Question: ReadAffy crashes on mac
0
gravatar for Nathan S. Watson-Haigh
11.3 years ago by
Nathan S. Watson-Haigh40 wrote:
I'm having a similar (i.e. a segfault when trying to read CEL files) problem reading v4 CEL files on a 64bit machine. Using any of the following methods results in a segfault (bottom): ReadAffy() read.celfile() read.celfile.header() read.celfile() The following methods seem to work ok: readCelHeader() readCel() Albeit readCelHeader() gives the following at the start of the output: -- start output -- R(5152): unaligned access to 0x200000000211c6ef, ip=0x200000000179c241 R(5152): unaligned access to 0x200000000211c6f7, ip=0x200000000179c241 R(5152): unaligned access to 0x200000000211c6ff, ip=0x200000000179c241 R(5152): unaligned access to 0x200000000211c707, ip=0x200000000179c241 R(5152): unaligned access to 0x200000000211c70f, ip=0x200000000179c241 $filename [1] "CEL/NA_7126_FG1.CEL" $version [1] 4 $cols [1] 732 $rows [1] 732 -- end output -- It should be noted that I transferred all these files from my windows machine to the linux machine via ftp. I transferred them back (in case they got corrupted) using the same method and the same commands on my windows machine did not have a problem. -- start segfault -- *** caught segfault *** address 0xa67fb0, cause 'memory not mapped' Traceback: 1: .Call("R_read_cel_file", filename, intensity.means.only, PACKAGE = "affyio") 2: read.celfile("CEL/NA_7126_FG1.CEL") Possible actions: 1: abort (with core dump, if enabled) 2: normal R exit 3: exit R without saving workspace 4: exit R saving workspace -- end segfault -- -- start sessionInfo() -- > sessionInfo() R version 2.7.1 (2008-06-23) ia64-unknown-linux-gnu locale: LC_CTYPE=en_AU;LC_NUMERIC=C;LC_TIME=en_AU;LC_COLLATE=en_AU;LC_MONETARY =C;LC_ MESSAGES=en_AU;LC_PAPER=en_AU;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC _MEASU REMENT=en_AU;LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] affxparser_1.12.2 -- end sessionInfo() -- -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Henrik Bengtsson Sent: Sunday, 20 July 2008 11:28 AM To: luo_weijun at yahoo.com Cc: Bioconductor at stat.math.ethz.ch Subject: Re: [BioC] ReadAffy crashes on mac Hi, The version 1 CEL file format is actually the most recent one from Affymetrix - it is a binary format known as the Calvin file format or the Command Console (CC) format. The old ASCII format is reported as version 3 and the binary (XDA) format is reported as version 4. ReadAffy of 'affy' utilized the 'affyio' package to read CEL files. I think that affyio supports the CC (v1) file format as well, but I can't bet on it. So for further troubleshooting I would recommend that start a fresh R session and only load 'affyio' and try its function to read the CEL files. Try with read.celfile.header(), read.celfile() and read.celfile.probeintensity.matrices() and see if they crash as well. That will help Ben Bolstad to troubleshoot affyio. If worse comes to worse, you can indeed convert the CEL files to v4 (binary; XDA) and the load it in. But, ideally you shouldn't have to convert files. Also, you should avoid working ASCII files - that's old school slow and memory consuming. My $1.02 /Henrik On Sat, Jul 19, 2008 at 5:43 PM, Luo Weijun <luo_weijun at="" yahoo.com=""> wrote: > Thanks a lot, Henrik, > I tried affxparser. Both readCelHeader() and readCel() worked well on either single or multiple CEL files. These binary CEL files. I think they should be version 4, but the readCelHeader read as version 1 (see the results). > I am wondering is there any way to create an AffyBatch object from the readCel() result object? I need to use special preprocessing method which takes AffyBatch as input. Or I may convert these CEL files to version 3 CEL format, where ReadAffy works fine. convertCel only writes version 4. > Weijun > > #header information >> header <- readCelHeader(celFile) >> header > $filename > [1] "~/bmpEarly/a1hr_6314.CEL" > > $version > [1] 1 > > $cols > [1] 1164 > > $rows > [1] 1164 > > $total > [1] 1354896 > > $algorithm > [1] "Feature