Oligo package crlmm method
1
0
Entering edit mode
Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 5 months ago
United States
Hi, I am using the crlmm function in Oligo package to make SNP calls. I encountered the following segfault error. Could you please let me know what could be the cause and how to tackle the problem? Thanks so much for your help! Kind regards, Julie library("oligo") library("pd.mapping250k.sty") fullFilenames <- list.celfiles("Sty_CEL_CML", full.names = TRUE) outputDir <- file.path(getwd(), "crlmmResults_StyCML") if (!file.exists(outputDir)) crlmm(fullFilenames, outputDir) *** caught segfault *** address 0x12de80000, cause 'memory not mapped' Traceback: 1: .Call("R_affx_get_cel_file_header", filename, PACKAGE = "affxparser") 2: readCelHeader(x) 3: FUN(c("Sty_CEL_CML/CML-#1-BC-250ksty.CEL", "Sty_CEL_CML/CML-#1-CP-250ksty.CEL", "Sty_CEL_CML/CML-#10-AP- 250ksty.CEL", "Sty_CEL_CML/CML-#10-CP-250ksty.CEL", "Sty_CEL_CML/CML-#11-AP- 250ksty.CEL", "Sty_CEL_CML/CML-#11-CP-250ksty.CEL", "Sty_CEL_CML/CML-#12-AP- 250ksty.CEL", "Sty_CEL_CML/CML-#12-CP-250ksty.CEL", "Sty_CEL_CML/CML-#12-CP2-250ksty.CEL", "Sty_CEL_CML/CML-#13-CP-250ksty.CEL", "Sty_CEL_CML/CML-#13-CP2-250ksty.CEL", "Sty_CEL_CML/CML-#14-BC-250ksty.CEL", "Sty_CEL_CML/CML-#14-Rem- 250ksty.CEL", "Sty_CEL_CML/CML-#15-BC-250ksty.CEL", "Sty_CEL_CML/CML-#15-CP- 250ksty.CEL", "Sty_CEL_CML/CML-#15-CP2-250ksty.CEL", "Sty_CEL_CML/CML-#16-BC- 250ksty.CEL", "Sty_CEL_CML/CML-#16-BC-GL-250ksty.CEL", "Sty_CEL_CML/CML-#16-CP-250ksty.CEL", "Sty_CEL_CML/CML-#16-CP2-250ksty.CEL", "Sty_CEL_CML/CML-#17-AP-250ksty.CEL", "Sty_CEL_CML/CML-#17-CP- 250ksty.CEL", "Sty_CEL_CML/CML-#18-BC-250ksty.CEL", "Sty_CEL_CML/CML-#19-BC- 250ksty.CEL", "Sty_CEL_CML/CML-#19-BC-GL-250ksty.CEL", "Sty_CEL_CML/CML-#19-CP-250ksty.CEL", "Sty_CEL_CML/CML-#2-CP- 250ksty.CEL", "Sty_CEL_CML/CML-#2-CP2-250ksty.CEL", "Sty_CEL_CML/CML-#20-AP- 250ksty.CEL", "Sty_CEL_CML/CML-#20-BC-250ksty.CEL", "Sty_CEL_CML/CML-#20-CP- 250ksty.CEL", "Sty_CEL_CML/CML-#21-CP-250ksty.CEL", "Sty_CEL_CML/CML-#21-CP2-250ksty.CEL", "Sty_CEL_CML/CML-#22-BC-250ksty.CEL", "Sty_CEL_CML/CML-#22-BC-GL-250ksty.CEL", "Sty_CEL_CML/CML-#22-CP-250ksty.CEL", "Sty_CEL_CML/CML-#23-BC- 250ksty.CEL", "Sty_CEL_CML/CML-#23-BC-GL-250ksty.CEL", "Sty_CEL_CML/CML-#23-CP-250ksty.CEL", "Sty_CEL_CML/CML-#3-AP- 250ksty.CEL", "Sty_CEL_CML/CML-#3-BC-250ksty.CEL", "Sty_CEL_CML/CML-#4-BC- 250ksty.CEL", "Sty_CEL_CML/CML-#4-CP-250ksty.CEL", "Sty_CEL_CML/CML-#4-Rem- 250ksty.CEL", "Sty_CEL_CML/CML-#5-BC-250ksty.CEL", "Sty_CEL_CML/CML-#5-BC-GL- 250ksty.CEL", "Sty_CEL_CML/CML-#5-Rem-250ksty.CEL", "Sty_CEL_CML/CML-#6-BC- 250ksty.CEL", "Sty_CEL_CML/CML-#6-BC-GL-250ksty.CEL", "Sty_CEL_CML/CML-#6-CP- 250ksty.CEL", "Sty_CEL_CML/CML-#7-BC-250ksty.CEL", "Sty_CEL_CML/CML-#7-CP- 250ksty.CEL", "Sty_CEL_CML/CML-#8-AP-250ksty.CEL", "Sty_CEL_CML/CML-#8-CP- 250ksty.CEL", "Sty_CEL_CML/CML-#9-BC-250ksty.CEL", "Sty_CEL_CML/CML-#9-BC-GL-250ksty.CEL")[[16L]], ...) 