[aroma.affymetrix] No write permissions error

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[aroma.affymetrix] No write permissions error

Elsa Chacko
$byChipType(chipType)
print(cdf)
cs <- AffymetrixCelSet$byName("tissues", cdf=cdf)
print(cs)
bc <- RmaBackgroundCorrection(cs, tag="coreR2")
csBC <- process(bc,verbose=verbose)
qn <- QuantileNormalization(csBC, typesToUpdate="pm")
print(qn)
csN <- process(qn, verbose=verbose)

I get stuck at this point. I keep gettng an error
[2010-11-10 09:16:33] Exception: No write permission for directory:
probeData/tissues,coreR2,QN
  at throw(Exception(...))
  at throw.default("No write permission for directory: ", path)
  at throw("No write permission for directory: ", path)
  at method(static, ...)
  at Arguments$getWritablePathname(path)
  at normalizeQuantile.AffymetrixCelFile(df, path = path,
subsetToUpdate = subse
  at normalizeQuantile(df, path = path, subsetToUpdate =
subsetToUpdate, typesTo
  at normalizeQuantile.AffymetrixCelSet(NA, path = "probeData/tissues,
  at normalizeQuantile(NA, path = "probeData/tissues,coreR2,QN/HuEx-1_
  at do.call("normalizeQuantile", args = args)
  at process.QuantileNormalization(qn, verbose = verbose)
  at process(qn, verbose = verbose)
In addition: Warning messages:
1: In writeBin(con = con, rawAll) : problem writing to connection
2: In writeBin(con = con, rawAll) : problem writing to connection
3: In fileAccess.default(pathT, mode = 2) :
  file.access(..., mode=2) and file(..., open="ab") gives different
results (0 != -1). Will use the file() results: probeData/
tissues,coreR2,QN/K
20101110 09:17:22|   Array #2...done
20101110 09:17:22|  Normalizing 30 arrays...done
20101110 09:17:22| Normalizing data towards target distribution...done
20101110 09:17:22|Quantile normalizing data set...done

I did get a similar error for csBC <- process(bc,verbose=verbose), but
i fixed it by giving universal write permission n the probeData
folder. But this didn't work for csN <- process(qn, verbose=verbose).

> sessionInfo()
R version 2.10.1 (2009-12-14)
x86_64-pc-linux-gnu

locale:
 [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8
 [5] LC_MONETARY=C              LC_MESSAGES=en_AU.UTF-8
 [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] Biobase_2.6.1          aroma.affymetrix_1.7.3 aroma.apd_0.1.7
 [4] affxparser_1.18.0      R.huge_0.2.0           aroma.core_1.7.4
 [7] aroma.light_1.18.2     matrixStats_0.2.2      R.rsp_0.4.0
[10] R.cache_0.3.0          R.filesets_0.9.0       digest_0.4.2
[13] R.utils_1.5.6          R.oo_1.7.4             affy_1.24.2
[16] R.methodsS3_1.2.1

loaded via a namespace (and not attached):
[1] affyio_1.14.0        preprocessCore_1.8.0 tools_2.10.1

> traceback()
No traceback available

I did follow a previous forum message regarding a similar problem and
get the following outputs.