Extraction Cell Generation" > . > > > > --- On Sat, 7/19/08, Henrik Bengtsson <hb at="" stat.berkeley.edu=""> wrote: > >> From: Henrik Bengtsson <hb at="" stat.berkeley.edu=""> >> Subject: Re: [BioC] ReadAffy crashes on mac >> To: luo_weijun at yahoo.com >> Cc: Bioconductor at stat.math.ethz.ch >> Date: Saturday, July 19, 2008, 5:53 PM >> Hints for more troubleshooting: >> >> * Your example use two CEL files. Can you reproduce the >> error for a >> single CEL file? >> * What chip type? >> * Are these ASCII or binary CEL files? >> * Try to use affxparser to read the buggy CEL file, e.g. >> readCelHeader(), readCel() etc. Does that also give an >> error? >> >> Basically, can it be because the CEL file is corrupt? It >> should core >> dump, but it is a start. >> >> My $0.02 >> >> /Henrik >> >> >> On Sat, Jul 19, 2008 at 11:56 AM, Luo Weijun >> <luo_weijun at="" yahoo.com=""> wrote: >> > Dear all, >> > I use BioConductor affy package on a Mac OS X 10.4 >> machine, ReadAffy crashes R. The same problem has been >> reported earlier by another user (see >> http://thread.gmane.org/gmane.science.biology.informatics.conductor/16 747), >> but no solution has been suggested yet. >> > Here I show you the error message, session and debug >> information for R 2.7.1, but the same problem has been >> observed under R 2.6.0 (both 32 bit and 64 bit versions). >> > Please let me know if you have any >> ideas/comments/suggestions. Thanks a lot! >> > Weijun >> > >> > >> > >> > ##error message >> >> library(affy) >> > ... >> >> fns <- >> list.celfiles(path='/bmpEarly',full.names=TRUE) >> >> hmscBmp<- ReadAffy(filenames=fns[1:2]) >> > >> > *** caught bus error *** >> > address 0x2008000, cause 'invalid alignment' >> > >> > *** caught segfault *** >> > address 0x40568008, cause 'memory not mapped' >> > >> > ##session >> >> sessionInfo() >> > R version 2.7.1 (2008-06-23) >> > powerpc-apple-darwin8.10.1 >> > >> > locale: >> > C >> > >> > attached base packages: >> > [1] tools stats graphics grDevices utils >> datasets methods >> > [8] base >> > >> > other attached packages: >> > [1] affy_1.18.2 preprocessCore_1.2.0 >> affyio_1.8.0 >> > [4] Biobase_2.0.1 >> > >> > >> > ##debug information >> > luow$ r -d gdb --vanilla >> > GNU gdb 6.1-20040303 (Apple version gdb-437) (Sun Dec >> 25 08:31:29 GMT 2005) >> > Copyright 2004 Free Software Foundation, Inc. >> > GDB is free software, covered by the GNU General >> Public License, and you are >> > welcome to change it and/or distribute copies of it >> under certain conditions. >> > Type "show copying" to see the conditions. >> > There is absolutely no warranty for GDB. Type >> "show warranty" for details. >> > This GDB was configured as >> "powerpc-apple-darwin"...unable to read unknown >> load command 0x1b >> > unable to read unknown load command 0x1b >> > unable to read unknown load command 0x1b >> > unable to read unknown load command 0x1b >> > bfd_mach_o_scan: unknown architecture 0x1000007/0x3 >> > Reading symbols for shared libraries ..... done >> > unable to read unknown load command 0x1b >> > >> > (gdb) run >> > Starting program: >> /Library/Frameworks/R.framework/Versions/2.7/Resources/bin/exec/ppc/R >> --vanilla >> > bfd_mach_o_scan: unknown architecture 0x1000007/0x3 >> > Reading symbols for shared libraries >> .......+...........+ done >> > unable to read unknown load command 0x1b >> > Reading symbols for shared libraries . done >> > >> > R version 2.7.1 (2008-06-23) >> > Copyright (C) 2008 The R Foundation for Statistical >> Computing >> > ISBN 3-900051-07-0 >> > >> > Reading symbols for shared libraries . done >> > R is free software and comes with ABSOLUTELY NO >> WARRANTY. >> > You are welcome to redistribute it under certain >> conditions. >> > Type 'license()' or 'licence()' for >> distribution details. >> > >> > Natural language support but running in an English >> locale >> > >> > R is a collaborative project with many contributors. >> > Type 'contributors()' for more information and >> > 'citation()' on how to cite R or R packages in >> publications. >> > >> > Type 'demo()' for some demos, 'help()' >> for on-line help, or >> > 'help.start()' for an HTML browser interface >> to help. >> > Type 'q()' to quit R. >> > >> > unable to read unknown load command 0x1b >> > Reading symbols for shared libraries >> ........................................................ >> done >> > unable to read unknown load command 0x1b >> > Reading symbols for shared libraries . done >> >> library(affy) >> > Loading required package: Biobase >> > Loading required package: tools >> > unable to read unknown load command 0x1b >> > Reading symbols for shared libraries . done >> > unable to read unknown load command 0x1b >> > Reading symbols for shared libraries . done >> > >> > Welcome to Bioconductor >> > >> > Vignettes contain introductory material. To view, >> type >> > 'openVignette()'. To cite Bioconductor, see >> > 'citation("Biobase")' and for >> packages 'citation(pkgname)'. >> > >> > Loading required package: affyio >> > unable to read unknown load command 0x1b >> > Reading symbols for shared libraries . done >> > Loading required package: preprocessCore >> > unable to read unknown load command 0x1b >> > unable to read unknown load command 0x1b >> > Reading symbols for shared libraries .. done >> > unable to read unknown load command 0x1b >> > Reading symbols for shared libraries . done >> >> fns <- >> list.celfiles(path='/Users/luow/project/microarraydata/celfiles/Mike/b mpEarl y',full.names=TRUE) >> >> hmscBmp<- ReadAffy(filenames=fns[1:2]) >> > Could not find OSO file: "" >> > (gdb) >> > >> > _______________________________________________ >> > 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 COMMENTlink modified 11.3 years ago by Ben Bolstad1.2k • written 11.3 years ago by Nathan S. Watson-Haigh40
Answer: ReadAffy crashes on mac
0
gravatar for Ben Bolstad
11.3 years ago by
Ben Bolstad1.2k
Ben Bolstad1.2k wrote:
You didn't give the relevant sessionInfo() to know which version of affyio you are using but I will give you the benefit of the doubt that you are using the most recent version. What you are observing is unrelated to the previous issue because 1) you are on a Linux of some kind not a PPC mac 2) You have a GCOS/binary format CEL file, not a command console format CEL file 3) The previous issue was fixed on (affyio 1.8.1/1.9.1) It is not likely a 64 bit problem, but perhaps more directly a IA64 problem, since plenty of people have been using this code on X86_64 type machines. Without something like a gdb backtrace to start looking into it I can not be of further help. Ben On Fri, 2008-08-15 at 10:36 +1000, Nathan S. Watson-Haigh wrote: > I'm having a similar (i.e. a segfault when trying to read CEL files) problem > reading v4 CEL files on a 64bit machine. > > Using any of the following methods results in a segfault (bottom): > ReadAffy() > read.celfile() > read.celfile.header() > read.celfile() > > The following methods seem to work ok: > readCelHeader() > readCel() > > Albeit readCelHeader() gives the following at the start of the output: > -- start output -- > R(5152): unaligned access to 0x200000000211c6ef, ip=0x200000000179c241 > R(5152): unaligned access to 0x200000000211c6f7, ip=0x200000000179c241 > R(5152): unaligned access to 0x200000000211c6ff, ip=0x200000000179c241 > R(5152): unaligned access to 0x200000000211c707, ip=0x200000000179c241 > R(5152): unaligned access to 0x200000000211c70f, ip=0x200000000179c241 > $filename > [1] "CEL/NA_7126_FG1.CEL" > > $version > [1] 4 > > $cols > [1] 732 > > $rows > [1] 732 > -- end output -- > > > It should be noted that I transferred all these files from my windows > machine to the linux machine via ftp. I transferred them back (in case they > got corrupted) using the same method and the same commands on my windows > machine did not have a problem. > > > -- start segfault -- > *** caught segfault *** > address 0xa67fb0, cause 'memory not mapped' > > Traceback: > 1: .Call("R_read_cel_file", filename, intensity.means.only, PACKAGE = > "affyio") > 2: read.celfile("CEL/NA_7126_FG1.CEL") > > Possible actions: > 1: abort (with core dump, if enabled) > 2: normal R exit > 3: exit R without saving workspace > 4: exit R saving workspace > -- end segfault -- > > -- start sessionInfo() -- > > sessionInfo() > R version 2.7.1 (2008-06-23) > ia64-unknown-linux-gnu > > locale: > LC_CTYPE=en_AU;LC_NUMERIC=C;LC_TIME=en_AU;LC_COLLATE=en_AU;LC_MONETA RY=C;LC_ > MESSAGES=en_AU;LC_PAPER=en_AU;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C; LC_MEASU > REMENT=en_AU;LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] affxparser_1.12.2 > -- end sessionInfo() -- > >