4: lapply(X, FUN, ...) 5: sapply(filenames, function(x) readCelHeader(x)$chiptype) 6: justCRLMMv3(filenames, outdir, batch_size = batch_size, recalibrate = recalibrate, minLLRforCalls = minLLRforCalls, balance = balance, verbose = verbose) 7: crlmm(fullFilenames, outputDir) Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace Selection: sessionInfo() R version 2.11.1 (2010-05-31) x86_64-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] pd.mapping250k.sty_1.0.0 RSQLite_0.9-2 DBI_0.2-5 [4] oligo_1.12.2 oligoClasses_1.10.0 Biobase_2.8.0 loaded via a namespace (and not attached): [1] affxparser_1.20.0 affyio_1.16.0 Biostrings_2.16.9 IRanges_1.6.11 [5] preprocessCore_1.10.0 splines_2.11.1
SNP oligo crlmm SNP oligo crlmm • 902 views
ADD COMMENT •
0
Entering edit mode
@benilton-carvalho-1375
Last seen 4.1 years ago
Brazil/Campinas/UNICAMP
Start a new session of R and try the following: cels = list.files("Sty_CEL_CML", pattern="CEL$", full=TRUE) library(affxparser) table(sapply(cels, function(x) readCelHeader(x)[["chiptype"]])) and let me know what you get. b On 15 September 2010 16:27, Zhu, Julie <julie.zhu at="" umassmed.edu=""> wrote: > Hi, > > I am using the crlmm function in Oligo package to make SNP calls. I > encountered the following segfault error. Could you please let me know what > could be the cause and how to tackle the problem? > > Thanks so much for your help! > > Kind regards, > > Julie > > library("oligo") > library("pd.mapping250k.sty") > fullFilenames <- list.celfiles("Sty_CEL_CML", full.names = TRUE) > outputDir <- file.path(getwd(), "crlmmResults_StyCML") > if (!file.exists(outputDir)) crlmm(fullFilenames, outputDir) > > ?*** caught segfault *** > address 0x12de80000, cause 'memory not mapped' > > Traceback: > ?1: .Call("R_affx_get_cel_file_header", filename, PACKAGE = "affxparser") > ?2: readCelHeader(x) > ?3: FUN(c("Sty_CEL_CML/CML-#1-BC-250ksty.CEL", > "Sty_CEL_CML/CML-#1-CP-250ksty.CEL", "Sty_CEL_CML/CML-#10-AP- 250ksty.CEL", > "Sty_CEL_CML/CML-#10-CP-250ksty.CEL", "Sty_CEL_CML/CML-#11-AP- 250ksty.CEL", > "Sty_CEL_CML/CML-#11-CP-250ksty.CEL", "Sty_CEL_CML/CML-#12-AP- 250ksty.CEL", > "Sty_CEL_CML/CML-#12-CP-250ksty.CEL", "Sty_CEL_CML/CML-#12-CP2-250ksty.CEL", > "Sty_CEL_CML/CML-#13-CP-250ksty.CEL", "Sty_CEL_CML/CML-#13-CP2-250ksty.CEL", > "Sty_CEL_CML/CML-#14-BC-250ksty.CEL", "Sty_CEL_CML/CML-#14-Rem- 250ksty.CEL", > "Sty_CEL_CML/CML-#15-BC-250ksty.CEL", "Sty_CEL_CML/CML-#15-CP- 250ksty.CEL", > "Sty_CEL_CML/CML-#15-CP2-250ksty.CEL", "Sty_CEL_CML/CML-#16-BC- 250ksty.CEL", > "Sty_CEL_CML/CML-#16-BC-GL-250ksty.CEL", > "Sty_CEL_CML/CML-#16-CP-250ksty.CEL", "Sty_CEL_CML/CML-#16-CP2-250ksty.CEL", > "Sty_CEL_CML/CML-#17-AP-250ksty.CEL", "Sty_CEL_CML/CML-#17-CP- 250ksty.CEL", > "Sty_CEL_CML/CML-#18-BC-250ksty.CEL", "Sty_CEL_CML/CML-#19-BC- 