and other options, go to
>>>>>>> http://www.aroma-project.org/forum/
>>>>
>>>>>>>
>>>>
>>>>>>
>>>>
>>>>>> --
>>>>
>>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>>>> latest version of the package, 2) to report the output of sessionInfo()
>>>>>> and
>>>>>> traceback(), and 3) to post a complete code example.
>>>>
>>>>>>
>>>>
>>>>>>
>>>>
>>>>>> You received this message because you are subscribed to the Google
>>>>>> Groups
>>>>>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>>>>
>>>>>> To post to this group, send email to [hidden email]
>>>>
>>>>>> To unsubscribe and other options, go to
>>>>>> http://www.aroma-project.org/forum/
>>>>
>>>>>>
>>>>
>>>>>> --
>>>>
>>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>>>> latest version of the package, 2) to report the output of sessionInfo()
>>>>>> and
>>>>>> traceback(), and 3) to post a complete code example.
>>>>
>>>>>>
>>>>
>>>>>>
>>>>
>>>>>> You received this message because you are subscribed to the Google
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>>>>
>>>>>> To post to this group, send email to [hidden email]
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>>>>>> To unsubscribe and other options, go to
>>>>>> http://www.aroma-project.org/forum/
>>>>
>>>>>>
>>>>
>>>>>
>>>>
>>>>> --
>>>>
>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>>> latest version of the package, 2) to report the output of sessionInfo()
>>>>> and
>>>>> traceback(), and 3) to post a complete code example.
>>>>
>>>>>
>>>>
>>>>>
>>>>
>>>>> You received this message because you are subscribed to the Google
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>>>>
>>>>> To post to this group, send email to [hidden email]
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>>>>> To unsubscribe and other options, go to
>>>>> http://www.aroma-project.org/forum/
>>>>
>>>>>
>>>>
>>>>> --
>>>>
>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>>> latest version of the package, 2) to report the output of sessionInfo()
>>>>> and
>>>>> traceback(), and 3) to post a complete code example.
>>>>
>>>>>
>>>>
>>>>>
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>>>>> You received this message because you are subscribed to the Google
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>>>>
>>>>> To post to this group, send email to [hidden email]
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>>>>> To unsubscribe and other options, go to
>>>>> http://www.aroma-project.org/forum/
>>>>
>>>>>
>>>>
>>>> --
>>>>
>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>> latest
>>>> version of the package, 2) to report the output of sessionInfo() and
>>>> traceback(), and 3) to post a complete code example.
>>>>
>>>> You received this message because you are subscribed to the Google Groups
>>>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>>>>
>>>> To post to this group, send email to [hidden email]
>>>>
>>>> To unsubscribe and other options, go to
>>>> http://www.aroma-project.org/forum/
>>>>
>>>> --
>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>> latest
>>>> version of the package, 2) to report the output of sessionInfo() and
>>>> traceback(), and 3) to post a complete code example.
>>>>
>>>>
>>>> You received this message because you are subscribed to the Google Groups
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>>>> To post to this group, send email to [hidden email]
>>>> To unsubscribe and other options, go to
>>>> http://www.aroma-project.org/forum/
>>>>
>>>
>>> --
>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>> latest version of the package, 2) to report the output of sessionInfo() and
>>> traceback(), and 3) to post a complete code example.
>>>
>>>
>>> You received this message because you are subscribed to the Google Groups
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>>> To post to this group, send email to [hidden email]
>>> To unsubscribe and other options, go to
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>>>
>>> --
>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>> latest version of the package, 2) to report the output of sessionInfo() and
>>> traceback(), and 3) to post a complete code example.
>>>
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>>> You received this message because you are subscribed to the Google Groups
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>>> To post to this group, send email to [hidden email]
>>> To unsubscribe and other options, go to
>>> http://www.aroma-project.org/forum/
>>>
>>
>> --
>> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
>> version of the package, 2) to report the output of sessionInfo() and
>> traceback(), and 3) to post a complete code example.
>>
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>> You received this message because you are subscribed to the Google Groups
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>> To post to this group, send email to [hidden email]
>> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>>
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to [hidden email]
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
>
>
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RE: [aroma.affymetrix] DNA segmentation result

