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
<http://aroma-project.org/setup/QuickSummaryOfRequiredFileStructure>:
> 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
--
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