250ksty.CEL", > "Sty_CEL_CML/CML-#19-BC-GL-250ksty.CEL", > "Sty_CEL_CML/CML-#19-CP-250ksty.CEL", "Sty_CEL_CML/CML-#2-CP- 250ksty.CEL", > "Sty_CEL_CML/CML-#2-CP2-250ksty.CEL", "Sty_CEL_CML/CML-#20-AP- 250ksty.CEL", > "Sty_CEL_CML/CML-#20-BC-250ksty.CEL", "Sty_CEL_CML/CML-#20-CP- 250ksty.CEL", > "Sty_CEL_CML/CML-#21-CP-250ksty.CEL", "Sty_CEL_CML/CML-#21-CP2-250ksty.CEL", > "Sty_CEL_CML/CML-#22-BC-250ksty.CEL", > "Sty_CEL_CML/CML-#22-BC-GL-250ksty.CEL", > "Sty_CEL_CML/CML-#22-CP-250ksty.CEL", "Sty_CEL_CML/CML-#23-BC- 250ksty.CEL", > "Sty_CEL_CML/CML-#23-BC-GL-250ksty.CEL", > "Sty_CEL_CML/CML-#23-CP-250ksty.CEL", "Sty_CEL_CML/CML-#3-AP- 250ksty.CEL", > "Sty_CEL_CML/CML-#3-BC-250ksty.CEL", "Sty_CEL_CML/CML-#4-BC- 250ksty.CEL", > "Sty_CEL_CML/CML-#4-CP-250ksty.CEL", "Sty_CEL_CML/CML-#4-Rem- 250ksty.CEL", > "Sty_CEL_CML/CML-#5-BC-250ksty.CEL", "Sty_CEL_CML/CML-#5-BC-GL- 250ksty.CEL", > "Sty_CEL_CML/CML-#5-Rem-250ksty.CEL", "Sty_CEL_CML/CML-#6-BC- 250ksty.CEL", > "Sty_CEL_CML/CML-#6-BC-GL-250ksty.CEL", "Sty_CEL_CML/CML-#6-CP- 250ksty.CEL", > "Sty_CEL_CML/CML-#7-BC-250ksty.CEL", "Sty_CEL_CML/CML-#7-CP- 250ksty.CEL", > "Sty_CEL_CML/CML-#8-AP-250ksty.CEL", "Sty_CEL_CML/CML-#8-CP- 250ksty.CEL", > "Sty_CEL_CML/CML-#9-BC-250ksty.CEL", > "Sty_CEL_CML/CML-#9-BC-GL-250ksty.CEL")[[16L]], ...) > ?4: lapply(X, FUN, ...) > ?5: sapply(filenames, function(x) readCelHeader(x)$chiptype) > ?6: justCRLMMv3(filenames, outdir, batch_size = batch_size, recalibrate = > recalibrate, ? ? minLLRforCalls = minLLRforCalls, balance = balance, verbose > = verbose) > ?7: crlmm(fullFilenames, outputDir) > > 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: > > sessionInfo() > R version 2.11.1 (2010-05-31) > x86_64-apple-darwin9.8.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 > > attached base packages: > [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base > > other attached packages: > [1] pd.mapping250k.sty_1.0.0 RSQLite_0.9-2 ? ? ? ? ? ?DBI_0.2-5 > [4] oligo_1.12.2 ? ? ? ? ? ? oligoClasses_1.10.0 ? ? ?Biobase_2.8.0 > > loaded via a namespace (and not attached): > [1] affxparser_1.20.0 ? ? affyio_1.16.0 ? ? ? ? Biostrings_2.16.9 > IRanges_1.6.11 > [5] preprocessCore_1.10.0 splines_2.11.1 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD COMMENT •
0
Entering edit mode
Benilton, Thank you so much for such a quick response! I tried the following code and got the following error. Best regards, Julie table(sapply(cels, function(x) readCelHeader(x)[["chiptype"]])) *** caught segfault *** address 0x1abb9000, cause 'memory not mapped' Traceback: 1: .Call("R_affx_get_cel_file_header", filename, PACKAGE = "affxparser") 2: readCelHeader(x) 3: FUN(c("Sty_CEL_CML/CML-#1-BC-250ksty.CEL", "Sty_CEL_CML/CML-#1-CP-250ksty.CEL", "Sty_CEL_CML/CML-#10-AP- 250ksty.CEL", "Sty_CEL_CML/CML-#10-CP-250ksty.CEL", "Sty_CEL_CML/CML-#11-AP- 250ksty.CEL", "Sty_CEL_CML/CML-#11-CP-250ksty.CEL", "Sty_CEL_CML/CML-#12-AP- 