Yan Jiao
Hi

Something strange on my machine,

I was running the copy number segmentation, I'm at the stage: process(ce.all,chromosomes=c(8,17),verbose=TRUE)
The computer has been running for almost a day, I got 604 samples, earlier when I check the CBS folder, I found all the .png file has been done, but no regions.xls file which summarize all the copy number information, but now when I check the folder, all the .png file has gone missing, the CBS folder got nothing inside, and R is still running (ce.all,chromosomes=c(8,17),verbose=TRUE)...

What is happening? Before I ran this 604 samples, I did have a trial run, which only include 3 samples and it's ok, I'm not sure whether I should continue waiting for the code to finish running, or I should kill it and rerun it? If I need to rerun it, do I need to delete all the folders?

Many thanks

yan

-----Original Message-----
From: [hidden email] [mailto:[hidden email]] On Behalf Of Pierre Neuvial
Sent: 29 November 2010 22:23
To: [hidden email]
Subject: Re: [aroma.affymetrix] DNA segmentation result

Hi,

Sure, it will be quicker.

In this case, you only have to setup the CBS segmentation model, and
fit it.  For example:

## define the segmentation model
## (and its parameters)
seg <- CbsModel(ds, min.width=5);

## perform the segmentation
## (possibly for a subset of arrays and chromosomes)
fit(seg, array=2, chromosome=5, verbose=TRUE);

There are other examples on the aroma project website, e.g.
http://aroma-project.org/vignettes/pairedTotalCopyNumberAnalysis

Best,

Pierre

On Mon, Nov 29, 2010 at 7:33 PM, Yan Jiao <[hidden email]> wrote:

> Hi,
>
> Sorry to bother you again
>
> If I don't need the chromosome Explorer as result, I just need that excel file with copy number in (regions.xls, in CBS folder), how should I set the parameter, I guess it will speed up the procedure as well, right?
>
> Many thanks
>
> yan
>
> -----Original Message-----
> From: [hidden email] [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
> Sent: 28 November 2010 22:57
> To: aroma-affymetrix
> Subject: Re: [aroma.affymetrix] DNAcopy parameter
>
> On Sun, Nov 28, 2010 at 6:01 AM, Pierre Neuvial
> <[hidden email]> wrote:
>> Hi,
>>
>> The parameters used are the default parameters of the 'segment'
>> function of the DNAcopy package.  If you search for 'DNAcopy
>> parameters' on the "Search forum" box at http://aroma-project.org, you
>> will find this recent thread which gives an example of how these
>> parameters can be changed:
>>
>> http://groups.google.com/group/aroma-affymetrix/browse_thread/thread/aa9db6ac7835d828/b6ab6b1c9786d9ff
>
> Note that I just posted a follow up on that thread clarified that it
> is now possible to specify optional arguments specific to
> DNAcopy::segment() as:
>
> seg <- CbsModel(ds, min.width=5);
>
> In order to find out which they are and what they do, see the specific
> segmentation method, i.e. help("segment", package="DNAcopy").
>
> /Henrik
>
>>
>> Hope this helps.
>>
>> Pierre
>>
>> On Wed, Nov 24, 2010 at 7:31 PM, Yan Jiao <[hidden email]> wrote:
>>> Thanks Henrik,
>>> I will update my R and aroma package,
>>> Another question is what kind of parameters of aroma use for copy number
>>> segmentation, if using DNAcopy as the algorithm?
>>>
>>> Many thanks
>>>
>>> yan
>>>
>>> -----Original Message-----
>>> From: [hidden email]
>>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>>> Sent: 24 November 2010 17:06
>>> To: aroma-affymetrix
>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>>
>>> Ok, after seing your sessionInfo();
>>>
>>> You need to update to R v2.12.0, especially since you're on Windows
>>> 64-bit.  Lots of work have been done by R core people to support
>>> Windows 64-bit on R v2.12.0 and beyond.  There is no shortcut to this.
>>>
>>> Update aroma.affymetrix to v1.8.0, cf. http://aroma-project.org/install
>>>
>>> Also, the Cairo package is not available for the 64-bit version of R
>>> on Windows.  If you try install.packages("Cairo") on your Windows
>>> machine, CRAN should report that package is not available.   Either
>>> you have installed it by other means or it incorrectly installed on R
>>> v2.11.0.
>>>
>>> /Henrik
>>>
>>>
>>> On Wed, Nov 24, 2010 at 8:58 AM, Yan Jiao <[hidden email]> wrote:
>>>> Hi Henrik,
>>>>
>>>> I did what you suggested:
>>>>
>>>>> traceback()
>>>>
>>>> 13: stop(gettextf("package '%s' is not installed for 'arch=%s'",
>>>>
>>>>         pkgname, r_arch), call. = FALSE, domain = NA)
>>>>
>>>> 12: testRversion(pkgInfo, package, pkgpath)
>>>>
>>>> 11: library(package, lib.loc = lib.loc, character.only = TRUE,
>>>> logical.return = TRUE,
>>>>
>>>>         warn.conflicts = warn.conflicts, keep.source = keep.source)
>>>>
>>>> 10: base::require(...)
>>>>
>>>> 9: require("Cairo")
>>>>
>>>> 8: findPngDevice.default(transparent = FALSE)
>>>>
>>>> 7: findPngDevice(transparent = FALSE)
>>>>
>>>> 6: plot.CopyNumberSegmentationModel(model, path = path, imageFormat =
>>>> "png",
>>>>
>>>>        plotband = plotband, arrays = arrays, ...)
>>>>
>>>> 5: plot(model, path = path, imageFormat = "png", plotband = plotband,
>>>>
>>>>        arrays = arrays, ...)
>>>>
>>>> 4: writeGraphs.ChromosomeExplorer(this, arrays = arrays, chromosomes =
>>>> chromosomes,
>>>>
>>>>        zooms = zooms, ..., verbose = less(verbose))
