memory corruption in make.cdf.package() reading binary CDF with BioC 2.3
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Don Maszle ▴ 10
@don-maszle-3135
Last seen 7.0 years ago
I just upgraded from R-2.3.0 / BioC 2.? (Biobase version 1.10.1 from June 2006) to R-2.8.0 / BioC 2.3 and cannot rebuild my cdf environments for two binary CDFs. A number of plain text CDFs rebuilt without a problem. System information and a backtrace are provided below. I'm hoping that this is due to something like the comments in read_cdf_xda.c which foretells of a future problem. Note, I have cleaned some names from this trace as this is a proprietary chip design. This of course means that I cannot pass the CDF to you for testing, however I am happy to do what I can on this end. The chip is an Affymetrix oligonucleotide array with 1.3 million features for 84000 probeset using a slide dimension of 1162x1162. Please let me know what else I can provide. Sincerely, Don Maszle Sr. Computational Biologist, Manager Mendel Biotechnology, Inc. ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++ # uname -a Linux ray 2.6.9-42.ELsmp #1 SMP Wed Jul 12 23:32:02 EDT 2006 x86_64 x86_64 x86_64 GNU/Linux # R -d gdb GNU gdb Red Hat Linux (6.3.0.0-1.132.EL4rh) ... This GDB was configured as "x86_64-redhat-linux-gnu"... Using host libthread_db library "/lib64/tls/libthread_db.so.1". (gdb) run Starting program: /usr/local/lib64/R/bin/exec/R R version 2.8.0 (2008-10-20) Copyright (C) 2008 The R Foundation for Statistical Computing ISBN 3-900051-07-0 ... > version _ platform x86_64-unknown-linux-gnu arch x86_64 os linux-gnu system x86_64, linux-gnu status major 2 minor 8.0 year 2008 month 10 day 20 svn rev 46754 language R version.string R version 2.8.0 (2008-10-20) > dirLib <- 'path-to-lib'; > dirPkg <- 'path-to-packages'; > library(makecdfenv) Loading required package: Biobase Loading required package: tools ... Loading required package: affy [Thread debugging using libthread_db enabled] [New Thread 182895468000 (LWP 5281)] Loading required package: affyio > fn <- 'file.cdf'; > make.cdf.package(cdf.path=dirLib, + package.path=dirPkg, + compress=TRUE, + species='species', + filename=fn, + author='D.R.Maszle', + maintainer='D.R.Maszle <dmaszle at="" mendelbio.com="">') *** glibc detected *** malloc(): memory corruption: 0x0000000001f9cbd0 *** Program received signal SIGABRT, Aborted. [Switching to Thread 182895468000 (LWP 7083)] 0x00000035cdf2e21d in raise () from /lib64/tls/libc.so.6 (gdb) backtrace #0 0x00000035cdf2e21d in raise () from /lib64/tls/libc.so.6 #1 0x00000035cdf2fa1e in abort () from /lib64/tls/libc.so.6 #2 0x00000035cdf63291 in __libc_message () from /lib64/tls/libc.so.6 #3 0x00000035cdf69881 in _int_malloc () from /lib64/tls/libc.so.6 #4 0x00000035cdf6b272 in malloc () from /lib64/tls/libc.so.6 #5 0x0000000000418748 in Rf_allocVector (type=14, length=40) at memory.c:1999 #6 0x00000000004c5a61 in Rf_allocMatrix (mode=14, nrow=20, ncol=2) at array.c:171 #7 0x0000002a992bdd57 in ReadCDFFile (filename=Variable "filename" is not available. ) at read_cdf_xda.c:738 #8 0x000000000050e47a in do_dotcall (call=0x21730e0, op=Variable "op" is not available. ) at dotcode.c:856 #9 0x000000000053b5c3 in Rf_eval (e=0x21730e0, rho=0x2174b10) at eval.c:487 #10 0x000000000053d316 in do_set (call=0x2172220, op=0x825858, args=0x21721e8, rho=0x2174b10) at eval.c:1422 #11 0x000000000053b487 in Rf_eval (e=0x2172220, rho=0x2174b10) at eval.c:461 #12 0x000000000053d39c in do_begin (call=0x2172290, op=0x825660, args=0x2172258, rho=0x2174b10) at eval.c:1174 #13 0x000000000053b487 in Rf_eval (e=0x2172290, rho=0x2174b10) at eval.c:461 #14 0x000000000053b487 in Rf_eval (e=0x216c268, rho=0x2174b10) at