250ksty.CEL", "Sty_CEL_CML/CML-#12-CP-250ksty.CEL", "Sty_CEL_CML/CML-#12-CP2-250ksty.CEL", "Sty_CEL_CML/CML-#13-CP-250ksty.CEL", "Sty_CEL_CML/CML-#13-CP2-250ksty.CEL", "Sty_CEL_CML/CML-#14-BC-250ksty.CEL", "Sty_CEL_CML/CML-#14-Rem- 250ksty.CEL", "Sty_CEL_CML/CML-#15-BC-250ksty.CEL", "Sty_CEL_CML/CML-#15-CP- 250ksty.CEL", "Sty_CEL_CML/CML-#15-CP2-250ksty.CEL", "Sty_CEL_CML/CML-#16-BC- 250ksty.CEL", "Sty_CEL_CML/CML-#16-BC-GL-250ksty.CEL", "Sty_CEL_CML/CML-#16-CP-250ksty.CEL", "Sty_CEL_CML/CML-#16-CP2-250ksty.CEL", "Sty_CEL_CML/CML-#17-AP-250ksty.CEL", "Sty_CEL_CML/CML-#17-CP- 250ksty.CEL", "Sty_CEL_CML/CML-#18-BC-250ksty.CEL", "Sty_CEL_CML/CML-#19-BC- 250ksty.CEL", "Sty_CEL_CML/CML-#19-BC-GL-250ksty.CEL", "Sty_CEL_CML/CML-#19-CP-250ksty.CEL", "Sty_CEL_CML/CML-#2-CP- 250ksty.CEL", "Sty_CEL_CML/CML-#2-CP2-250ksty.CEL", "Sty_CEL_CML/CML-#20-AP- 250ksty.CEL", "Sty_CEL_CML/CML-#20-BC-250ksty.CEL", "Sty_CEL_CML/CML-#20-CP- 250ksty.CEL", "Sty_CEL_CML/CML-#21-CP-250ksty.CEL", "Sty_CEL_CML/CML-#21-CP2-250ksty.CEL", "Sty_CEL_CML/CML-#22-BC-250ksty.CEL", "Sty_CEL_CML/CML-#22-BC-GL-250ksty.CEL", "Sty_CEL_CML/CML-#22-CP-250ksty.CEL", "Sty_CEL_CML/CML-#23-BC- 250ksty.CEL", "Sty_CEL_CML/CML-#23-BC-GL-250ksty.CEL", "Sty_CEL_CML/CML-#23-CP-250ksty.CEL", "Sty_CEL_CML/CML-#3-AP- 250ksty.CEL", "Sty_CEL_CML/CML-#3-BC-250ksty.CEL", "Sty_CEL_CML/CML-#4-BC- 250ksty.CEL", "Sty_CEL_CML/CML-#4-CP-250ksty.CEL", "Sty_CEL_CML/CML-#4-Rem- 250ksty.CEL", "Sty_CEL_CML/CML-#5-BC-250ksty.CEL", "Sty_CEL_CML/CML-#5-BC-GL- 250ksty.CEL", "Sty_CEL_CML/CML-#5-Rem-250ksty.CEL", "Sty_CEL_CML/CML-#6-BC- 250ksty.CEL", "Sty_CEL_CML/CML-#6-BC-GL-250ksty.CEL", "Sty_CEL_CML/CML-#6-CP- 250ksty.CEL", "Sty_CEL_CML/CML-#7-BC-250ksty.CEL", "Sty_CEL_CML/CML-#7-CP- 250ksty.CEL", "Sty_CEL_CML/CML-#8-AP-250ksty.CEL", "Sty_CEL_CML/CML-#8-CP- 250ksty.CEL", "Sty_CEL_CML/CML-#9-BC-250ksty.CEL", "Sty_CEL_CML/CML-#9-BC-GL-250ksty.CEL")[[12L]], ...) 4: lapply(X, FUN, ...) 5: sapply(cels, function(x) readCelHeader(x)[["chiptype"]]) 6: table(sapply(cels, function(x) readCelHeader(x)[["chiptype"]])) 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: On 9/15/10 11:43 AM, "Benilton Carvalho" <beniltoncarvalho at="" gmail.com=""> wrote: > Start a new session of R and try the following: > > cels = list.files("Sty_CEL_CML", pattern="CEL$", full=TRUE) > library(affxparser) > table(sapply(cels, function(x) readCelHeader(x)[["chiptype"]])) > > and let me know what you get. > > b > > On 15 September 2010 16:27, Zhu, Julie <julie.zhu at="" umassmed.edu=""> wrote: >> Hi, >> >> I am using the crlmm function in Oligo package to make SNP calls. I >> encountered the following segfault error. Could you please let me know what >> could be the cause and how to tackle the problem? >> >> Thanks so much for your help! >> >> Kind regards, >> >> Julie >> >> library("oligo") >> library("pd.mapping250k.sty") >> fullFilenames <- list.celfiles("Sty_CEL_CML", full.names = TRUE) >> outputDir <- file.path(getwd(), "crlmmResults_StyCML") >> if (!file.exists(outputDir)) crlmm(fullFilenames, outputDir) >> >> ?