>>>>
>>>> 3: writeGraphs(this, arrays = arrays, chromosomes = chromosomes,
>>>>
>>>>        zooms = zooms, ..., verbose = less(verbose))
>>>>
>>>> 2: process.ChromosomeExplorer(ce.all, verbose = TRUE)
>>>>
>>>> 1: process(ce.all, verbose = TRUE)
>>>>
>>>>> sessionInfo()
>>>>
>>>> R version 2.11.0 (2010-04-22)
>>>>
>>>> x86_64-pc-mingw32
>>>>
>>>> locale:
>>>>
>>>> [1] LC_COLLATE=English_United Kingdom.1252  LC_CTYPE=English_United
>>>> Kingdom.1252    LC_MONETARY=English_United Kingdom.1252
>>>> LC_NUMERIC=C
>>>>
>>>> [5] LC_TIME=English_United Kingdom.1252
>>>>
>>>> attached base packages:
>>>>
>>>> [1] stats     graphics  grDevices utils     datasets  methods   base
>>>>
>>>> other attached packages:
>>>>
>>>>  [1] RColorBrewer_1.0-2     DNAcopy_1.22.1         preprocessCore_1.10.0
>>>> sfit_0.1.9             aroma.affymetrix_1.7.0 aroma.apd_0.1.7
>>>> affxparser_1.20.0
>>>>
>>>>  [8] R.huge_0.2.0           aroma.core_1.7.0       aroma.light_1.16.1
>>>> matrixStats_0.2.2      R.rsp_0.4.0            R.cache_0.3.0
>>>> R.filesets_0.9.0
>>>>
>>>> [15] digest_0.4.2           R.utils_1.5.3          R.oo_1.7.4
>>>> R.methodsS3_1.2.1
>>>>
>>>> loaded via a namespace (and not attached):
>>>>
>>>> [1] tools_2.11.0
>>>>
>>>>>
>>>>
>>>> process(ce,chromosomes=c(1,8,17), verbose=-10)
>>>>
>>>> Generating ChromosomeExplorer report...
>>>>
>>>>  Setting up ChromosomeExplorer report files...
>>>>
>>>>   Copying template files...
>>>>
>>>>    Source path:
>>>> C:/Users/rmhkyji/R/win64-library/2.11/aroma.core/reports/includes
>>>>
>>>>    Destination path: reports/includes
>>>>
>>>>   Copying template files...done
>>>>
>>>>  Setting up ChromosomeExplorer report files...done
>>>>
>>>>  Explorer output version: 3
>>>>
>>>>  Compiling ChromosomeExplorer.onLoad.js.rsp...
>>>>
>>>>   Source:
>>>>
>>>> C:/Users/rmhkyji/R/win64-library/2.11/aroma.core/reports/templates/rsp/ChromosomeExplorer3/ChromosomeExplorer.onLoad.js.rsp
>>>>
>>>>   Output path: reports/Fockens_1/ACC,-XY,RMA,+300,A+B,FLN,-XY
>>>>
>>>>   Scanning directories for available chip types...
>>>>
>>>>    Detected chip types: Mapping50K_Hind240
>>>>
>>>>   Scanning directories for available chip types...done
>>>>
>>>>   Scanning image files for available zooms...
>>>>
>>>>    Detected (or default) zooms: 1, 2, 4, 8, 16, 32, 64
>>>>
>>>>   Scanning image files for available zooms...done
>>>>
>>>>   Scanning directory for subdirectories...
>>>>
>>>>    Detected (or default) sets: cbs
>>>>
>>>>   Scanning directory for subdirectories...done
>>>>
>>>>   Compiling RSP...
>>>>
>>>>            member data.class dimension objectSize
>>>>
>>>>    1    chipTypes  character         1        120
>>>>
>>>>    2    chrLayers  character         0         40
>>>>
>>>>    3 sampleLabels  character         3        240
>>>>
>>>>    4 sampleLayers  character         0         40
>>>>
>>>>    5      samples  character         3        240
>>>>
>>>>    6         sets  character         1         96
>>>>
>>>>    7        zooms    numeric         7         72
>>>>
>>>>    Sample names:
>>>>
>>>>    [1] "GSM255038" "GSM255039" "GSM255040"
>>>>
>>>>    Full sample names:
>>>>
>>>>    [1] "GSM255038,total" "GSM255039,total" "GSM255040,total"
>>>>
>>>>   Compiling RSP...done
>>>>
>>>>  Compiling ChromosomeExplorer.onLoad.js.rsp...done
>>>>
>>>> Loading required package: Cairo
>>>>
>>>> Error: package 'Cairo' is not installed for 'arch=x64'
>>>>
>>>> Generating ChromosomeExplorer report...done
>>>>
>>>>
>>>> -----Original Message-----
>>>> From: [hidden email]
>>>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>>>> Sent: 24 November 2010 16:50
>>>> To: aroma-affymetrix
