[aroma.affymetrix] Error writing to connection

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[aroma.affymetrix] Error writing to connection

Karyn Meltz Steinberg
Hello,

I am running doCRMAv2 on 8 CytoScanHD .CEL files. I get the following error in the  CRMAv2/Export to technology-independent data files...
step:

Error in base_save(file = fh, object, compress = compress, ...) :
  error writing to connection
In addition: Warning message:
In readRDS(con) : error reading from connection
          Saving to file cache...done
         Getting (unit, group, cell) map...done
        Extracting (total, freqB)...done
       Reading data...done
      Exporting CnChipEffectFile as an AromaUnitTotalCnBinaryFile...done
     Exporting (total, fracB) data...done
    Array #1 ('GBD-035') of 8...done
   Exporting CnChipEffectSet as AromaUnitTotalCnBinarySet...done

I have enough space on the disk and the correct permissions. I am running version 3.1.0 on R3.4.0. Any advice would be greatly appreciated

Best,
Karyn

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Re: [aroma.affymetrix] Error writing to connection

Henrik Bengtsson-2
Hi.  From your verbose output, I think two things can have happened:

1. This error happens when it tries to write to the file cache, which
is located under ~/.Rcache/.  It could be that this cache is using up
your home drive/folder/account.  Not sure what OS you're on, but to
find where `~` is use `normalizePath("~").   If that is indeed full,
and you're on Unix/macOS, the easiest is to simply point `~/.Rcache/`
to another drive via symbol links, e.g. `mkdir -p /scratch/$USER; mv
~/.Rcache /scratch/$USER/; ln -s /scratch/$USER/ ~/.Rcache`.

2. Alternatively, it could just be a hiccup on your system, which
means you can just rerun the script (it should quickly skip everything
already processed in previous runs).

I think (1) is the most likely reason, because the error is in
`base_save(file = fh, object, compress = compress, ...)` which happens
after two very similar calls to the same file which did _not_ fail,
cf. https://github.com/HenrikBengtsson/R.cache/blob/0.12.0/R/saveCache.R#L111.
(I'll see if I can add a more informative error message in a future
version of R.cache, e.g. including the problematic filename.)

Hope this helps

Henrik

On Mon, Dec 18, 2017 at 3:25 PM, Karyn Meltz Steinberg
<[hidden email]> wrote:

> Hello,
>
> I am running doCRMAv2 on 8 CytoScanHD .CEL files. I get the following error
> in the  CRMAv2/Export to technology-independent data files...
> step:
>
> Error in base_save(file = fh, object, compress = compress, ...) :
>   error writing to connection
> In addition: Warning message:
> In readRDS(con) : error reading from connection
>           Saving to file cache...done
>          Getting (unit, group, cell) map...done
>         Extracting (total, freqB)...done
>        Reading data...done
>       Exporting CnChipEffectFile as an AromaUnitTotalCnBinaryFile...done
>      Exporting (total, fracB) data...done
>     Array #1 ('GBD-035') of 8...done
>    Exporting CnChipEffectSet as AromaUnitTotalCnBinarySet...done
>
> I have enough space on the disk and the correct permissions. I am running
> version 3.1.0 on R3.4.0. Any advice would be greatly appreciated
>
> Best,
> Karyn
>
> --
> --
> 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/
>
> ---
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group.
> To unsubscribe from this group and stop receiving emails from it, send an
> email to [hidden email].
> For more options, visit https://groups.google.com/d/optout.

--
--
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] Error writing to connection

Karyn Meltz Steinberg
Thank you so much--Number 1 was indeed the issue. I truly appreciate your quick response.

