Hi,
interesting. A quick guess is that the input file, i.e.
rawData/NIK_2014/HuEx-1_0-st-v2/GSM709330_HSB194-S1C-L.CEL
is write protected (e.g. file owned by someone else). This could be
the reason, because internally that file is copied and used as a
template and the copy may inherit the file permissions. What does ls
-l say about the above file?
If this is the case, I need to update the copying such that the new
file has proper permissions.
Thanks for the report
Henrik
On Thu, Sep 4, 2014 at 10:15 AM, Taylor Raborn <taylor.rab...@gmail.com> wrote:
> Hi Henrik:
>
> I just come across an unusual error when using aroma.affymetrix on our
> high-memory HPC machine. It may or may not be platform-specific, and I'll
> give you all the information I can in the hopes of isolating and identifying
> the error.
>
> Traceback:
>
>> traceback()
>
> 18: stop(cond)
>
> 17: throw.Exception(Exception(...))
>
> 16: throw(Exception(...))
>
> 15: throw.default("No permission to modify existing file: ", pathname)
>
> 14: throw("No permission to modify existing file: ", pathname)
>
> 13: getWritablePathname.Arguments(static, ...)
>
> 12: getWritablePathname(static, ...) at <text>#1
>
> 11: Arguments$getWritablePathname(pathname, mustExist = TRUE)
>
> 10: renameFile.default(srcPathname, pathname, ...)
>
> 9: renameFile(srcPathname, pathname, ...)
>
> 8: renameTo.GenericDataFile(res, filename = pathname, verbose =
> less(verbose))
>
> 7: renameTo(res, filename = pathname, verbose = less(verbose))
>
> 6: createFrom.AffymetrixCelFile(this, filename = pathnameT, path = NULL,
>
> verbose = less(verbose))
>
> 5: createFrom(this, filename = pathnameT, path = NULL, verbose =
> less(verbose))
>
> 4: bgAdjustRma.AffymetrixCelFile(df, path = outputPath, pmonly = pmonly,
>
> addJitter = addJitter, jitterSd = jitterSd, overwrite = force,
>
> verbose = verbose, .deprecated = FALSE)
>
> 3: bgAdjustRma(df, path = outputPath, pmonly = pmonly, addJitter =
> addJitter,
>
> jitterSd = jitterSd, overwrite = force, verbose = verbose,
>
> .deprecated = FALSE)
>
> 2: process.RmaBackgroundCorrection(bc, verbose = verbose)
>
> 1: process(bc, verbose = verbose)
>
>
> ----
>
> sessionInfo:
>
>> sessionInfo()
>
> R version 3.0.1 (2013-05-16)
>
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
>
> locale:
>
> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>
> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>
> [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
>
> [7] LC_PAPER=C LC_NAME=C
>
> [9] LC_ADDRESS=C LC_TELEPHONE=C
>
> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>
>
> attached base packages:
>
> [1] tools parallel stats graphics grDevices utils datasets
>
> [8] methods base
>
>
> other attached packages:
>
> [1] R.cache_0.10.0 base64enc_0.1-2 aroma.apd_0.5.0
>
> [4] preprocessCore_1.24.0 affyio_1.30.0 Biobase_2.20.1
>
> [7] BiocGenerics_0.6.0 aroma.light_1.32.0 matrixStats_0.10.0
>
> [10] aroma.affymetrix_2.12.0 aroma.core_2.12.1 R.devices_2.11.0
>
> [13] R.filesets_2.6.0 R.utils_1.33.0 R.oo_1.18.0
>
> [16] affxparser_1.34.2 affy_1.40.0 R.methodsS3_1.6.1
>
> [19] PSCBS_0.43.0 DNAcopy_1.36.0 BiocInstaller_1.12.1
>
>
> loaded via a namespace (and not attached):
>
> [1] digest_0.6.4 R.huge_0.8.0 R.rsp_0.19.0 zlibbioc_1.11.1
>
>
>
> Here's how I produced the error. Note that my directory structure matches
> that on the aroma-project.org site, shown here:
>
>> chipType <- "HuEx-1_0-st-v2"
>
>
>> cdf <- AffymetrixCdfFile$byChipType(chipType, tags="coreR3,A20071112,EP")
>
>
>> print(cdf)
>
> AffymetrixCdfFile:
>
> Path: annotationData/chipTypes/HuEx-1_0-st-v2
>
> Filename: HuEx-1_0-st-v2,coreR3,A20071112,EP.cdf
>
> File size: 38.25 MB (40108891 bytes)
>
> Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP
>
> RAM: 0.00MB
>
> File format: v4 (binary; XDA)
>
> Dimension: 2560x2560
>
> Number of cells: 6553600
>
> Number of units: 18708
>
> Cells per unit: 350.31
>
> Number of QC units: 1
>
>
>> cs <- AffymetrixCelSet$byName("NIK_2014", cdf=cdf)
>
>
>> print(cs)
>
> AffymetrixCelSet:
>
> Name: NIK_2014
>
> Tags:
>
> Path: rawData/NIK_2014/HuEx-1_0-st-v2
>
> Platform: Affymetrix
>
> Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP
>
> Number of arrays: 9
>
> Names: GSM709330_HSB194-S1C-L, GSM709331_HSB194-S1C-R,
> GSM709332_HSB194-STC-L, ..., GSM709338_HSB194-VFC-R [9]
>
> Time period: 2011-01-25 12:15:03 -- 2011-01-25 13:48:02
>
> Total file size: 564.87MB
>
> RAM: 0.02MB
>
>
>> csBC <- process(bc,verbose=verbose)
>
> Background correcting data set...