>>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>>>
>>>> Hi.
>>>>
>>>> On Wed, Nov 24, 2010 at 8:10 AM, Yan Jiao <[hidden email]> wrote:
>>>>
>>>>> Hi Henrik,
>>>>
>>>>>
>>>>
>>>>> Another question, I was trying to only do segmentation on 3 chromosomes,
>>>>> how should I do it, I tried:
>>>>
>>>>> process(ce,chromosomes=c(1,8,17), verbose=TRUE);
>>>>
>>>>>
>>>>
>>>>> but got error message:
>>>>
>>>>>
>>>>
>>>>> Generating ChromosomeExplorer report...
>>>>
>>>>> Loading required package: Cairo
>>>>
>>>>> Error: package 'Cairo' is not installed for 'arch=x64'
>>>>
>>>>> Generating ChromosomeExplorer report...done
>>>>
>>>> Odd, because specifying a subset of chromosomes shouldn't be any
>>>>
>>>> different from running all, as you did before.
>>>>
>>>> So, there seem to be several packages that install on R 64-bit in
>>>>
>>>> Windows, but when trying to use then fails.  The Cairo package is
>>>>
>>>> actually "deprecated" (replaced with similar function builtin in R),
>>>>
>>>> but we've kept support for backward compatibilities.  It seems like
>>>>
>>>> you're facing these issues - and not that many people are running
>>>>
>>>> 64-bit Windows yet so you seem to be the one hitting the bumps.
>>>>
>>>> What does traceback() give when you get the error?
>>>>
>>>> What is your sessionInfo()?
>>>>
>>>> Can you use process(ce,chromosomes=c(1,8,17), verbose=-10) in order to
>>>>
>>>> narrow down where the error occurs.
>>>>
>>>> /Henrik
>>>>
>>>>>
>>>>
>>>>>
>>>>
>>>>> Many thanks
>>>>
>>>>>
>>>>
>>>>> yan
>>>>
>>>>>
>>>>
>>>>>
>>>>
>>>>>
>>>>
>>>>> -----Original Message-----
>>>>
>>>>> From: [hidden email]
>>>>> [mailto:[hidden email]] On Behalf Of Henrik Bengtsson
>>>>
>>>>> Sent: 24 November 2010 15:08
>>>>
>>>>> To: aroma-affymetrix
>>>>
>>>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>>>
>>>>>
>>>>
>>>>> Hi,
>>>>
>>>>>
>>>>
>>>>> great.  Contrary to error messages, warnings are alright to get.
>>>>
>>>>>
>>>>
>>>>> /H
>>>>
>>>>>
>>>>
>>>>> On Wed, Nov 24, 2010 at 2:51 AM, Yan Jiao <[hidden email]> wrote:
>>>>
>>>>>> Thank you Henrik,
>>>>
>>>>>> It works now, but I got some warning:
>>>>
>>>>>>
>>>>
>>>>>> process(ce, verbose=TRUE);
>>>>
>>>>>> Generating ChromosomeExplorer report...
>>>>
>>>>>> Loading required package: Cairo
>>>>
>>>>>> Generating ChromosomeExplorer report...done
>>>>
>>>>>> [1] TRUE
>>>>
>>>>>> Warning messages:
>>>>
>>>>>> 1: In library(package, lib.loc = lib.loc, character.only = TRUE,
>>>>>> logical.return = TRUE,  :
>>>>
>>>>>>  there is no package called 'Cairo'
>>>>
>>>>>> 2: In method(static, ...) :
>>>>
>>>>>>  Ghostscript not found. Searched directories: C:/gs, C:\Program
>>>>>> Files/gs,
>>>>>> /gs, C:\Program Files\Common Files/gs
>>>>
>>>>>>
>>>>
>>>>>> Are those warning messages serious? Could I ignore them?
>>>>
>>>>>>
>>>>
>>>>>>
>>>>
>>>>>> Yan
>>>>
>>>>>>
>>>>
>>>>>> -----Original Message-----
>>>>
>>>>>> From: [hidden email]
>>>>>> [mailto:[hidden email]] On Behalf Of Henrik
>>>>>> Bengtsson
>>>>
>>>>>> Sent: 23 November 2010 21:53
>>>>
>>>>>> To: aroma-affymetrix
>>>>
>>>>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>>>
>>>>>>
>>>>
>>>>>> Hi.
>>>>
>>>>>>
>>>>
>>>>>> On Tue, Nov 23, 2010 at 11:51 AM, Yan Jiao <[hidden email]> wrote:
>>>>
>>>>>>> Hi Henrik,
>>>>
>>>>>>>
>>>>
>>>>>>> Sorry, the error is after
>>>>
>>>>>>> cbs <- CbsModel(ds);
>>>>
>>>>>>> ce <- ChromosomeExplorer(cbs);
>>>>
>>>>>>> process(ce, verbose=TRUE);
>>>>
>>>>>>
>>>>
>>>>>> Ok, now the error message makes a bit more sense (it was my suspicion
>>>>
>>>>>> but I didn't want make guesses).
>>>>
>>>>>>
>>>>
>>>>>>>
>>>>
>>>>>>>
>>>>
>>>>>>> Generating ChromosomeExplorer report...