> library("R.utils");
> path <- "/home/elsa/probeData/tissues,coreR2,
annotationData/ .cshrc          probeData/      .Rcache/
.bash_history   .login          rawData/        .ssh/
> path <- "/home/elsa/probeData/tissues,coreR2,
annotationData/ .cshrc          probeData/      .Rcache/
.bash_history   .login          rawData/        .ssh/
> path <- "/home/elsa/probeData/tissues,coreR2,QN
+ "
> path <- "/home/elsa/probeData/tissues,coreR2,QN"
> print(path)
[1] "/home/elsa/probeData/tissues,coreR2,QN"
> str(file.info(path));
'data.frame':   1 obs. of  10 variables:
 $ size  : num 3
 $ isdir : logi TRUE
 $ mode  :Class 'octmode'  int 1535
 $ mtime : POSIXct, format: "2010-11-10 09:15:13"
 $ ctime : POSIXct, format: "2010-11-10 09:16:37"
 $ atime : POSIXct, format: "2010-11-10 09:16:37"
 $ uid   : int 341178
 $ gid   : int 341178
 $ uname : chr "elsa"
 $ grname: chr "elsa"
> print(file.access(path, mode=0));
/home/elsa/probeData/tissues,coreR2,QN
                                                 0
> print(file.access(path, mode=1));
/home/elsa/probeData/tissues,coreR2,QN
                                                 0
> print(file.access(path, mode=2));
/home/elsa/probeData/tissues,coreR2,QN
                                                 0
> print(file.access(path, mode=4));
/home/elsa/probeData/tissues,coreR2,QN
                                                 0
> print(fileAccess(path,mode=0));
[1] 0
> print(fileAccess(path,mode=1));
[1] 0
> print(fileAccess(path,mode=2));
[1] -1
Warning message:
In fileAccess.default(path, mode = 2) :
  file.access(..., mode=2) and file(..., open="ab") gives different
results (0 != -1). Will use the file() results: /home/elsa/probeData/
tissues,coreR2,QN/B
> print(fileAccess(path,mode=4));
[1] 0

> print(isDirectory(path));
[1] TRUE
> print(isFile(path));
[1] FALSE


Looks like R.util does not have write permissions on the folder. I am
just not sure how i ca fix this problem.

Any help is very much appreciated.

Regards
Elsa Chacko
PhD student
Macquarie University



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Re: [aroma.affymetrix] No write permissions error

Henrik Bengtsson-4
Hi,

the fileAccess() write-permission test actually tries to write a small
file to the directory to assert you have write permission to it.  It
seems like it cannot create a file and write to it in that directory.
That provides an additional test on top of what file.access() does.
(The filename 'K' is randomly generated, hence
probeData/tissues,coreR2,QN/K in that error message).

Q1. Are you sure you're not out of disk space?

Q2. If you start a new R session, does the following work?

path <- "/home/elsa/probeData/tissues,coreR2,QN";
pathname <- file.path(path, "dummy.txt");
cat("Hello world!", file=pathname);

str(file.info(pathname));
print(readLines(pathname));

/Henrik

PS. Independent of the above, you probably want to use tag="*,coreR2"
instead of tag="coreR2" in order for the tags to reflect what steps
have been made.

On Tue, Nov 9, 2010 at 9:10 PM, Elsa Chacko <[hidden email]> wrote:

> $byChipType(chipType)
> print(cdf)
> cs <- AffymetrixCelSet$byName("tissues", cdf=cdf)
> print(cs)
> bc <- RmaBackgroundCorrection(cs, tag="coreR2")
> csBC <- process(bc,verbose=verbose)
> qn <- QuantileNormalization(csBC, typesToUpdate="pm")
> print(qn)
> csN <- process(qn, verbose=verbose)
>
> I get stuck at this point. I keep gettng an error
> [2010-11-10 09:16:33] Exception: No write permission for directory:
> probeData/tissues,coreR2,QN
>  at throw(Exception(...))
>  at throw.default("No write permission for directory: ", path)
>  at throw("No write permission for directory: ", path)
>  at method(static, ...)
>  at Arguments$getWritablePathname(path)
>  at normalizeQuantile.AffymetrixCelFile(df, path = path,
> subsetToUpdate = subse
>  at normalizeQuantile(df, path = path, subsetToUpdate =
> subsetToUpdate, typesTo
>  at normalizeQuantile.AffymetrixCelSet(NA, path = "probeData/tissues,
>  at normalizeQuantile(NA, path = "probeData/tissues,coreR2,QN/HuEx-1_
>  at do.call("normalizeQuantile", args = args)
>  at process.QuantileNormalization(qn, verbose = verbose)
>  at process(qn, verbose = verbose)
> In addition: Warning messages:
> 1: In writeBin(con = con, rawAll) : problem writing to connection
> 2: In writeBin(con = con, rawAll) : problem writing to connection
> 3: In fileAccess.default(pathT, mode = 2) :
>  file.access(..., mode=2) and file(..., open="ab") gives different
> results (0 != -1). Will use the file() results: probeData/
> tissues,coreR2,QN/K
> 20101110 09:17:22|   Array #2...done
> 20101110 09:17:22|  Normalizing 30 arrays...done
> 20101110 09:17:22| Normalizing data towards target distribution...done
> 20101110 09:17:22|Quantile normalizing data set...done
>
> I did get a similar error for csBC <- process(bc,verbose=verbose), but
> i fixed it by giving universal write permission n the probeData
> folder. But this didn't work for csN <- process(qn, verbose=verbose).
>
>> sessionInfo()
> R version 2.10.1 (2009-12-14)
> x86_64-pc-linux-gnu
>
> locale:
>  [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=en_AU.UTF-8
>  [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] Biobase_2.6.1          aroma.affymetrix_1.7.3 aroma.apd_0.1.7
>  [4] affxparser_1.18.0      R.huge_0.2.0           aroma.core_1.7.4
>  [7] aroma.light_1.18.2     matrixStats_0.2.2      R.rsp_0.4.0
> [10] R.cache_0.3.0          R.filesets_0.9.0       digest_0.4.2
> [13] R.utils_1.5.6          R.oo_1.7.4             affy_1.24.2
> [16] R.methodsS3_1.2.1
>
> loaded via a namespace (and not attached):
> [1] affyio_1.14.0        preprocessCore_1.8.0 tools_2.10.1
>
>> traceback()
> No traceback available
>
> I did follow a previous forum message regarding a similar problem and
> get the following outputs.
>
>> library("R.utils");
[snip]

>> path <- "/home/elsa/probeData/tissues,coreR2,QN"
>> print(path)
> [1] "/home/elsa/probeData/tissues,coreR2,QN"
>> str(file.info(path));
> 'data.frame':   1 obs. of  10 variables:
>  $ size  : num 3
>  $ isdir : logi TRUE
>  $ mode  :Class 'octmode'  int 1535
>  $ mtime : POSIXct, format: "2010-11-10 09:15:13"
>  $ ctime : POSIXct, format: "2010-11-10 09:16:37"
>  $ atime : POSIXct, format: "2010-11-10 09:16:37"
>  $ uid   : int 341178
>  $ gid   : int 341178
>  $ uname : chr "elsa"
>  $ grname: chr "elsa"
>> print(file.access(path, mode=0));
> /home/elsa/probeData/tissues,coreR2,QN
>                                                 0
>> print(file.access(path, mode=1));
> /home/elsa/probeData/tissues,coreR2,QN
>                                                 0
>> print(file.access(path, mode=2));
> /home/elsa/probeData/tissues,coreR2,QN
>                                                 0
>> print(file.access(path, mode=4));
> /home/elsa/probeData/tissues,coreR2,QN
>                                                 0
>> print(fileAccess(path,mode=0));
> [1] 0
>> print(fileAccess(path,mode=1));
> [1] 0
>> print(fileAccess(path,mode=2));
> [1] -1
> Warning message:
> In fileAccess.default(path, mode = 2) :
>  file.access(..., mode=2) and file(..., open="ab") gives different
> results (0 != -1). Will use the file() results: /home/elsa/probeData/
> tissues,coreR2,QN/B
>> print(fileAccess(path,mode=4));
> [1] 0
>
>> print(isDirectory(path));
> [1] TRUE
>> print(isFile(path));
> [1] FALSE
>
>
> Looks like R.util does not have write permissions on the folder. I am
> just not sure how i ca fix this problem.
>
> Any help is very much appreciated.
>
> Regards
> Elsa Chacko
> PhD student
> Macquarie University
>
>
>
> --
> 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] Re: No write permissions error

Elsa Chacko
Hi Henrik,

Thanks for the help. I fixed the issue by running the fileAccess patch
available at http://www.braju.com/R/patches/R.utils/20100905/fileAccess.R.
But then i came across a Disk quota exceeded, which i guess is upto
the sys admin to fix...

