>From the traceback it is quite clear that the problem occurs solely in affxparser (has nothing to do with aroma.*), so a minimum reproducible example should be:
library("affxparser"); pathname <- "rawData/GSE19804/GenomeWideSNP_6/Lung32T.CEL"; print(file.info(pathname)); hdr <- readCelHeader(pathname); str(hdr); If you have more CEL files, you may have to locate the one causing the problem, unless all of them causes R to crash. My guess is that it is indeed a faulty CEL file. If it works with one version of R/affxparser but not another, that may indicate a faulty affxparser build. See if you can reproduce with a more recent version of R - if you can, then we'll look into the details. No one will (nor will be able to) bug fix anything before affxparser v1.24.0. /Henrik On Thu, Oct 6, 2011 at 3:05 PM, Johan Staaf <johan.st...@med.lu.se> wrote: > Hi Henrik > Below is the same output including sessionInfo() when it did not work, as > well as when it worked. Sorry for the inconvenience. Thanks! > > Johan > > ##### Worked on Mac ##### >> library(aroma.affymetrix) > Loading required package: R.utils > Loading required package: R.oo > Loading required package: R.methodsS3 > R.methodsS3 v1.2.0 (2010-03-13) successfully loaded. See ?R.methodsS3 for > help. > R.oo v1.7.3 (2010-06-04) successfully loaded. See ?R.oo for help. > R.utils v1.5.0 (2010-08-04) successfully loaded. See ?R.utils for help. > Loading required package: R.filesets > Loading required package: digest > R.filesets v0.8.3 (2010-07-06) successfully loaded. See ?R.filesets for help. > Loading required package: aroma.core > Loading required package: R.cache > R.cache v0.3.0 (2010-03-13) successfully loaded. See ?R.cache for help. > Loading required package: R.rsp > R.rsp v0.3.6 (2009-09-16) successfully loaded. See ?R.rsp for help. > Type browseRsp() to open the RSP main menu in your browser. > Loading required package: matrixStats > matrixStats v0.2.1 (2010-04-05) successfully loaded. See ?matrixStats for > help. > Loading required package: aroma.light > aroma.light v1.16.1 (2010-06-23) successfully loaded. See ?aroma.light for > help. > aroma.core v1.7.0 (2010-07-26) successfully loaded. See ?aroma.core for help. > Loading required package: aroma.apd > Loading required package: R.huge > R.huge v0.2.0 (2009-10-16) successfully loaded. See ?R.huge for help. > Loading required package: affxparser > aroma.apd v0.1.7 (2009-10-16) successfully loaded. See ?aroma.apd for help. > aroma.affymetrix v1.7.0 (2010-07-26) successfully loaded. See > ?aroma.affymetrix for help. > Warning message: > 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible >> >> ####### Read and check that CDFs etc is ok ##### >> verbose <- Arguments$getVerbose(-8, timestamp=TRUE) >> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full") >> print(cdf) > AffymetrixCdfFile: > Path: annotationData/chipTypes/GenomeWideSNP_6 > Filename: GenomeWideSNP_6,Full.cdf > Filesize: 470.44MB > Chip type: GenomeWideSNP_6,Full > RAM: 0.00MB > File format: v4 (binary; XDA) > Dimension: 2572x2680 > Number of cells: 6892960 > Number of units: 1881415 > Cells per unit: 3.66 > Number of QC units: 4 >> >> gi <- getGenomeInformation(cdf) >> print(gi) > UgpGenomeInformation: > Name: GenomeWideSNP_6 > Tags: Full,na26,HB20080821 > Full name: GenomeWideSNP_6,Full,na26,HB20080821 > Pathname: > annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na26,HB20080821.ugp > File size: 8.97 MB (9407937 bytes) > RAM: 0.00 MB > Chip type: GenomeWideSNP_6,Full >> >> acs <- AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE)) >> print(acs) > AromaCellSequenceFile: > Name: GenomeWideSNP_6 > Tags: HB20080710 > Full name: GenomeWideSNP_6,HB20080710 > Pathname: > annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,HB20080710.acs > File size: 170.92 MB (179217531 bytes) > RAM: 0.00 MB > Number of data rows: 6892960 > File format: v1 > Dimensions: 6892960x26 > Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, > raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw > Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, > 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 > Footer: <createdOn>20080710 22:47:02 > PDT</createdOn><platform>Affymetrix</platform><chipType>GenomeWideSNP_6</chipType><srcFile><filename>GenomeWideSNP_6.probe_tab</filename><filesize>341479928</filesize><checksum>2037c033c09fd8f7c06bd042a77aef15</checksum></srcFile><srcFile2><filename>GenomeWideSNP_6.CN_probe_tab</filename><filesize>96968290</filesize><checksum>3dc2d3178f5eafdbea9c8b6eca88a89c</checksum></srcFile2> > Chip type: GenomeWideSNP_6 > Platform: Affymetrix >> ########### >> sessionInfo() > R version 2.11.1 (2010-05-31) > x86_64-apple-darwin9.8.0 > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] aroma.affymetrix_1.7.0 aroma.apd_0.1.7 affxparser_1.20.0 > R.huge_0.2.0 aroma.core_1.7.0 > [6] aroma.light_1.16.1 matrixStats_0.2.1 R.rsp_0.3.6 > R.cache_0.3.0 R.filesets_0.8.3 > [11] digest_0.4.2 R.utils_1.5.0 R.oo_1.7.3 > R.methodsS3_1.2.0 > > loaded via a namespace (and not attached): > [1] tools_2.11.1 > Warning message: > 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible > > ################# > > > > ##### DID NOT WORK Unix ### > library(aroma.affymetrix) > Loading required package: R.filesets > Loading required package: digest > R.filesets v1.1.0 (2011-07-24) successfully loaded. See ?R.filesets for help. > Loading required package: aroma.core > Loading required package: R.cache > R.cache v0.5.1 (2011-08-31) successfully loaded. See ?R.cache for help. > > > Attaching package: 'R.cache' > > The following object(s) are masked from 'package:R.filesets': > > getChecksum > > Loading required package: R.rsp > R.rsp v0.6.2 (2011-07-27) successfully loaded. See ?R.rsp for help. > Type browseRsp() to open the RSP main menu in your browser. > Loading required package: matrixStats > matrixStats v0.2.2 (2010-10-06) successfully loaded. See ?matrixStats for > help. > Loading required package: aroma.light > aroma.light v1.20.0 (2011-04-12) successfully loaded. See ?aroma.light for > help. > > aroma.core v2.2.0 (2011-09-01) successfully loaded. See ?aroma.core for help. > > Attaching package: 'aroma.core' > > The following object(s) are masked from 'package:base': > > .Machine, append, apply, cat, colMeans, colSums, getOption, lapply, > library, require, sapply > > Loading required package: aroma.apd > Loading required package: R.huge > R.huge v0.3.0 (2011-07-23) successfully loaded. See ?R.huge for help. > Loading required package: affxparser > aroma.apd v0.2.0 (2011-07-23) successfully loaded. See ?aroma.apd for help. > aroma.affymetrix v2.2.0 (2011-09-01) successfully loaded. See > ?aroma.affymetrix for help. >> library("ACNE"); > Loading required package: MASS > ACNE v0.4.2 (2010-09-28) successfully loaded. See ?ACNE for help. > > >> sessionInfo() > R