Best,
KMS

On Monday, December 18, 2017 at 10:49:06 PM UTC-6, Henrik Bengtsson wrote:
Hi.  From your verbose output, I think two things can have happened:

1. This error happens when it tries to write to the file cache, which
is located under ~/.Rcache/.  It could be that this cache is using up
your home drive/folder/account.  Not sure what OS you're on, but to
find where `~` is use `normalizePath("~").   If that is indeed full,
and you're on Unix/macOS, the easiest is to simply point `~/.Rcache/`
to another drive via symbol links, e.g. `mkdir -p /scratch/$USER; mv
~/.Rcache /scratch/$USER/; ln -s /scratch/$USER/ ~/.Rcache`.

2. Alternatively, it could just be a hiccup on your system, which
means you can just rerun the script (it should quickly skip everything
already processed in previous runs).

I think (1) is the most likely reason, because the error is in
`base_save(file = fh, object, compress = compress, ...)` which happens
after two very similar calls to the same file which did _not_ fail,
cf. <a href="https://github.com/HenrikBengtsson/R.cache/blob/0.12.0/R/saveCache.R#L111" target="_blank" rel="nofollow" onmousedown="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FHenrikBengtsson%2FR.cache%2Fblob%2F0.12.0%2FR%2FsaveCache.R%23L111\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHnlOlekj2HmdjBu40r1ZcGv66-Ew&#39;;return true;" onclick="this.href=&#39;https://www.google.com/url?q\x3dhttps%3A%2F%2Fgithub.com%2FHenrikBengtsson%2FR.cache%2Fblob%2F0.12.0%2FR%2FsaveCache.R%23L111\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHnlOlekj2HmdjBu40r1ZcGv66-Ew&#39;;return true;">https://github.com/HenrikBengtsson/R.cache/blob/0.12.0/R/saveCache.R#L111.
(I'll see if I can add a more informative error message in a future
version of R.cache, e.g. including the problematic filename.)

Hope this helps

Henrik

On Mon, Dec 18, 2017 at 3:25 PM, Karyn Meltz Steinberg
<<a href="javascript:" target="_blank" gdf-obfuscated-mailto="c3amHgHcCQAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">karyn.s...@...> wrote:

> Hello,
>
> I am running doCRMAv2 on 8 CytoScanHD .CEL files. I get the following error
> in the  CRMAv2/Export to technology-independent data files...
> step:
>
> Error in base_save(file = fh, object, compress = compress, ...) :
>   error writing to connection
> In addition: Warning message:
> In readRDS(con) : error reading from connection
>           Saving to file cache...done
>          Getting (unit, group, cell) map...done
>         Extracting (total, freqB)...done
>        Reading data...done
>       Exporting CnChipEffectFile as an AromaUnitTotalCnBinaryFile...done
>      Exporting (total, fracB) data...done
>     Array #1 ('GBD-035') of 8...done
>    Exporting CnChipEffectSet as AromaUnitTotalCnBinarySet...done
>
> I have enough space on the disk and the correct permissions. I am running
> version 3.1.0 on R3.4.0. Any advice would be greatly appreciated
>
> Best,
> Karyn
>
> --
> --
> 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 <a href="http://www.aroma-project.org/" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.aroma-project.org%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGgFm4_bwjITDRdF-uORwY5SRzKjA&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.aroma-project.org%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGgFm4_bwjITDRdF-uORwY5SRzKjA&#39;;return true;">http://www.aroma-project.org/.
> To post to this group, send email to <a href="javascript:" target="_blank" gdf-obfuscated-mailto="c3amHgHcCQAJ" rel="nofollow" onmousedown="this.href=&#39;javascript:&#39;;return true;" onclick="this.href=&#39;javascript:&#39;;return true;">aroma-af...@googlegroups.com
> To unsubscribe and other options, go to <a href="http://www.aroma-project.org/forum/" target="_blank" rel="nofollow" onmousedown="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.aroma-project.org%2Fforum%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHDHkQUDcBfAJzIqTbjSXZqyWgITA&#39;;return true;" onclick="this.href=&#39;http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.aroma-project.org%2Fforum%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHDHkQUDcBfAJzIqTbjSXZqyWgITA&#39;;return true;">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]
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