Thanks again..

Regards
Elsa


On Nov 10, 4:50 pm, Henrik Bengtsson <henrik.bengts...@aroma-
project.org> wrote:

> Hi,
>
> the fileAccess() write-permission test actually tries to write a small
> file to the directory to assert you have write permission to it.  It
> seems like it cannot create a file and write to it in that directory.
> That provides an additional test on top of what file.access() does.
> (The filename 'K' is randomly generated, hence
> probeData/tissues,coreR2,QN/K in that error message).
>
> Q1. Are you sure you're not out of disk space?
>
> Q2. If you start a new R session, does the following work?
>
> path <- "/home/elsa/probeData/tissues,coreR2,QN";
> pathname <- file.path(path, "dummy.txt");
> cat("Hello world!", file=pathname);
>
> str(file.info(pathname));
> print(readLines(pathname));
>
> /Henrik
>
> PS. Independent of the above, you probably want to use tag="*,coreR2"
> instead of tag="coreR2" in order for the tags to reflect what steps
> have been made.
>
>
>
> On Tue, Nov 9, 2010 at 9:10 PM, Elsa Chacko <[hidden email]> wrote:
> > $byChipType(chipType)
> > print(cdf)
> > cs <- AffymetrixCelSet$byName("tissues", cdf=cdf)
> > print(cs)
> > bc <- RmaBackgroundCorrection(cs, tag="coreR2")
> > csBC <- process(bc,verbose=verbose)
> > qn <- QuantileNormalization(csBC, typesToUpdate="pm")
> > print(qn)
> > csN <- process(qn, verbose=verbose)
>
> > I get stuck at this point. I keep gettng an error
> > [2010-11-10 09:16:33] Exception: No write permission for directory:
> > probeData/tissues,coreR2,QN
> >  at throw(Exception(...))
> >  at throw.default("No write permission for directory: ", path)
> >  at throw("No write permission for directory: ", path)
> >  at method(static, ...)
> >  at Arguments$getWritablePathname(path)
> >  at normalizeQuantile.AffymetrixCelFile(df, path = path,
> > subsetToUpdate = subse
> >  at normalizeQuantile(df, path = path, subsetToUpdate =
> > subsetToUpdate, typesTo
> >  at normalizeQuantile.AffymetrixCelSet(NA, path = "probeData/tissues,
> >  at normalizeQuantile(NA, path = "probeData/tissues,coreR2,QN/HuEx-1_
> >  at do.call("normalizeQuantile", args = args)
> >  at process.QuantileNormalization(qn, verbose = verbose)
> >  at process(qn, verbose = verbose)
> > In addition: Warning messages:
> > 1: In writeBin(con = con, rawAll) : problem writing to connection
> > 2: In writeBin(con = con, rawAll) : problem writing to connection
> > 3: In fileAccess.default(pathT, mode = 2) :
> >  file.access(..., mode=2) and file(..., open="ab") gives different
> > results (0 != -1). Will use the file() results: probeData/
> > tissues,coreR2,QN/K
> > 20101110 09:17:22|   Array #2...done
> > 20101110 09:17:22|  Normalizing 30 arrays...done
> > 20101110 09:17:22| Normalizing data towards target distribution...done
> > 20101110 09:17:22|Quantile normalizing data set...done
>
> > I did get a similar error for csBC <- process(bc,verbose=verbose), but
> > i fixed it by giving universal write permission n the probeData
> > folder. But this didn't work for csN <- process(qn, verbose=verbose).
>
> >> sessionInfo()
> > R version 2.10.1 (2009-12-14)
> > x86_64-pc-linux-gnu
>
> > locale:
> >  [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C