>>>>
>>>>>>> Loading required package: Cairo
>>>>
>>>>>>> <simpleError in inDL(x, as.logical(local), as.logical(now), ...):
>>>>>>> unable
>>>>
>>>>>>> to load shared library
>>>>
>>>>>>> 'C:/Users/rmhkyji/R/win64-library/2.11/GLAD/libs/x64/GLAD.dll':
>>>>
>>>>>>>  LoadLibrary failure:  The specified module could not be found.
>>>>
>>>>>>>
>>>>
>>>>>>> And there  is a pop out window saying: The program can't start because
>>>>
>>>>>>> libgsl-0.dll I smissing from your computer. Try reinstalling the
>>>>>>> program
>>>>
>>>>>>> to fix this program.
>>>>
>>>>>>
>>>>
>>>>>> I can reproduce this on 64-bit Windows 7 - you get the same error if
>>>>
>>>>>> you try library("GLAD").  It is because we utilize part of the GLAD
>>>>
>>>>>> package, if and only if it is *installed*, and otherwise we turn to
>>>>
>>>>>> backup solutions.  What happens here is that *GLAD is installed but
>>>>
>>>>>> doesn't load*, which causes the error so that backup solutions doesn't
>>>>
>>>>>> kick in.   In the next release I'll try to make sure the backup
>>>>
>>>>>> solutions will also work when there is an error load GLAD.  In
>>>>
>>>>>> meanwhile, you can do this:
>>>>
>>>>>>
>>>>
>>>>>> WORKAROUND:
>>>>
>>>>>>
>>>>
>>>>>> 1. Uninstall the GLAD package (it doesn't work anyway):
>>>>
>>>>>>
>>>>
>>>>>>> remove.packages("GLAD")
>>>>
>>>>>> Removing package(s) from 'C:\Users\hb\R\win-library\2.12'
>>>>
>>>>>> (as 'lib' is unspecified)
>>>>
>>>>>>
>>>>
>>>>>>> library("GLAD")
>>>>
>>>>>> Error in library("GLAD") : there is no package called 'GLAD'
>>>>
>>>>>>
>>>>
>>>>>> That should do it.  Let me know if it works for you.
>>>>
>>>>>>
>>>>
>>>>>> TECHNICAL DETAILS: It happens because the GNU Scientific Library (GSL)
>>>>
>>>>>> is not installed on the system (hence the 'gsl' part of
>>>>
>>>>>> 'libgsl-0.dll'). There is a hard-to-find note that you need GSL in
>>>>
>>>>>> order to use the GLAD package, cf.
>>>>
>>>>>> http://bioconductor.org/packages/release/bioc/html/GLAD.html.  There
>>>>
>>>>>> exist 32-bit binaries of GSL at
>>>>
>>>>>> http://gnuwin32.sourceforge.net/packages/gsl.htm.  Unfortunately, it
>>>>
>>>>>> does not work for the 64-bit version of R on Windows 64-bit.  It works
>>>>
>>>>>> if you do tricks an run the 32-bit version of R, but that is a rather
>>>>
>>>>>> inconvenient workaround.
>>>>
>>>>>>
>>>>
>>>>>> /Henrik
>>>>
>>>>>>
>>>>
>>>>>>>
>>>>
>>>>>>>
>>>>
>>>>>>> Yan
>>>>
>>>>>>>
>>>>
>>>>>>> -----Original Message-----
>>>>
>>>>>>> From: [hidden email]
>>>>
>>>>>>> [mailto:[hidden email]] On Behalf Of Henrik
>>>>>>> Bengtsson
>>>>
>>>>>>> Sent: 23 November 2010 18:50
>>>>
>>>>>>> To: aroma-affymetrix
>>>>
>>>>>>> Subject: Re: [aroma.affymetrix] libgsl-0.dll missing error
>>>>
>>>>>>>
>>>>
>>>>>>> Hi.
>>>>
>>>>>>>
>>>>
>>>>>>> On Tue, Nov 23, 2010 at 10:05 AM, Yan Jiao <[hidden email]> wrote:
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>> Dear all,
>>>>
>>>>>>>>
>>>>
>>>>>>>> I'm trying to do DNA segmentation,
>>>>
>>>>>>>>
>>>>
>>>>>>>> This is what I'm doing:
>>>>
>>>>>>>>
>>>>
>>>>>>>> ds <- doCRMAv1("Fockens_1", chipType="Mapping50K_Hind240",
>>>>
>>>>>>> verbose=TRUE);
>>>>
>>>>>>>>
>>>>
>>>>>>>> ###this is done sucessfully
>>>>
>>>>>>>>
>>>>
>>>>>>>> # Segmentation
>>>>
>>>>>>>>
>>>>
>>>>>>>> cbs <- CbsModel(ds);
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>> I got error libgsl-0.dll is missing, I think it's using GLAD, but I'm
>>>>
>>>>>>> trying
>>>>
>>>>>>>> to use DNAcopy for segmentation.
>>>>
>>>>>>>
>>>>
>>>>>>> Is it really the case that you get that error when you do:
>>>>
>>>>>>>
>>>>
>>>>>>> cbs <- CbsModel(ds);
>>>>
>>>>>>>
>>>>
>>>>>>> or do you do anything else?  Is suspect you do something more.