ADD COMMENTlink written 11.3 years ago by Ben Bolstad1.2k
Sorry, I gave you the wrong sessionInfo()! Yes, It's a brand new install of BioC. As it turns out, BioC was compiled using the Intel compiler. Using the GNU compilers, the problem disappears. Has anyone got the Intel compilers to work? Cheers, Nathan -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of Ben Bolstad Sent: Friday, 15 August 2008 1:42 PM To: Nathan S. Watson-Haigh Cc: luo_weijun at yahoo.com; Bioconductor at stat.math.ethz.ch Subject: Re: [BioC] ReadAffy crashes on mac You didn't give the relevant sessionInfo() to know which version of affyio you are using but I will give you the benefit of the doubt that you are using the most recent version. What you are observing is unrelated to the previous issue because 1) you are on a Linux of some kind not a PPC mac 2) You have a GCOS/binary format CEL file, not a command console format CEL file 3) The previous issue was fixed on (affyio 1.8.1/1.9.1) It is not likely a 64 bit problem, but perhaps more directly a IA64 problem, since plenty of people have been using this code on X86_64 type machines. Without something like a gdb backtrace to start looking into it I can not be of further help. Ben On Fri, 2008-08-15 at 10:36 +1000, Nathan S. Watson-Haigh wrote: > I'm having a similar (i.e. a segfault when trying to read CEL files) problem > reading v4 CEL files on a 64bit machine. > > Using any of the following methods results in a segfault (bottom): > ReadAffy() > read.celfile() > read.celfile.header() > read.celfile() > > The following methods seem to work ok: > readCelHeader() > readCel() > > Albeit readCelHeader() gives the following at the start of the output: > -- start output -- > R(5152): unaligned access to 0x200000000211c6ef, ip=0x200000000179c241 > R(5152): unaligned access to 0x200000000211c6f7, ip=0x200000000179c241 > R(5152): unaligned access to 0x200000000211c6ff, ip=0x200000000179c241 > R(5152): unaligned access to 0x200000000211c707, ip=0x200000000179c241 > R(5152): unaligned access to 0x200000000211c70f, ip=0x200000000179c241 > $filename > [1] "CEL/NA_7126_FG1.CEL" > > $version > [1] 4 > > $cols > [1] 732 > > $rows > [1] 732 > -- end output -- > > > It should be noted that I transferred all these files from my windows > machine to the linux machine via ftp. I transferred them back (in case they > got corrupted) using the same method and the same commands on my windows > machine did not have a problem. > > > -- start segfault -- > *** caught segfault *** > address 0xa67fb0, cause 'memory not mapped' > > Traceback: > 1: .Call("R_read_cel_file", filename, intensity.means.only, PACKAGE = > "affyio") > 2: read.celfile("CEL/NA_7126_FG1.CEL") > > Possible actions: > 1: abort (with core dump, if enabled) > 2: normal R exit > 3: exit R without saving workspace > 4: exit R saving workspace > -- end segfault -- > > -- start sessionInfo() -- > > sessionInfo() > R version 2.7.1 (2008-06-23) > ia64-unknown-linux-gnu > > locale: > LC_CTYPE=en_AU;LC_NUMERIC=C;LC_TIME=en_AU;LC_COLLATE=en_AU;LC_MONETARY =C;LC_ > MESSAGES=en_AU;LC_PAPER=en_AU;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC _MEASU > REMENT=en_AU;LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] affxparser_1.12.2 > -- end sessionInfo() -- > > _______________________________________________ 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 REPLYlink written 11.3 years ago by Nathan S. Watson-Haigh40
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