> >  [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8
> >  [5] LC_MONETARY=C              LC_MESSAGES=en_AU.UTF-8
> >  [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C
> >  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> > [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
>
> > attached base packages:
> > [1] stats     graphics  grDevices utils     datasets  methods   base
>
> > other attached packages:
> >  [1] Biobase_2.6.1          aroma.affymetrix_1.7.3 aroma.apd_0.1.7
> >  [4] affxparser_1.18.0      R.huge_0.2.0           aroma.core_1.7.4
> >  [7] aroma.light_1.18.2     matrixStats_0.2.2      R.rsp_0.4.0
> > [10] R.cache_0.3.0          R.filesets_0.9.0       digest_0.4.2
> > [13] R.utils_1.5.6          R.oo_1.7.4             affy_1.24.2
> > [16] R.methodsS3_1.2.1
>
> > loaded via a namespace (and not attached):
> > [1] affyio_1.14.0        preprocessCore_1.8.0 tools_2.10.1
>
> >> traceback()
> > No traceback available
>
> > I did follow a previous forum message regarding a similar problem and
> > get the following outputs.
>
> >> library("R.utils");
> [snip]
> >> path <- "/home/elsa/probeData/tissues,coreR2,QN"
> >> print(path)
> > [1] "/home/elsa/probeData/tissues,coreR2,QN"
> >> str(file.info(path));
> > 'data.frame':   1 obs. of  10 variables:
> >  $ size  : num 3
> >  $ isdir : logi TRUE
> >  $ mode  :Class 'octmode'  int 1535
> >  $ mtime : POSIXct, format: "2010-11-10 09:15:13"
> >  $ ctime : POSIXct, format: "2010-11-10 09:16:37"
> >  $ atime : POSIXct, format: "2010-11-10 09:16:37"
> >  $ uid   : int 341178
> >  $ gid   : int 341178
> >  $ uname : chr "elsa"
> >  $ grname: chr "elsa"
> >> print(file.access(path, mode=0));
> > /home/elsa/probeData/tissues,coreR2,QN
> >                                                 0
> >> print(file.access(path, mode=1));
> > /home/elsa/probeData/tissues,coreR2,QN
> >                                                 0
> >> print(file.access(path, mode=2));
> > /home/elsa/probeData/tissues,coreR2,QN
> >                                                 0
> >> print(file.access(path, mode=4));
> > /home/elsa/probeData/tissues,coreR2,QN
> >                                                 0
> >> print(fileAccess(path,mode=0));
> > [1] 0
> >> print(fileAccess(path,mode=1));
> > [1] 0
> >> print(fileAccess(path,mode=2));
> > [1] -1
> > Warning message:
> > In fileAccess.default(path, mode = 2) :
> >  file.access(..., mode=2) and file(..., open="ab") gives different
> > results (0 != -1). Will use the file() results: /home/elsa/probeData/
> > tissues,coreR2,QN/B
> >> print(fileAccess(path,mode=4));
> > [1] 0
>
> >> print(isDirectory(path));
> > [1] TRUE
> >> print(isFile(path));
> > [1] FALSE
>
> > Looks like R.util does not have write permissions on the folder. I am
> > just not sure how i ca fix this problem.
>
> > Any help is very much appreciated.
>
> > Regards
> > Elsa Chacko
> > PhD student
> > Macquarie University
>
> > --
> > 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 websitehttp://www.aroma-project.org/.
> > To post to this group, send email to [hidden email]
> > To unsubscribe and other options, go tohttp://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] Re: No write permissions error