*** caught segfault *** >> address 0x12de80000, cause 'memory not mapped' >> >> Traceback: >> ?1: .Call("R_affx_get_cel_file_header", filename, PACKAGE = "affxparser") >> ?2: readCelHeader(x) >> ?3: FUN(c("Sty_CEL_CML/CML-#1-BC-250ksty.CEL", >> "Sty_CEL_CML/CML-#1-CP-250ksty.CEL", "Sty_CEL_CML/CML-#10-AP- 250ksty.CEL", >> "Sty_CEL_CML/CML-#10-CP-250ksty.CEL", "Sty_CEL_CML/CML-#11-AP- 250ksty.CEL", >> "Sty_CEL_CML/CML-#11-CP-250ksty.CEL", "Sty_CEL_CML/CML-#12-AP- 250ksty.CEL", >> "Sty_CEL_CML/CML-#12-CP-250ksty.CEL", "Sty_CEL_CML/CML-#12-CP2-250ksty.CEL", >> "Sty_CEL_CML/CML-#13-CP-250ksty.CEL", "Sty_CEL_CML/CML-#13-CP2-250ksty.CEL", >> "Sty_CEL_CML/CML-#14-BC-250ksty.CEL", "Sty_CEL_CML/CML-#14-Rem- 250ksty.CEL", >> "Sty_CEL_CML/CML-#15-BC-250ksty.CEL", "Sty_CEL_CML/CML-#15-CP- 250ksty.CEL", >> "Sty_CEL_CML/CML-#15-CP2-250ksty.CEL", "Sty_CEL_CML/CML-#16-BC- 250ksty.CEL", >> "Sty_CEL_CML/CML-#16-BC-GL-250ksty.CEL", >> "Sty_CEL_CML/CML-#16-CP-250ksty.CEL", "Sty_CEL_CML/CML-#16-CP2-250ksty.CEL", >> "Sty_CEL_CML/CML-#17-AP-250ksty.CEL", "Sty_CEL_CML/CML-#17-CP- 250ksty.CEL", >> "Sty_CEL_CML/CML-#18-BC-250ksty.CEL", "Sty_CEL_CML/CML-#19-BC- 250ksty.CEL", >> "Sty_CEL_CML/CML-#19-BC-GL-250ksty.CEL", >> "Sty_CEL_CML/CML-#19-CP-250ksty.CEL", "Sty_CEL_CML/CML-#2-CP- 250ksty.CEL", >> "Sty_CEL_CML/CML-#2-CP2-250ksty.CEL", "Sty_CEL_CML/CML-#20-AP- 250ksty.CEL", >> "Sty_CEL_CML/CML-#20-BC-250ksty.CEL", "Sty_CEL_CML/CML-#20-CP- 250ksty.CEL", >> "Sty_CEL_CML/CML-#21-CP-250ksty.CEL", "Sty_CEL_CML/CML-#21-CP2-250ksty.CEL", >> "Sty_CEL_CML/CML-#22-BC-250ksty.CEL", >> "Sty_CEL_CML/CML-#22-BC-GL-250ksty.CEL", >> "Sty_CEL_CML/CML-#22-CP-250ksty.CEL", "Sty_CEL_CML/CML-#23-BC- 250ksty.CEL", >> "Sty_CEL_CML/CML-#23-BC-GL-250ksty.CEL", >> "Sty_CEL_CML/CML-#23-CP-250ksty.CEL", "Sty_CEL_CML/CML-#3-AP- 250ksty.CEL", >> "Sty_CEL_CML/CML-#3-BC-250ksty.CEL", "Sty_CEL_CML/CML-#4-BC- 250ksty.CEL", >> "Sty_CEL_CML/CML-#4-CP-250ksty.CEL", "Sty_CEL_CML/CML-#4-Rem- 250ksty.CEL", >> "Sty_CEL_CML/CML-#5-BC-250ksty.CEL", "Sty_CEL_CML/CML-#5-BC-GL- 250ksty.CEL", >> "Sty_CEL_CML/CML-#5-Rem-250ksty.CEL", "Sty_CEL_CML/CML-#6-BC- 250ksty.CEL", >> "Sty_CEL_CML/CML-#6-BC-GL-250ksty.CEL", "Sty_CEL_CML/CML-#6-CP- 250ksty.CEL", >> "Sty_CEL_CML/CML-#7-BC-250ksty.CEL", "Sty_CEL_CML/CML-#7-CP- 250ksty.CEL", >> "Sty_CEL_CML/CML-#8-AP-250ksty.CEL", "Sty_CEL_CML/CML-#8-CP- 250ksty.CEL", >> "Sty_CEL_CML/CML-#9-BC-250ksty.CEL", >> "Sty_CEL_CML/CML-#9-BC-GL-250ksty.CEL")[[16L]], ...) >> ?4: lapply(X, FUN, ...) >> ?5: sapply(filenames, function(x) readCelHeader(x)$chiptype) >> ?6: justCRLMMv3(filenames, outdir, batch_size = batch_size, recalibrate = >> recalibrate, ? ? minLLRforCalls = minLLRforCalls, balance = balance, verbose >> = verbose) >> ?7: crlmm(fullFilenames, outputDir) >> >> 