rma of oligo feature set crashes R
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Ou, Jianhong ★ 1.3k
@ou-jianhong-4539
Last seen 7 days ago
United States
Hi all, When I do ram of oligo, R crashed. It is very similar to https://stat.ethz.ch/pipermail/bioconductor/2011-October/041567.html. Here is the output of console, > library(oligo) > library(limma) > library(pd.hugene.1.0.st.v1) Loading required package: RSQLite Loading required package: DBI > targets<-readTargets(file="filelist.txt",sep=" ",row.names="cel_files") > affyGeneFS <- read.celfiles(targets$cel_files) Platform design info loaded. Reading in : Control-1-1_(HuGene-1_0-st-v1).CEL Reading in : CONTROL-1-2-(HuGene-1_0-st-v1).CEL Reading in : Control-2-3_(HuGene-1_0-st-v1).CEL Reading in : CONTROL-2-4-(HuGene-1_0-st-v1).CEL Reading in : Control-3-5_(HuGene-1_0-st-v1).CEL Reading in : CONTROL-3-6-(HuGene-1_0-st-v1).CEL Reading in : kd-1_7-(HuGene-1_0-st-v1).CEL Reading in : KD-1-8_(HuGene-1_0-st-v1).CEL Reading in : kd-2_9-(HuGene-1_0-st-v1).CEL Reading in : KD-2-10_(HuGene-1_0-st-v1).CEL Reading in : kd-3_11-(HuGene-1_0-st-v1).CEL Reading in : KD-3-12_(HuGene-1_0-st-v1).CEL > sessionInfo() R version 3.0.0 (2013-04-03) Platform: x86_64-apple-darwin10.8.0 (64-bit) locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] parallel stats graphics grDevices utils datasets methods [8] base other attached packages: [1] pd.hugene.1.0.st.v1_3.8.0 RSQLite_0.11.3 [3] DBI_0.2-7 limma_3.16.3 [5] oligo_1.24.0 Biobase_2.20.0 [7] oligoClasses_1.22.0 BiocGenerics_0.6.0 loaded via a namespace (and not attached): [1] affxparser_1.32.0 affyio_1.28.0 BiocInstaller_1.10.1 [4] Biostrings_2.28.0 bit_1.1-10 codetools_0.2-8 [7] ff_2.2-11 foreach_1.4.0 GenomicRanges_1.12.2 [10] IRanges_1.18.0 iterators_1.0.6 preprocessCore_1.22.0 [13] splines_3.0.0 stats4_3.0.0 zlibbioc_1.6.0 > geneCore <- rma(affyGeneFS, target = "core") Background correcting *** caught segfault *** address 0x1029fb000, cause 'memory not mapped' Traceback: 1: .Call("rma_c_complete_copy", pmMat, pnVec, nPn, normalize, background, bgversion, verbose, PACKAGE = "oligo") 2: basicRMA(pms, pnVec, normalize, background) 3: .local(object, ...) 4: rma(affyGeneFS, target = "core") 5: rma(affyGeneFS, target = "core") Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection: 1 aborting ... Segmentation fault: 11 Any ideas? Yours sincerely, Jianhong Ou [[alternative HTML version deleted]]
oligo oligo • 1.9k views
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@benilton-carvalho-1375
Last seen 4.7 years ago
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Can you please try: pms = pm(affyGeneFS) apply(!is.finite(pms), 2, table) (if you see TRUE for any sample, that's not a good sign) Then compare the file sizes of the files for which you saw TRUE on the above command... Big divergences on file sizes may indication file corruption. b 2013/5/10 Ou, Jianhong <jianhong.ou at="" umassmed.edu="">: > Hi all, > > When I do ram of oligo, R crashed. It is very similar to https://stat.ethz.ch/pipermail/bioconductor/2011-October/041567.html. Here is the output of console, > >> library(oligo) >> library(limma) >> library(pd.hugene.1.0.st.v1) > Loading required package: RSQLite > Loading required package: DBI >> targets<-readTargets(file="filelist.txt",sep=" ",row.names="cel_files") >> affyGeneFS <- read.celfiles(targets$cel_files) > Platform design info loaded. > Reading in : Control-1-1_(HuGene-1_0-st-v1).CEL > Reading in : CONTROL-1-2-(HuGene-1_0-st-v1).CEL > Reading in : Control-2-3_(HuGene-1_0-st-v1).CEL > Reading in : CONTROL-2-4-(HuGene-1_0-st-v1).CEL > Reading in : Control-3-5_(HuGene-1_0-st-v1).CEL > Reading in : CONTROL-3-6-(HuGene-1_0-st-v1).CEL > Reading in : kd-1_7-(HuGene-1_0-st-v1).CEL > Reading in : KD-1-8_(HuGene-1_0-st-v1).CEL > Reading in : kd-2_9-(HuGene-1_0-st-v1).CEL > Reading in : KD-2-10_(HuGene-1_0-st-v1).CEL > Reading in : kd-3_11-(HuGene-1_0-st-v1).CEL > Reading in : KD-3-12_(HuGene-1_0-st-v1).CEL >> sessionInfo() > R version 3.0.0 (2013-04-03) > Platform: x86_64-apple-darwin10.8.0 (64-bit) > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] parallel stats graphics grDevices utils datasets methods > [8] base > > other attached packages: > [1] pd.hugene.1.0.st.v1_3.8.0 RSQLite_0.11.3 > [3] DBI_0.2-7 limma_3.16.3 > [5] oligo_1.24.0 Biobase_2.20.0 > [7] oligoClasses_1.22.0 BiocGenerics_0.6.0 > > loaded via a namespace (and not attached): > [1] affxparser_1.32.0 affyio_1.28.0 BiocInstaller_1.10.1 > [4] Biostrings_2.28.0 bit_1.1-10 codetools_0.2-8 > [7] ff_2.2-11 foreach_1.4.0 GenomicRanges_1.12.2 > [10] IRanges_1.18.0 iterators_1.0.6 preprocessCore_1.22.0 > [13] splines_3.0.0 stats4_3.0.0 zlibbioc_1.6.0 > >> geneCore <- rma(affyGeneFS, target = "core") > Background correcting > > *** caught segfault *** > address 0x1029fb000, cause 'memory not mapped' > > Traceback: > 1: .Call("rma_c_complete_copy", pmMat, pnVec, nPn, normalize, background, bgversion, verbose, PACKAGE = "oligo") > 2: basicRMA(pms, pnVec, normalize, background) > 3: .local(object, ...) > 4: rma(affyGeneFS, target = "core") > 5: rma(affyGeneFS, target = "core") > > Possible actions: > 1: abort (with core dump, if enabled) > 2: normal R exit > 3: exit R without saving workspace > 4: exit R saving workspace > Selection: 1 > aborting ... > Segmentation fault: 11 > > Any ideas? > > Yours sincerely, > > Jianhong Ou > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
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Dear Benilton, Yes, I found two files contain TRUE (485 and 138). However the file sizes are similar to the others. I will double check the md5 checksums. Thank you for your help. Yours sincerely, Jianhong Ou LRB 670A Program in Gene Function and Expression 364 Plantation Street Worcester, MA 01605 On 5/12/13 6:02 PM, "Benilton Carvalho" <beniltoncarvalho at="" gmail.com=""> wrote: >Can you please try: > >pms = pm(affyGeneFS) >apply(!is.finite(pms), 2, table) > >(if you see TRUE for any sample, that's not a good sign) > >Then compare the file sizes of the files for which you saw TRUE on the >above command... Big divergences on file sizes may indication file >corruption. > > >b > >2013/5/10 Ou, Jianhong <jianhong.ou at="" umassmed.edu="">: >> Hi all, >> >> When I do ram of oligo, R crashed. It is very similar to >>https://stat.ethz.ch/pipermail/bioconductor/2011-October/041567.html . >>Here is the output of console, >> >>> library(oligo) >>> library(limma) >>> library(pd.hugene.1.0.st.v1) >> Loading required package: RSQLite >> Loading required package: DBI >>> targets<-readTargets(file="filelist.txt",sep=" ",row.names="cel_files") >>> affyGeneFS <- read.celfiles(targets$cel_files) >> Platform design info loaded. >> Reading in : Control-1-1_(HuGene-1_0-st-v1).CEL >> Reading in : CONTROL-1-2-(HuGene-1_0-st-v1).CEL >> Reading in : Control-2-3_(HuGene-1_0-st-v1).CEL >> Reading in : CONTROL-2-4-(HuGene-1_0-st-v1).CEL >> Reading in : Control-3-5_(HuGene-1_0-st-v1).CEL >> Reading in : CONTROL-3-6-(HuGene-1_0-st-v1).CEL >> Reading in : kd-1_7-(HuGene-1_0-st-v1).CEL >> Reading in : KD-1-8_(HuGene-1_0-st-v1).CEL >> Reading in : kd-2_9-(HuGene-1_0-st-v1).CEL >> Reading in : KD-2-10_(HuGene-1_0-st-v1).CEL >> Reading in : kd-3_11-(HuGene-1_0-st-v1).CEL >> Reading in : KD-3-12_(HuGene-1_0-st-v1).CEL >>> sessionInfo() >> R version 3.0.0 (2013-04-03) >> Platform: x86_64-apple-darwin10.8.0 (64-bit) >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] parallel stats graphics grDevices utils datasets methods >> [8] base >> >> other attached packages: >> [1] pd.hugene.1.0.st.v1_3.8.0 RSQLite_0.11.3 >> [3] DBI_0.2-7 limma_3.16.3 >> [5] oligo_1.24.0 Biobase_2.20.0 >> [7] oligoClasses_1.22.0 BiocGenerics_0.6.0 >> >> loaded via a namespace (and not attached): >> [1] affxparser_1.32.0 affyio_1.28.0 BiocInstaller_1.10.1 >> [4] Biostrings_2.28.0 bit_1.1-10 codetools_0.2-8 >> [7] ff_2.2-11 foreach_1.4.0 GenomicRanges_1.12.2 >> [10] IRanges_1.18.0 iterators_1.0.6 preprocessCore_1.22.0 >> [13] splines_3.0.0 stats4_3.0.0 zlibbioc_1.6.0 >> >>> geneCore <- rma(affyGeneFS, target = "core") >> Background correcting >> >> *** caught segfault *** >> address 0x1029fb000, cause 'memory not mapped' >> >> Traceback: >> 1: .Call("rma_c_complete_copy", pmMat, pnVec, nPn, normalize, >>background, bgversion, verbose, PACKAGE = "oligo") >> 2: basicRMA(pms, pnVec, normalize, background) >> 3: .local(object, ...) >> 4: rma(affyGeneFS, target = "core") >> 5: rma(affyGeneFS, target = "core") >> >> Possible actions: >> 1: abort (with core dump, if enabled) >> 2: normal R exit >> 3: exit R without saving workspace >> 4: exit R saving workspace >> Selection: 1 >> aborting ... >> Segmentation fault: 11 >> >> Any ideas? >> >> Yours sincerely, >> >> Jianhong Ou >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at r-project.org >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >>http://news.gmane.org/gmane.science.biology.informatics.conductor
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You'll need to either find non-damaged copies of these files or remove them from analysis. b 2013/5/13 Ou, Jianhong <jianhong.ou at="" umassmed.edu="">: > Dear Benilton, > > Yes, I found two files contain TRUE (485 and 138). However the file sizes > are similar to the others. I will double check the md5 checksums. > Thank you for your help. > > Yours sincerely, > > Jianhong Ou > > LRB 670A > Program in Gene Function and Expression > 364 Plantation Street Worcester, > MA 01605 > > > > > On 5/12/13 6:02 PM, "Benilton Carvalho" <beniltoncarvalho at="" gmail.com=""> wrote: > >>Can you please try: >> >>pms = pm(affyGeneFS) >>apply(!is.finite(pms), 2, table) >> >>(if you see TRUE for any sample, that's not a good sign) >> >>Then compare the file sizes of the files for which you saw TRUE on the >>above command... Big divergences on file sizes may indication file >>corruption. >> >> >>b >> >>2013/5/10 Ou, Jianhong <jianhong.ou at="" umassmed.edu="">: >>> Hi all, >>> >>> When I do ram of oligo, R crashed. It is very similar to >>>https://stat.ethz.ch/pipermail/bioconductor/2011-October/041567.htm l. >>>Here is the output of console, >>> >>>> library(oligo) >>>> library(limma) >>>> library(pd.hugene.1.0.st.v1) >>> Loading required package: RSQLite >>> Loading required package: DBI >>>> targets<-readTargets(file="filelist.txt",sep=" ",row.names="cel_files") >>>> affyGeneFS <- read.celfiles(targets$cel_files) >>> Platform design info loaded. >>> Reading in : Control-1-1_(HuGene-1_0-st-v1).CEL >>> Reading in : CONTROL-1-2-(HuGene-1_0-st-v1).CEL >>> Reading in : Control-2-3_(HuGene-1_0-st-v1).CEL >>> Reading in : CONTROL-2-4-(HuGene-1_0-st-v1).CEL >>> Reading in : Control-3-5_(HuGene-1_0-st-v1).CEL >>> Reading in : CONTROL-3-6-(HuGene-1_0-st-v1).CEL >>> Reading in : kd-1_7-(HuGene-1_0-st-v1).CEL >>> Reading in : KD-1-8_(HuGene-1_0-st-v1).CEL >>> Reading in : kd-2_9-(HuGene-1_0-st-v1).CEL >>> Reading in : KD-2-10_(HuGene-1_0-st-v1).CEL >>> Reading in : kd-3_11-(HuGene-1_0-st-v1).CEL >>> Reading in : KD-3-12_(HuGene-1_0-st-v1).CEL >>>> sessionInfo() >>> R version 3.0.0 (2013-04-03) >>> Platform: x86_64-apple-darwin10.8.0 (64-bit) >>> >>> locale: >>> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 >>> >>> attached base packages: >>> [1] parallel stats graphics grDevices utils datasets methods >>> [8] base >>> >>> other attached packages: >>> [1] pd.hugene.1.0.st.v1_3.8.0 RSQLite_0.11.3 >>> [3] DBI_0.2-7 limma_3.16.3 >>> [5] oligo_1.24.0 Biobase_2.20.0 >>> [7] oligoClasses_1.22.0 BiocGenerics_0.6.0 >>> >>> loaded via a namespace (and not attached): >>> [1] affxparser_1.32.0 affyio_1.28.0 BiocInstaller_1.10.1 >>> [4] Biostrings_2.28.0 bit_1.1-10 codetools_0.2-8 >>> [7] ff_2.2-11 foreach_1.4.0 GenomicRanges_1.12.2 >>> [10] IRanges_1.18.0 iterators_1.0.6 preprocessCore_1.22.0 >>> [13] splines_3.0.0 stats4_3.0.0 zlibbioc_1.6.0 >>> >>>> geneCore <- rma(affyGeneFS, target = "core") >>> Background correcting >>> >>> *** caught segfault *** >>> address 0x1029fb000, cause 'memory not mapped' >>> >>> Traceback: >>> 1: .Call("rma_c_complete_copy", pmMat, pnVec, nPn, normalize, >>>background, bgversion, verbose, PACKAGE = "oligo") >>> 2: basicRMA(pms, pnVec, normalize, background) >>> 3: .local(object, ...) >>> 4: rma(affyGeneFS, target = "core") >>> 5: rma(affyGeneFS, target = "core") >>> >>> Possible actions: >>> 1: abort (with core dump, if enabled) >>> 2: normal R exit >>> 3: exit R without saving workspace >>> 4: exit R saving workspace >>> Selection: 1 >>> aborting ... >>> Segmentation fault: 11 >>> >>> Any ideas? >>> >>> Yours sincerely, >>> >>> Jianhong Ou >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at r-project.org >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>>http://news.gmane.org/gmane.science.biology.informatics.conductor >
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Hello, I also get a crash in oligo's background correction, in a different subroutine, though:

> eset.bg.normalized <- rma(dat,target="core",background=T,normalize=T)
Background correcting

 *** caught segfault ***
address 0x562729e52000, cause 'memory not mapped'

Traceback:
 1: basicRMA(pms, pnVec, normalize, background)
 2: .local(object, ...)
 3: rma(dat, target = "core", background = T, normalize = T)
 4: rma(dat, target = "core", background = T, normalize = T)

Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection: 1
R is aborting now ...
Segmentation fault (core dumped)

Confirmed it with Debian, conda+BiocManager and my own compliation of oligo 1.62.2.

> table(apply(pms, 2, function(X) all(is.finite(X))))

TRUE 
18

I tried bisecting through the samples but individually or in groups of sixes they all work. My work-around is to cbind the exprs of subsets, which somewhat affects the quantile normalization, I expect. Can I somehow help to track this down?

With many thanks! Steffen

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Please don't tack comments onto 10 year old posts! If you would like help, start a new post and supply a self-contained example, or at the very least provide the array type you are using.

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