version 2.12.1 (2010-12-16) > Platform: x86_64-redhat-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=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices datasets utils methods base > > other attached packages: > [1] ACNE_0.4.2 MASS_7.3-9 aroma.affymetrix_2.2.0 > [4] affxparser_1.22.1 aroma.apd_0.2.0 R.huge_0.3.0 > [7] aroma.core_2.2.0 aroma.light_1.20.0 matrixStats_0.2.2 > [10] R.rsp_0.6.2 R.cache_0.5.1 R.filesets_1.1.0 > [13] digest_0.5.1 R.utils_1.8.2 R.oo_1.8.2 > [16] R.methodsS3_1.2.1 >> >> >> ####### Read and check that CDFs etc is ok ##### >> verbose <- Arguments$getVerbose(-8, timestamp=TRUE) >> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full") >> print(cdf) > AffymetrixCdfFile: > Path: annotationData/chipTypes/GenomeWideSNP_6 > Filename: GenomeWideSNP_6,Full.cdf > Filesize: 470.44MB > Chip type: GenomeWideSNP_6,Full > RAM: 0.00MB > File format: v4 (binary; XDA) > Dimension: 2572x2680 > Number of cells: 6892960 > Number of units: 1881415 > Cells per unit: 3.66 > Number of QC units: 4 >> gi <- getGenomeInformation(cdf) >> print(gi) > UgpGenomeInformation: > Name: GenomeWideSNP_6 > Tags: Full,na26,HB20080821 > Full name: GenomeWideSNP_6,Full,na26,HB20080821 > Pathname: > annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na26,HB20080821.ugp > File size: 8.97 MB (9407937 bytes) > RAM: 0.00 MB > Chip type: GenomeWideSNP_6,Full >> acs <- AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE)) >> print(acs) > AromaCellSequenceFile: > Name: GenomeWideSNP_6 > Tags: HB20080710 > Full name: GenomeWideSNP_6,HB20080710 > Pathname: > annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,HB20080710.acs > File size: 170.92 MB (179217531 bytes) > RAM: 0.00 MB > Number of data rows: 6892960 > File format: v1 > Dimensions: 6892960x26 > Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, > raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw > Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, > 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 > Footer: <createdOn>20080710 22:47:02 > PDT</createdOn><platform>Affymetrix</platform><chipType>GenomeWideSNP_6</chipType><srcFile><filename>GenomeWideSNP_6.probe_tab</filename><filesize>341479928</filesize><checksum>2037c033c09fd8f7c06bd042a77aef15</checksum></srcFile><srcFile2><filename>GenomeWideSNP_6.CN_probe_tab</filename><filesize>96968290</filesize><checksum>3dc2d3178f5eafdbea9c8b6eca88a89c</checksum></srcFile2> > Chip type: GenomeWideSNP_6 > Platform: Affymetrix >> ####### >> >> >> data.set.name<-"GSE19804" >> print(paste("doing",data.set.name)) > [1] "doing GSE19804" >> >> cdf > AffymetrixCdfFile: > Path: annotationData/chipTypes/GenomeWideSNP_6 > Filename: GenomeWideSNP_6,Full.cdf > Filesize: 470.44MB > Chip type: GenomeWideSNP_6,Full > RAM: 0.00MB > File format: v4 (binary; XDA) > Dimension: 2572x2680 > Number of cells: 6892960 > Number of units: 1881415 > Cells per unit: 3.66 > Number of QC units: 4 >> cs <- AffymetrixCelSet$byName(data.set.name, cdf=cdf); >> cs <- extract(cs, !isDuplicated(cs)) > > > *** caught segfault *** > address 0x7f449b4b3850, cause 'invalid permissions' > > Traceback: > 1: .Call("R_affx_get_cel_file_header", filename, PACKAGE = "affxparser") > 2: readCelHeader(pathname) > 3: getHeader.AffymetrixCelFile(this) > 4: getHeader(this) > 5: getTimestamp.AffymetrixCelFile(X[[19L]], ...) > 6: FUN(X[[19L]], ...) > 7: base::lapply(this$files, ...) > 8: lapply.GenericDataFileSet(this, getTimestamp) > 9: lapply(this, getTimestamp) > 10: getTimestamps.AffymetrixCelSet(this) > 11: getTimestamps(this) > 12: isDuplicated.AffymetrixCelSet(cs) > 13: isDuplicated(cs) > 14: extract.GenericDataFileSet(cs, !isDuplicated(cs)) > 15: extract(cs, !isDuplicated(cs)) > > ________________________________________ > Från: aroma-affymetrix@googlegroups.com [aroma-affymetrix@googlegroups.com] > för Henrik Bengtsson [henrik.bengts...