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: >> >> sessionInfo() >> R version 2.11.1 (2010-05-31) >> x86_64-apple-darwin9.8.0 >> >> locale: >> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >> >> attached base packages: >> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >> >> other attached packages: >> [1] pd.mapping250k.sty_1.0.0 RSQLite_0.9-2 ? ? ? ? ? ?DBI_0.2-5 >> [4] oligo_1.12.2 ? ? ? ? ? ? oligoClasses_1.10.0 ? ? ?Biobase_2.8.0 >> >> loaded via a namespace (and not attached): >> [1] affxparser_1.20.0 ? ? affyio_1.16.0 ? ? ? ? Biostrings_2.16.9 >> IRanges_1.6.11 >> [5] preprocessCore_1.10.0 splines_2.11.1 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> >
ADD REPLY •
0
Entering edit mode
Benilton, Thanks for the debugging code! It helped me to get down to two files with unreadable header. Best regards, Julie On 9/15/10 11:55 AM, "Julie Zhu" <julie.zhu at="" umassmed.edu=""> wrote: > Benilton, > > Thank you so much for such a quick response! > > I tried the following code and got the following error. > > Best regards, > > Julie > > > table(sapply(cels, function(x) readCelHeader(x)[["chiptype"]])) > > *** caught segfault *** > address 0x1abb9000, cause 'memory not mapped' > > Traceback: > 1: .Call("R_affx_get_cel_file_header", filename, PACKAGE = "affxparser") > 2: readCelHeader(x) > 3: FUN(c("Sty_CEL_CML/CML-#1-BC-250ksty.CEL", > "Sty_CEL_CML/CML-#1-CP-250ksty.CEL", "Sty_CEL_CML/CML-#10-AP- 250ksty.CEL", > "Sty_CEL_CML/CML-#10-CP-250ksty.CEL", "Sty_CEL_CML/CML-#11-AP- 250ksty.CEL", > "Sty_CEL_CML/CML-#11-CP-250ksty.CEL", "Sty_CEL_CML/CML-#12-AP- 250ksty.CEL", > "Sty_CEL_CML/CML-#12-CP-250ksty.CEL", "Sty_CEL_CML/CML-#12-CP2-250ksty.CEL", > "Sty_CEL_CML/CML-#13-CP-250ksty.CEL", "Sty_CEL_CML/CML-#13-CP2-250ksty.CEL", > "Sty_CEL_CML/CML-#14-BC-250ksty.CEL", "Sty_CEL_CML/CML-#14-Rem- 250ksty.CEL", > "Sty_CEL_CML/CML-#15-BC-250ksty.CEL", "Sty_CEL_CML/CML-#15-CP- 250ksty.CEL", > "Sty_CEL_CML/CML-#15-CP2-250ksty.CEL", "Sty_CEL_CML/CML-#16-BC- 250ksty.CEL", > "Sty_CEL_CML/CML-#16-BC-GL-250ksty.CEL", > "Sty_CEL_CML/CML-#16-CP-250ksty.CEL", "Sty_CEL_CML/CML-#16-CP2-250ksty.CEL", > "Sty_CEL_CML/CML-#17-AP-250ksty.CEL", "Sty_CEL_CML/CML-#17-CP- 250ksty.CEL", > "Sty_CEL_CML/CML-#18-BC-250ksty.CEL", "Sty_CEL_CML/CML-#19-BC- 250ksty.CEL", > "Sty_CEL_CML/CML-#19-BC-GL-250ksty.CEL", > "Sty_CEL_CML/CML-#19-CP-250ksty.CEL", "Sty_CEL_CML/CML-#2-CP- 250ksty.CEL", > "Sty_CEL_CML/CML-#2-CP2-250ksty.CEL", "Sty_CEL_CML/CML-#20-AP- 250ksty.CEL", > "Sty_CEL_CML/CML-#20-BC-250ksty.CEL", "Sty_CEL_CML/CML-#20-CP- 250ksty.CEL", > "Sty_CEL_CML/CML-#21-CP-250ksty.CEL", "Sty_CEL_CML/CML-#21-CP2-250ksty.CEL", > "Sty_CEL_CML/CML-#22-BC-250ksty.CEL", > "Sty_CEL_CML/CML-#22-BC-GL-250ksty.CEL", > "Sty_CEL_CML/CML-#22-CP-250ksty.CEL", "Sty_CEL_CML/CML-#23-BC- 250ksty.CEL", > "Sty_CEL_CML/CML-#23-BC-GL-250ksty.CEL", > "Sty_CEL_CML/CML-#23-CP-250ksty.CEL", "Sty_CEL_CML/CML-#3-AP- 