eval.c:461 #15 0x000000000053d39c in do_begin (call=0x216b2e8, op=0x825660, args=0x216c2a0, rho=0x2174b10) at eval.c:1174 #16 0x000000000053b487 in Rf_eval (e=0x216b2e8, rho=0x2174b10) at eval.c:461 #17 0x000000000053ea74 in Rf_applyClosure (call=0x20efb58, op=0x21671b8, arglist=0x2174db0, rho=0x20f3438, suppliedenv=0x8478b0) at eval.c:667 #18 0x000000000053b39b in Rf_eval (e=0x20efb58, rho=0x20f3438) at eval.c:505 #19 0x000000000053d316 in do_set (call=0x20efc70, op=0x825858, args=0x20efc38, rho=0x20f3438) at eval.c:1422 #20 0x000000000053b487 in Rf_eval (e=0x20efc70, rho=0x20f3438) at eval.c:461 #21 0x000000000053d39c in do_begin (call=0x20ef4e8, op=0x825660, args=0x20efca8, rho=0x20f3438) at eval.c:1174 #22 0x000000000053b487 in Rf_eval (e=0x20ef4e8, rho=0x20f3438) at eval.c:461 #23 0x000000000053ea74 in Rf_applyClosure (call=0x20ecf88, op=0x20ecdc8, arglist=0x20f2a10, rho=0x847878, suppliedenv=0x8478b0) at eval.c:667 #24 0x000000000053b39b in Rf_eval (e=0x20ecf88, rho=0x847878) at eval.c:505 #25 0x0000000000414109 in Rf_ReplIteration (rho=0x847878, savestack=0, browselevel=0, state=0x7fbfffe770) at main.c:257 #26 0x0000000000414238 in R_ReplConsole (rho=0x847878, savestack=0, browselevel=0) at main.c:306 #27 0x00000000004144e2 in run_Rmainloop () at main.c:966 #28 0x00000000004125f8 in main (ac=Variable "ac" is not available. ) at Rmain.c:33 (gdb)
cdf db0 cdf db0 • 609 views
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@wolfgang-huber-3550
Last seen 7 weeks ago
EMBL European Molecular Biology Laborat…
Hi Don One guess: You say "updgraded" - are you using any of the old instances of packages? Or did you a clean new install of R, and of all the libraries that you want to use? (and remove any old libraries from R_LIBRARY_PATH) Using old libraries with newer versions of R is not recommended, and typically leads to problems as you described. Btw, as mentioned in the posting guide and many times on this list, please include the output of sessionInfo(). Best wishes Wolfgang ----------------------------------------------------- Wolfgang Huber EMBL-EBI http://www.ebi.ac.uk/huber Don Maszle wrote: > I just upgraded from R-2.3.0 / BioC 2.? (Biobase version 1.10.1 from > June 2006) > to R-2.8.0 / BioC 2.3 and cannot rebuild my cdf environments for two > binary CDFs. > A number of plain text CDFs rebuilt without a problem. System > information and > a backtrace are provided below. I'm hoping that this is due to > something like > the comments in read_cdf_xda.c which foretells of a future problem. > > Note, I have cleaned some names from this trace as this is a proprietary > chip > design. This of course means that I cannot pass the CDF to you for > testing, > however I am happy to do what I can on this end. The chip is an > Affymetrix > oligonucleotide array with 1.3 million features for 84000 probeset using a > slide dimension of 1162x1162. > > Please let me know what else I can provide. > > Sincerely, > > Don Maszle > Sr. Computational Biologist, Manager > Mendel Biotechnology, Inc. > > ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ +++++++++++ > > > # uname -a > Linux ray 2.6.9-42.ELsmp #1 SMP Wed Jul 12 23:32:02 EDT 2006 x86_64 > x86_64 x86_64 GNU/Linux > > # R -d gdb > GNU gdb Red Hat Linux (6.3.0.0-1.132.EL4rh) > ... > This GDB was configured as "x86_64-redhat-linux-gnu"... > Using host libthread_db library "/lib64/tls/libthread_db.so.1". > > (gdb) run > Starting program: /usr/local/lib64/R/bin/exec/R > > R version 2.8.0 (2008-10-20) > Copyright (C) 2008 The R Foundation for Statistical Computing > ISBN 3-900051-07-0 > ... > > version > _ > platform x86_64-unknown-linux-gnu > arch x86_64 > os linux-gnu > system x86_64, linux-gnu > status > major 