>
> Number of arrays: 9
>
> Array #1 ('GSM709330_HSB194-S1C-L') of 9...
>
> Adjusting PM signals only
>
> Obtaining signals...
>
> Obtaining signals...done
>
> Applying normal+exponential signal model...
>
> Applying normal+exponential signal model...done
>
> Writing adjusted probe signals...
>
> Adding temporary suffix from file...
>
> Pathname:
> probeData/NIK_2014,RBC,coreR3/HuEx-1_0-st-v2/GSM709330_HSB194-S1C-L.CEL
>
> Suffix: .tmp
>
> Rename existing file?: FALSE
>
> Temporary pathname:
> probeData/NIK_2014,RBC,coreR3/HuEx-1_0-st-v2/GSM709330_HSB194-S1C-L.CEL.tmp
>
> Adding temporary suffix from file...done
>
> Creating CEL file for results, if missing...
>
> [2014-09-04 12:38:54] Exception: No permission to modify existing file:
> probeData/NIK_2014,RBC,coreR3/HuEx-1_0-st-v2/GSM709330_HSB194-S1C-L.CEL.tmp.tmp
>
>
> at #13. getWritablePathname.Arguments(static, ...)
>
> - getWritablePathname.Arguments() is in environment 'R.utils'
>
>
> at #12. getWritablePathname(static, ...)
>
> - getWritablePathname() is in environment 'R.utils'
>
> - originating from '<text>'
>
>
> at #11. Arguments$getWritablePathname(pathname, mustExist = TRUE)
>
> - Arguments$getWritablePathname() is local of the calling function
>
>
> at #10. renameFile.default(srcPathname, pathname, ...)
>
> - renameFile.default() is in environment 'R.utils'
>
>
> at #09. renameFile(srcPathname, pathname, ...)
>
> - renameFile() is in environment 'R.utils'
>
>
> at #08. renameTo.GenericDataFile(res, filename = pathname, verbose =
> less(verbose))
>
> - renameTo.GenericDataFile() is in environment 'R.filesets'
>
>
> at #07. renameTo(res, filename = pathname, verbose = less(verbose))
>
> - renameTo() is in environment 'R.filesets'
>
>
> at #06. createFrom.AffymetrixCelFile(this, filename = pathnameT, path =
> NULL,
>
> verbose = less(verbose))
>
> - createFrom.AffymetrixCelFile() is in environment
> 'aroma.affymetrix'
>
>
> at #05. createFrom(this, filename = pathnameT, path = NULL, verbose =
> less(verbose))
>
> - createFrom() is in environment 'aroma.affymetrix'
>
>
> at #04. bgAdjustRma.AffymetrixCelFile(df, path = outputPath, pmonly =
> pmonly,
>
> addJitter = addJitter, jitterSd = jitterSd, overwrite = force,
>
> verbose = verbose, .deprecated = FALSE)
>
> - bgAdjustRma.AffymetrixCelFile() is in environment
> 'aroma.affymetrix'
>
>
> at #03. bgAdjustRma(df, path = outputPath, pmonly = pmonly, addJitter =
> addJitter,
>
> jitterSd = jitterSd, overwrite = force, verbose = verbose,
>
> .deprecated = FALSE)
>
> - bgAdjustRma() is in environment 'aroma.affymetrix'
>
>
> at #02. process.RmaBackgroundCorrection(bc, verbose = verbose)
>
> - process.RmaBackgroundCorrection() is in environment
> 'aroma.affymetrix'
>
>
> at #01. process(bc, verbose = verbose)
>
> - process() is in environment 'aroma.core'
>
>
> Error: No permission to modify existing file:
> probeData/NIK_2014,RBC,coreR3/HuEx-1_0-st-v2/GSM709330_HSB194-S1C-L.CEL.tmp.tmp
>
> Creating CEL file for results, if missing...done
>
> Writing adjusted probe signals...done
>
> Array #1 ('GSM709330_HSB194-S1C-L') of 9...done
>
> Background correcting data set...done
>
> --------------------
>
>
> I tried to find a solution from the group archives and other places to no
> avail. It's worth mentioning that I get this problem even if I open up
> permissions to the entire directory. The *CEL.tmp.tmp file appears to be
> written with write-protections, which is baffling to me. The machine is a
> large, high-memory cluster from my institution, and the error may be
> associated with this.
>
>
> Thanks in advance for any insight you can provide with this.
>
>
> Best regards,
>
>
> Taylor
>
>
> --
> --
> 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
"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/
---
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