>>>>
>>>>>>>
>>>>
>>>>>>> Also, after you got the error, could you cut'n'paste the verbose
>>>>
>>>>>>> output including any error messages you get and send it to us?   Also,
>>>>
>>>>>>> make sure to report what print(traceback()) gives immediate after
>>>>
>>>>>>> getting the error.
>>>>
>>>>>>>
>>>>
>>>>>>> /Henrik
>>>>
>>>>>>>
>>>>
>>>>>>> PS. The 'GLAD' package may indeed be used regardless of segmentation
>>>>
>>>>>>> method because it contains information about cytobands.
>>>>
>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>> How to change it?
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>> Many thanks
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>> yan
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>>>>> **********************************************************************
>>>>
>>>>>>>>
>>>>
>>>>>>>> This email and any files transmitted with it are confidential and
>>>>
>>>>>>>>
>>>>
>>>>>>>> intended solely for the use of the individual or entity to whom they
>>>>
>>>>>>>>
>>>>
>>>>>>>> are addressed. If you have received this email in error please notify
>>>>
>>>>>>>>
>>>>
>>>>>>>> the system manager ([hidden email]).
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>>>>> **********************************************************************
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>> --
>>>>
>>>>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>>
>>>>>>> latest
>>>>
>>>>>>>> version of the package, 2) to report the output of sessionInfo() and
>>>>
>>>>>>>> traceback(), and 3) to post a complete code example.
>>>>
>>>>>>>>
>>>>
>>>>>>>>
>>>>
>>>>>>>> You received this message because you are subscribed to the Google
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>>>>
>>>>>>>> To post to this group, send email to
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>>>>>>>>
>>>>
>>>>>>>
>>>>
>>>>>>> --
>>>>
>>>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>>
>>>>>>> latest version of the package, 2) to report the output of
>>>>>>> sessionInfo()
>>>>
>>>>>>> and traceback(), and 3) to post a complete code example.
>>>>
>>>>>>>
>>>>
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>>>>>>> You received this message because you are subscribed to the Google
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>>>>>>> Groups "aroma.affymetrix" group with website
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>>>>
>>>>>>>
>>>>
>>>>>>> --
>>>>
>>>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>>>>> latest version of the package, 2) to report the output of
>>>>>>> sessionInfo() and
>>>>>>> traceback(), and 3) to post a complete code example.
>>>>
>>>>>>>
>>>>
>>>>>>>
>>>>
>>>>>>> You received this message because you are subscribed to the Google
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>>>>>>> http://www.aroma-project.org/.
>>>>
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>>>>>>> http://www.aroma-project.org/forum/
>>>>
>>>>>>>
>>>>
>>>>>>
>>>>
>>>>>> --
>>>>
>>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>>>> latest version of the package, 2) to report the output of sessionInfo()
>>>>>> and
>>>>>> traceback(), and 3) to post a complete code example.
>>>>
>>>>>>
>>>>
>>>>>>
>>>>
>>>>>> You received this message because you are subscribed to the Google
>>>>>> Groups
>>>>>> "aroma.affymetrix" group with website http://www.aroma-project.org/.
>>>>
>>>>>> To post to this group, send email to [hidden email]
>>>>
>>>>>> To unsubscribe and other options, go to
>>>>>> http://www.aroma-project.org/forum/
>>>>
>>>>>>
>>>>
>>>>>> --
>>>>