Henrik Bengtsson-4
Hi.

On Wed, Nov 10, 2010 at 12:58 AM, Elsa Chacko <[hidden email]> wrote:
> Hi Henrik,
>
> Thanks for the help. I fixed the issue by running the fileAccess patch
> available at http://www.braju.com/R/patches/R.utils/20100905/fileAccess.R.

That was a patch for R.utils 1.5.1 and you've already got R.utils
1.5.6.  Using that code had no affect on your issue.

> But then i came across a Disk quota exceeded, which i guess is upto
> the sys admin to fix...

So that was the real cause.

Thanks for reporting back.

/Henrik

>
> Thanks again..
>
> Regards
> Elsa
>
>
> On Nov 10, 4:50 pm, Henrik Bengtsson <henrik.bengts...@aroma-
> project.org> wrote:
>> Hi,
>>
>> the fileAccess() write-permission test actually tries to write a small
>> file to the directory to assert you have write permission to it.  It
>> seems like it cannot create a file and write to it in that directory.
>> That provides an additional test on top of what file.access() does.
>> (The filename 'K' is randomly generated, hence
>> probeData/tissues,coreR2,QN/K in that error message).
>>
>> Q1. Are you sure you're not out of disk space?
>>
>> Q2. If you start a new R session, does the following work?
>>
>> path <- "/home/elsa/probeData/tissues,coreR2,QN";
>> pathname <- file.path(path, "dummy.txt");
>> cat("Hello world!", file=pathname);
>>
>> str(file.info(pathname));
>> print(readLines(pathname));
>>
>> /Henrik
>>
>> PS. Independent of the above, you probably want to use tag="*,coreR2"
>> instead of tag="coreR2" in order for the tags to reflect what steps
>> have been made.
>>
>>
>>
>> On Tue, Nov 9, 2010 at 9:10 PM, Elsa Chacko <[hidden email]> wrote:
>> > $byChipType(chipType)
>> > print(cdf)
>> > cs <- AffymetrixCelSet$byName("tissues", cdf=cdf)
>> > print(cs)
>> > bc <- RmaBackgroundCorrection(cs, tag="coreR2")
>> > csBC <- process(bc,verbose=verbose)
>> > qn <- QuantileNormalization(csBC, typesToUpdate="pm")
>> > print(qn)
>> > csN <- process(qn, verbose=verbose)
>>
>> > I get stuck at this point. I keep gettng an error
>> > [2010-11-10 09:16:33] Exception: No write permission for directory:
>> > probeData/tissues,coreR2,QN
>> >  at throw(Exception(...))
>> >  at throw.default("No write permission for directory: ", path)
>> >  at throw("No write permission for directory: ", path)
>> >  at method(static, ...)
>> >  at Arguments$getWritablePathname(path)
>> >  at normalizeQuantile.AffymetrixCelFile(df, path = path,
>> > subsetToUpdate = subse
>> >  at normalizeQuantile(df, path = path, subsetToUpdate =
>> > subsetToUpdate, typesTo
>> >  at normalizeQuantile.AffymetrixCelSet(NA, path = "probeData/tissues,
>> >  at normalizeQuantile(NA, path = "probeData/tissues,coreR2,QN/HuEx-1_
>> >  at do.call("normalizeQuantile", args = args)
>> >  at process.QuantileNormalization(qn, verbose = verbose)
>> >  at process(qn, verbose = verbose)
>> > In addition: Warning messages:
>> > 1: In writeBin(con = con, rawAll) : problem writing to connection
>> > 2: In writeBin(con = con, rawAll) : problem writing to connection
>> > 3: In fileAccess.default(pathT, mode = 2) :
>> >  file.access(..., mode=2) and file(..., open="ab") gives different
>> > results (0 != -1). Will use the file() results: probeData/
>> > tissues,coreR2,QN/K
>> > 20101110 09:17:22|   Array #2...done
>> > 20101110 09:17:22|  Normalizing 30 arrays...done
>> > 20101110 09:17:22| Normalizing data towards target distribution...done
>> > 20101110 09:17:22|Quantile normalizing data set...done
>>
>> > I did get a similar error for csBC <- process(bc,verbose=verbose), but