250ksty.CEL", > "Sty_CEL_CML/CML-#3-BC-250ksty.CEL", "Sty_CEL_CML/CML-#4-BC- 250ksty.CEL", > "Sty_CEL_CML/CML-#4-CP-250ksty.CEL", "Sty_CEL_CML/CML-#4-Rem- 250ksty.CEL", > "Sty_CEL_CML/CML-#5-BC-250ksty.CEL", "Sty_CEL_CML/CML-#5-BC-GL- 250ksty.CEL", > "Sty_CEL_CML/CML-#5-Rem-250ksty.CEL", "Sty_CEL_CML/CML-#6-BC- 250ksty.CEL", > "Sty_CEL_CML/CML-#6-BC-GL-250ksty.CEL", "Sty_CEL_CML/CML-#6-CP- 250ksty.CEL", > "Sty_CEL_CML/CML-#7-BC-250ksty.CEL", "Sty_CEL_CML/CML-#7-CP- 250ksty.CEL", > "Sty_CEL_CML/CML-#8-AP-250ksty.CEL", "Sty_CEL_CML/CML-#8-CP- 250ksty.CEL", > "Sty_CEL_CML/CML-#9-BC-250ksty.CEL", > "Sty_CEL_CML/CML-#9-BC-GL-250ksty.CEL")[[12L]], ...) > 4: lapply(X, FUN, ...) > 5: sapply(cels, function(x) readCelHeader(x)[["chiptype"]]) > 6: table(sapply(cels, function(x) readCelHeader(x)[["chiptype"]])) > > 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: > > > On 9/15/10 11:43 AM, "Benilton Carvalho" <beniltoncarvalho at="" gmail.com=""> wrote: > >> Start a new session of R and try the following: >> >> cels = list.files("Sty_CEL_CML", pattern="CEL$", full=TRUE) >> library(affxparser) >> table(sapply(cels, function(x) readCelHeader(x)[["chiptype"]])) >> >> and let me know what you get. >> >> b >> >> On 15 September 2010 16:27, Zhu, Julie <julie.zhu at="" umassmed.edu=""> wrote: >>> Hi, >>> >>> I am using the crlmm function in Oligo package to make SNP calls. I >>> encountered the following segfault error. Could you please let me know what >>> could be the cause and how to tackle the problem? >>> >>> Thanks so much for your help! >>> >>> Kind regards, >>> >>> Julie >>> >>> library("oligo") >>> library("pd.mapping250k.sty") >>> fullFilenames <- list.celfiles("Sty_CEL_CML", full.names = TRUE) >>> outputDir <- file.path(getwd(), "crlmmResults_StyCML") >>> if (!file.exists(outputDir)) crlmm(fullFilenames, outputDir) >>> >>> ?*** caught segfault *** >>> address 0x12de80000, cause 'memory not mapped' >>> >>> Traceback: >>> ?1: .Call("R_affx_get_cel_file_header", filename, PACKAGE = "affxparser") >>> ?2: readCelHeader(x) >>> ?3: FUN(c("Sty_CEL_CML/CML-#1-BC-250ksty.CEL", >>> "Sty_CEL_CML/CML-#1-CP-250ksty.CEL", "Sty_CEL_CML/CML-#10-AP- 250ksty.CEL", >>> "Sty_CEL_CML/CML-#10-CP-250ksty.CEL", "Sty_CEL_CML/CML-#11-AP- 250ksty.CEL", >>> "Sty_CEL_CML/CML-#11-CP-250ksty.CEL", "Sty_CEL_CML/CML-#12-AP- 250ksty.CEL", >>> "Sty_CEL_CML/CML-#12-CP-250ksty.CEL", "Sty_CEL_CML/CML-#12-CP2-250ksty.CEL", >>> "Sty_CEL_CML/CML-#13-CP-250ksty.CEL", "Sty_CEL_CML/CML-#13-CP2-250ksty.CEL", >>> "Sty_CEL_CML/CML-#14-BC-250ksty.CEL", "Sty_CEL_CML/CML-#14-Rem- 250ksty.CEL", >>> "Sty_CEL_CML/CML-#15-BC-250ksty.CEL", "Sty_CEL_CML/CML-#15-CP- 250ksty.CEL", >>> "Sty_CEL_CML/CML-#15-CP2-250ksty.CEL", "Sty_CEL_CML/CML-#16-BC- 250ksty.CEL", >>> "Sty_CEL_CML/CML-#16-BC-GL-250ksty.CEL", >>> "Sty_CEL_CML/CML-#16-CP-250ksty.CEL", "Sty_CEL_CML/CML-#16-CP2-250ksty.CEL", >>> "Sty_CEL_CML/CML-#17-AP-250ksty.CEL", "Sty_CEL_CML/CML-#17-CP- 