>>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>>>> latest version of the package, 2) to report the output of sessionInfo()
>>>>>> and
>>>>>> traceback(), and 3) to post a complete code example.
>>>>
>>>>>>
>>>>
>>>>>>
>>>>
>>>>>> You received this message because you are subscribed to the Google
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>>>>
>>>>>> To post to this group, send email to [hidden email]
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>>>>
>>>>>>
>>>>
>>>>>
>>>>
>>>>> --
>>>>
>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>>> latest version of the package, 2) to report the output of sessionInfo()
>>>>> and
>>>>> traceback(), and 3) to post a complete code example.
>>>>
>>>>>
>>>>
>>>>>
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>>>>
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>>>>>
>>>>
>>>>> --
>>>>
>>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>>> latest version of the package, 2) to report the output of sessionInfo()
>>>>> and
>>>>> traceback(), and 3) to post a complete code example.
>>>>
>>>>>
>>>>
>>>>>
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>>>>
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>>>>>
>>>>
>>>> --
>>>>
>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>> latest
>>>> version of the package, 2) to report the output of sessionInfo() and
>>>> traceback(), and 3) to post a complete code example.
>>>>
>>>> You received this message because you are subscribed to the Google Groups
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>>>>
>>>> To post to this group, send email to [hidden email]
>>>>
>>>> To unsubscribe and other options, go to
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>>>>
>>>> --
>>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>>> latest
>>>> version of the package, 2) to report the output of sessionInfo() and
>>>> traceback(), and 3) to post a complete code example.
>>>>
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>>>> You received this message because you are subscribed to the Google Groups
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>>>
>>> --
>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>> latest version of the package, 2) to report the output of sessionInfo() and
>>> traceback(), and 3) to post a complete code example.
>>>
>>>
>>> You received this message because you are subscribed to the Google Groups
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>>>
>>> --
>>> When reporting problems on aroma.affymetrix, make sure 1) to run the
>>> latest version of the package, 2) to report the output of sessionInfo() and
>>> traceback(), and 3) to post a complete code example.
>>>
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>>> You received this message because you are subscribed to the Google Groups
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>>>
>>
>> --
>> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
>> version of the package, 2) to report the output of sessionInfo() and
>> traceback(), and 3) to post a complete code example.
>>
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>> You received this message because you are subscribed to the Google Groups
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>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest version of the package, 2) to report the output of sessionInfo() and traceback(), and 3) to post a complete code example.
>
>
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> To post to this group, send email to [hidden email]
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>
> --
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>
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12