>> > i fixed it by giving universal write permission n the probeData
>> > folder. But this didn't work for csN <- process(qn, verbose=verbose).
>>
>> >> sessionInfo()
>> > R version 2.10.1 (2009-12-14)
>> > x86_64-pc-linux-gnu
>>
>> > locale:
>> >  [1] LC_CTYPE=en_AU.UTF-8       LC_NUMERIC=C
>> >  [3] LC_TIME=en_AU.UTF-8        LC_COLLATE=en_AU.UTF-8
>> >  [5] LC_MONETARY=C              LC_MESSAGES=en_AU.UTF-8
>> >  [7] LC_PAPER=en_AU.UTF-8       LC_NAME=C
>> >  [9] LC_ADDRESS=C               LC_TELEPHONE=C
>> > [11] LC_MEASUREMENT=en_AU.UTF-8 LC_IDENTIFICATION=C
>>
>> > attached base packages:
>> > [1] stats     graphics  grDevices utils     datasets  methods   base
>>
>> > other attached packages:
>> >  [1] Biobase_2.6.1          aroma.affymetrix_1.7.3 aroma.apd_0.1.7
>> >  [4] affxparser_1.18.0      R.huge_0.2.0           aroma.core_1.7.4
>> >  [7] aroma.light_1.18.2     matrixStats_0.2.2      R.rsp_0.4.0
>> > [10] R.cache_0.3.0          R.filesets_0.9.0       digest_0.4.2
>> > [13] R.utils_1.5.6          R.oo_1.7.4             affy_1.24.2
>> > [16] R.methodsS3_1.2.1
>>
>> > loaded via a namespace (and not attached):
>> > [1] affyio_1.14.0        preprocessCore_1.8.0 tools_2.10.1
>>
>> >> traceback()
>> > No traceback available
>>
>> > I did follow a previous forum message regarding a similar problem and
>> > get the following outputs.
>>
>> >> library("R.utils");
>> [snip]
>> >> path <- "/home/elsa/probeData/tissues,coreR2,QN"
>> >> print(path)
>> > [1] "/home/elsa/probeData/tissues,coreR2,QN"
>> >> str(file.info(path));
>> > 'data.frame':   1 obs. of  10 variables:
>> >  $ size  : num 3
>> >  $ isdir : logi TRUE
>> >  $ mode  :Class 'octmode'  int 1535
>> >  $ mtime : POSIXct, format: "2010-11-10 09:15:13"
>> >  $ ctime : POSIXct, format: "2010-11-10 09:16:37"
>> >  $ atime : POSIXct, format: "2010-11-10 09:16:37"
>> >  $ uid   : int 341178
>> >  $ gid   : int 341178
>> >  $ uname : chr "elsa"
>> >  $ grname: chr "elsa"
>> >> print(file.access(path, mode=0));
>> > /home/elsa/probeData/tissues,coreR2,QN
>> >                                                 0
>> >> print(file.access(path, mode=1));
>> > /home/elsa/probeData/tissues,coreR2,QN
>> >                                                 0
>> >> print(file.access(path, mode=2));
>> > /home/elsa/probeData/tissues,coreR2,QN
>> >                                                 0
>> >> print(file.access(path, mode=4));
>> > /home/elsa/probeData/tissues,coreR2,QN
>> >                                                 0
>> >> print(fileAccess(path,mode=0));
>> > [1] 0
>> >> print(fileAccess(path,mode=1));
>> > [1] 0
>> >> print(fileAccess(path,mode=2));
>> > [1] -1
>> > Warning message:
>> > In fileAccess.default(path, mode = 2) :
>> >  file.access(..., mode=2) and file(..., open="ab") gives different
>> > results (0 != -1). Will use the file() results: /home/elsa/probeData/
>> > tissues,coreR2,QN/B
>> >> print(fileAccess(path,mode=4));
>> > [1] 0
>>
>> >> print(isDirectory(path));
>> > [1] TRUE
>> >> print(isFile(path));
>> > [1] FALSE
>>
>> > Looks like R.util does not have write permissions on the folder. I am
>> > just not sure how i ca fix this problem.
>>
>> > Any help is very much appreciated.
>>
>> > Regards
>> > Elsa Chacko
>> > PhD student
>> > Macquarie University
>>
>> > --
>> > 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 websitehttp://www.aroma-project.org/.
>> > To post to this group, send email to [hidden email]
>> > To unsubscribe and other options, go tohttp://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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