250ksty.CEL", >>> "Sty_CEL_CML/CML-#18-BC-250ksty.CEL", "Sty_CEL_CML/CML-#19-BC- 250ksty.CEL", >>> "Sty_CEL_CML/CML-#19-BC-GL-250ksty.CEL", >>> "Sty_CEL_CML/CML-#19-CP-250ksty.CEL", "Sty_CEL_CML/CML-#2-CP- 250ksty.CEL", >>> "Sty_CEL_CML/CML-#2-CP2-250ksty.CEL", "Sty_CEL_CML/CML-#20-AP- 250ksty.CEL", >>> "Sty_CEL_CML/CML-#20-BC-250ksty.CEL", "Sty_CEL_CML/CML-#20-CP- 250ksty.CEL", >>> "Sty_CEL_CML/CML-#21-CP-250ksty.CEL", "Sty_CEL_CML/CML-#21-CP2-250ksty.CEL", >>> "Sty_CEL_CML/CML-#22-BC-250ksty.CEL", >>> "Sty_CEL_CML/CML-#22-BC-GL-250ksty.CEL", >>> "Sty_CEL_CML/CML-#22-CP-250ksty.CEL", "Sty_CEL_CML/CML-#23-BC- 250ksty.CEL", >>> "Sty_CEL_CML/CML-#23-BC-GL-250ksty.CEL", >>> "Sty_CEL_CML/CML-#23-CP-250ksty.CEL", "Sty_CEL_CML/CML-#3-AP- 250ksty.CEL", >>> "Sty_CEL_CML/CML-#3-BC-250ksty.CEL", "Sty_CEL_CML/CML-#4-BC- 250ksty.CEL", >>> "Sty_CEL_CML/CML-#4-CP-250ksty.CEL", "Sty_CEL_CML/CML-#4-Rem- 250ksty.CEL", >>> "Sty_CEL_CML/CML-#5-BC-250ksty.CEL", "Sty_CEL_CML/CML-#5-BC-GL- 250ksty.CEL", >>> "Sty_CEL_CML/CML-#5-Rem-250ksty.CEL", "Sty_CEL_CML/CML-#6-BC- 250ksty.CEL", >>> "Sty_CEL_CML/CML-#6-BC-GL-250ksty.CEL", "Sty_CEL_CML/CML-#6-CP- 250ksty.CEL", >>> "Sty_CEL_CML/CML-#7-BC-250ksty.CEL", "Sty_CEL_CML/CML-#7-CP- 250ksty.CEL", >>> "Sty_CEL_CML/CML-#8-AP-250ksty.CEL", "Sty_CEL_CML/CML-#8-CP- 250ksty.CEL", >>> "Sty_CEL_CML/CML-#9-BC-250ksty.CEL", >>> "Sty_CEL_CML/CML-#9-BC-GL-250ksty.CEL")[[16L]], ...) >>> ?4: lapply(X, FUN, ...) >>> ?5: sapply(filenames, function(x) readCelHeader(x)$chiptype) >>> ?6: justCRLMMv3(filenames, outdir, batch_size = batch_size, recalibrate = >>> recalibrate, ? ? minLLRforCalls = minLLRforCalls, balance = balance, verbose >>> = verbose) >>> ?7: crlmm(fullFilenames, outputDir) >>> >>> 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: >>> >>> sessionInfo() >>> R version 2.11.1 (2010-05-31) >>> x86_64-apple-darwin9.8.0 >>> >>> locale: >>> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 >>> >>> attached base packages: >>> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >>> >>> other attached packages: >>> [1] pd.mapping250k.sty_1.0.0 RSQLite_0.9-2 ? ? ? ? ? ?DBI_0.2-5 >>> [4] oligo_1.12.2 ? ? ? ? ? ? oligoClasses_1.10.0 ? ? ?Biobase_2.8.0 >>> >>> loaded via a namespace (and not attached): >>> [1] affxparser_1.20.0 ? ? affyio_1.16.0 ? ? ? ? Biostrings_2.16.9 >>> IRanges_1.6.11 >>> [5] preprocessCore_1.10.0 splines_2.11.1 >>> >>> _______________________________________________ >>> Bioconductor mailing list >>> Bioconductor at stat.math.ethz.ch >>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>> Search the archives: >>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>> >> > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >
ADD REPLY •

Login before adding your answer.

Similar Posts
Loading Similar Posts
Traffic: 831 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6