2 > minor 8.0 > year 2008 > month 10 > day 20 > svn rev 46754 > language R > version.string R version 2.8.0 (2008-10-20) > > > dirLib <- 'path-to-lib'; > > dirPkg <- 'path-to-packages'; > > library(makecdfenv) > Loading required package: Biobase > Loading required package: tools > ... > Loading required package: affy > [Thread debugging using libthread_db enabled] > [New Thread 182895468000 (LWP 5281)] > Loading required package: affyio > > fn <- 'file.cdf'; > > make.cdf.package(cdf.path=dirLib, > + package.path=dirPkg, > + compress=TRUE, > + species='species', > + filename=fn, > + author='D.R.Maszle', > + maintainer='D.R.Maszle <dmaszle at="" mendelbio.com="">') > *** glibc detected *** malloc(): memory corruption: 0x0000000001f9cbd0 *** > > Program received signal SIGABRT, Aborted. > [Switching to Thread 182895468000 (LWP 7083)] > 0x00000035cdf2e21d in raise () from /lib64/tls/libc.so.6 > (gdb) backtrace > #0 0x00000035cdf2e21d in raise () from /lib64/tls/libc.so.6 > #1 0x00000035cdf2fa1e in abort () from /lib64/tls/libc.so.6 > #2 0x00000035cdf63291 in __libc_message () from /lib64/tls/libc.so.6 > #3 0x00000035cdf69881 in _int_malloc () from /lib64/tls/libc.so.6 > #4 0x00000035cdf6b272 in malloc () from /lib64/tls/libc.so.6 > #5 0x0000000000418748 in Rf_allocVector (type=14, length=40) at > memory.c:1999 > #6 0x00000000004c5a61 in Rf_allocMatrix (mode=14, nrow=20, ncol=2) > at array.c:171 > #7 0x0000002a992bdd57 in ReadCDFFile (filename=Variable "filename" is > not available. > ) at read_cdf_xda.c:738 > #8 0x000000000050e47a in do_dotcall (call=0x21730e0, op=Variable "op" > is not available. > ) at dotcode.c:856 > #9 0x000000000053b5c3 in Rf_eval (e=0x21730e0, rho=0x2174b10) at > eval.c:487 > #10 0x000000000053d316 in do_set (call=0x2172220, op=0x825858, > args=0x21721e8, > rho=0x2174b10) at eval.c:1422 > #11 0x000000000053b487 in Rf_eval (e=0x2172220, rho=0x2174b10) at > eval.c:461 > #12 0x000000000053d39c in do_begin (call=0x2172290, op=0x825660, > args=0x2172258, rho=0x2174b10) at eval.c:1174 > #13 0x000000000053b487 in Rf_eval (e=0x2172290, rho=0x2174b10) at > eval.c:461 > #14 0x000000000053b487 in Rf_eval (e=0x216c268, rho=0x2174b10) at > eval.c:461 > #15 0x000000000053d39c in do_begin (call=0x216b2e8, op=0x825660, > args=0x216c2a0, rho=0x2174b10) at eval.c:1174 > #16 0x000000000053b487 in Rf_eval (e=0x216b2e8, rho=0x2174b10) at > eval.c:461 > #17 0x000000000053ea74 in Rf_applyClosure (call=0x20efb58, op=0x21671b8, > arglist=0x2174db0, rho=0x20f3438, suppliedenv=0x8478b0) at eval.c:667 > #18 0x000000000053b39b in Rf_eval (e=0x20efb58, rho=0x20f3438) at > eval.c:505 > #19 0x000000000053d316 in do_set (call=0x20efc70, op=0x825858, > args=0x20efc38, > rho=0x20f3438) at eval.c:1422 > #20 0x000000000053b487 in Rf_eval (e=0x20efc70, rho=0x20f3438) at > eval.c:461 > #21 0x000000000053d39c in do_begin (call=0x20ef4e8, op=0x825660, > args=0x20efca8, rho=0x20f3438) at eval.c:1174 > #22 0x000000000053b487 in Rf_eval (e=0x20ef4e8, rho=0x20f3438) at > eval.c:461 > #23 0x000000000053ea74 in Rf_applyClosure (call=0x20ecf88, op=0x20ecdc8, > arglist=0x20f2a10, rho=0x847878, suppliedenv=0x8478b0) at eval.c:667 > #24 0x000000000053b39b in Rf_eval (e=0x20ecf88, rho=0x847878) at eval.c:505 > #25 0x0000000000414109 in Rf_ReplIteration (rho=0x847878, savestack=0, > browselevel=0, state=0x7fbfffe770) at main.c:257 > #26 0x0000000000414238 in R_ReplConsole (rho=0x847878, savestack=0, > browselevel=0) at main.c:306 > #27 0x00000000004144e2 in run_Rmainloop () at main.c:966 > #28 0x00000000004125f8 in main (ac=Variable "ac" is not available. > ) at Rmain.c:33 > (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
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