@aroma-project.org] > Skickat: den 6 oktober 2011 23:43 > Till: aroma-affymetrix@googlegroups.com > Ämne: Re: [aroma.affymetrix] Problems loading Affymetrix 6.0 CEL files using > AffymetrixCelSet$byName > > Hi. > > On Thu, Oct 6, 2011 at 2:36 PM, Johan Staaf <johan.st...@med.lu.se> wrote: >> Hi Henrik >> I have come across a problem loading Affymetrix 6.0 CEL files using the >> AffymetrixCelSet$byName function as described below on a unix 64-bit >> machine. >> >> Interestingly, the same code has worked before on the same machine with 6.0 >> CEL files, and I can load the actual CEL files successfully on a MacBook Pro >> laptop using the same code. >> >> the rights for the folders the CEL files are in are: >> drwxrwxr-x. 3 johans johans 4096 Oct 6 07:05 GSE19804 >> drwxrwxr-x. 3 johans johans 4096 Oct 6 21:03 GenomeWideSNP_6 >> -rwxr-xr-x. 1 johans johans 69104164 Oct 6 20:47 Lung32T.CEL >> >> >> ? >> >> Thanks! >> >> Best regards >> Johan >> >> Session info: > > Almost, but need to see versions etc of everything (especially R > itself and affxparser), so sessionInfo() please. > > /Henrik > >> >> library(aroma.affymetrix) >> Loading required package: R.filesets >> Loading required package: digest >> R.filesets v1.1.0 (2011-07-24) successfully loaded. See ?R.filesets for >> help. >> Loading required package: aroma.core >> Loading required package: R.cache >> R.cache v0.5.1 (2011-08-31) successfully loaded. See ?R.cache for help. >> >> >> Attaching package: 'R.cache' >> >> The following object(s) are masked from 'package:R.filesets': >> >> getChecksum >> >> Loading required package: R.rsp >> R.rsp v0.6.2 (2011-07-27) successfully loaded. See ?R.rsp for help. >> Type browseRsp() to open the RSP main menu in your browser. >> Loading required package: matrixStats >> matrixStats v0.2.2 (2010-10-06) successfully loaded. See ?matrixStats for >> help. >> Loading required package: aroma.light >> aroma.light v1.20.0 (2011-04-12) successfully loaded. See ?aroma.light for >> help. >> >> aroma.core v2.2.0 (2011-09-01) successfully loaded. See ?aroma.core for >> help. >> >> Attaching package: 'aroma.core' >> >> The following object(s) are masked from 'package:base': >> >> .Machine, append, apply, cat, colMeans, colSums, getOption, lapply, >> library, require, sapply >> >> Loading required package: aroma.apd >> Loading required package: R.huge >> R.huge v0.3.0 (2011-07-23) successfully loaded. See ?R.huge for help. >> Loading required package: affxparser >> aroma.apd v0.2.0 (2011-07-23) successfully loaded. See ?aroma.apd for help. >> aroma.affymetrix v2.2.0 (2011-09-01) successfully loaded. See >> ?aroma.affymetrix for help. >>> library("ACNE"); >> Loading required package: MASS >> ACNE v0.4.2 (2010-09-28) successfully loaded. See ?ACNE for help. >>> >>> ####### Read and check that CDFs etc is ok ##### >>> verbose <- Arguments$getVerbose(-8, timestamp=TRUE) >>> cdf <- AffymetrixCdfFile$byChipType("GenomeWideSNP_6", tags="Full") >>> print(cdf) >> AffymetrixCdfFile: >> Path: annotationData/chipTypes/GenomeWideSNP_6 >> Filename: GenomeWideSNP_6,Full.cdf >> Filesize: 470.44MB >> Chip type: GenomeWideSNP_6,Full >> RAM: 0.00MB >> File format: v4 (binary; XDA) >> Dimension: 2572x2680 >> Number of cells: 6892960 >> Number of units: 1881415 >> Cells per unit: 3.66 >> Number of QC units: 4 >>> gi <- getGenomeInformation(cdf) >>> print(gi) >> UgpGenomeInformation: >> Name: GenomeWideSNP_6 >> Tags: Full,na26,HB20080821 >> Full name: GenomeWideSNP_6,Full,na26,HB20080821 >> Pathname: >> annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,Full,na26,HB20080821.ugp >> File size: 8.97 MB (9407937 bytes) >> RAM: 0.00 MB >> Chip type: GenomeWideSNP_6,Full >>> acs <- AromaCellSequenceFile$byChipType(getChipType(cdf, fullname=FALSE)) >>> print(acs) >> AromaCellSequenceFile: >> Name: GenomeWideSNP_6 >> Tags: HB20080710 >> Full name: GenomeWideSNP_6,HB20080710 >> Pathname: >> annotationData/chipTypes/GenomeWideSNP_6/GenomeWideSNP_6,HB20080710.acs >> File size: 170.92 MB (179217531 bytes) >> RAM: 0.00 MB >> Number of data rows: 6892960 >> File format: v1 >> Dimensions: 6892960x26 >> Column classes: raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, >> raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw, raw >> Number of bytes per column: 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, >> 1, 1, 1, 1, 1, 1, 1, 1, 1, 1 >> Footer: <createdOn>20080710 22:47:02 >> PDT</createdOn><platform>Affymetrix</platform><chipType>GenomeWideSNP_6</chipType><srcFile><filename>GenomeWideSNP_6.probe_tab</filename><filesize>341479928</filesize><checksum>2037c033c09fd8f7c06bd042a77aef15</checksum></srcFile><srcFile2><filename>GenomeWideSNP_6.CN_probe_tab</filename><filesize>96968290</filesize><checksum>3dc2d3178f5eafdbea9c8b6eca88a89c</checksum></srcFile2> >> Chip type: GenomeWideSNP_6 >> Platform: Affymetrix >>> ####### >>> >>> >>> data.set.name<-"GSE19804" >>> print(paste("doing",data.set.name)) >> [1] "doing GSE19804" >>> >>> cdf >> AffymetrixCdfFile: >> Path: annotationData/chipTypes/GenomeWideSNP_6 >> Filename: GenomeWideSNP_6,Full.cdf >> Filesize: 470.44MB >> Chip type: GenomeWideSNP_6,Full >> RAM: 0.00MB >> File format: v4 (binary; XDA) >> Dimension: 2572x2680 >> Number of cells: 6892960 >> Number of units: 1881415 >> Cells per unit: 3.66 >> Number of QC units: 4 >>> cs <- AffymetrixCelSet$byName(data.set.name, cdf=cdf); >>> cs <- extract(cs, !isDuplicated(cs)) >> >> >> *** caught segfault *** >> address 0x7f449b4b3850, cause 'invalid permissions' >> >> Traceback: >> 1: .Call("R_affx_get_cel_file_header", filename, PACKAGE = "affxparser") >> 2: readCelHeader(pathname) >> 3: getHeader.AffymetrixCelFile(this) >> 4: getHeader(this) >> 5: getTimestamp.AffymetrixCelFile(X[[19L]], ...) >> 6: FUN(X[[19L]], ...) >> 7: base::lapply(this$files, ...) >> 8: lapply.GenericDataFileSet(this, getTimestamp) >> 9: lapply(this, getTimestamp) >> 10: getTimestamps.AffymetrixCelSet(this) >> 11: getTimestamps(this) >> 12: isDuplicated.AffymetrixCelSet(cs) >> 13: isDuplicated(cs) >> 14: extract.GenericDataFileSet(cs, !isDuplicated(cs)) >> 15: extract(cs, !isDuplicated(cs)) >> >> -- >> 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/ >> > > -- > 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/ > > -- > 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/ > -- 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/