Kasper, thanks. Btw. is there anything against reading in the raw data from the .chp files, besides the called genotype? I have a patch for this if you are interested. Best, Gabor On Mon, May 11, 2009 at 2:14 AM, Kasper Daniel Hansen <khansen at="" stat.berkeley.edu=""> wrote: > Fixed in the devel branch, affxparser version 1.17.2 > > Kasper > > On May 1, 2009, at 9:18 , G?bor Cs?rdi wrote: > >> Dear All, >> >> I am trying to read in a .chp file with readChp from the affxparser >> package, without much success. It used to work fine, but for this new >> file (and a lot of other new files as well) it segfaults. >> >> The file is for the Affymetrix 5.0 SNP chip, and it was produced by >> Affymetrix Power Tools. I have uploaded it here: >> http://www2.unil.ch/cbg/readChp_segfault.chp.gz >> >> Sometimes it segfaults for the first read attempt, sometimes only for >> the second: >>> >>> library(affxparser) >>> chp <- readChp("readChp_segfault.chp") >> >> *** caught segfault *** >> address 0x1ab8000, cause 'memory not mapped' >> >> Traceback: >> 1: .Call("R_affx_get_chp_file", filename, withQuant) >> 2: readChp("readChp_segfault.chp") >> >> 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: >> >> A more detailed backtrace: >> >>> library(affxparser) >>> chp <- readChp("readChp_segfault.chp") >> >> Program received signal SIGSEGV, Segmentation fault. >> 0x0000003d53a70c2e in strlen () from /lib64/tls/libc.so.6 >> (gdb) bt >> #0 ?0x0000003d53a70c2e in strlen () from /lib64/tls/libc.so.6 >> #1 ?0x0000002a95606029 in Rf_mkChar ( >> ? name=0x1a35988 "./apt-probeset-genotype -o >> /home/zoltan/apt-1.10.1-20081103-amd64-pc-linux/results/ --cdf-file >> GenomeWideSNP_5.cdf --chrX-snps GenomeWideSNP_5.chrx >> --read-models-brlmmp GenomeWideSNP_5.models --output"...) >> ? at envir.c:3238 >> #2 ?0x0000002a9562ba93 in Rf_mkString ( >> ? s=0x1a35988 "./apt-probeset-genotype -o >> /home/zoltan/apt-1.10.1-20081103-amd64-pc-linux/results/ --cdf-file >> GenomeWideSNP_5.cdf --chrX-snps GenomeWideSNP_5.chrx >> --read-models-brlmmp GenomeWideSNP_5.models --output"...) >> ? at ../../src/include/Rinlinedfuns.h:537 >> #3 ?0x0000002a9948a191 in R_affx_GetList (params= >> >> {<std::_list_base<affymetrix_calvin_parameter::parameternamevaluety pe,std::allocator<affymetrix_calvin_parameter::parameternamevaluetype=""> >>>> >>>> = {_M_impl = >> >> >> {<std::allocator<std::_list_node<affymetrix_calvin_parameter::param eternamevaluetype=""> >>>> >>>> = >>>> {<__gnu_cxx::new_allocator<std::_list_node<affymetrix_calvin_para meter::parameternamevaluetype=""> >>>> = {<no data="" fields="">}, <no data="" fields="">}, _M_node = {_M_next = >> >> 0x1968ca0, _M_prev = 0x1a1f510}}}, <no data="" fields="">}) >> ? at R_affx_chp_parser.cpp:122 >> #4 ?0x0000002a9948d76f in R_affx_ReadCHP (chp=0xf878b0, isBrief=false) >> ? at R_affx_chp_parser.cpp:789 >> #5 ?0x0000002a9948e0d5 in R_affx_get_chp_file (fname=0x69a588, >> ? withQuantifications=0xfcc1a8) at R_affx_chp_parser.cpp:917 >> ---Type <return> to continue, or q <return> to quit--- >> #6 ?0x0000002a955e515a in do_dotcall (call=0x192b970, op=Variable "op" >> is not available. >> ) at dotcode.c:859 >> #7 ?0x0000002a9561359a in Rf_eval (e=0x1a35988, rho=0x192b778) at >> eval.c:487 >> #8 ?0x0000002a95616d20 in Rf_applyClosure (call=0x192aa98, op=0x192a830, >> ? arglist=0x192b820, rho=0x544aa8, suppliedenv=0x544ae0) at eval.c:667 >> #9 ?0x0000002a95613359 in Rf_eval (e=0x192aa98, rho=0x544aa8) at >> eval.c:505 >> #10 0x0000002a956154a3 in do_set (call=0x192a9f0, op=0x522a88, >> args=0x192aa28, >> ? rho=0x544aa8) at eval.c:1422 >> #11 0x0000002a95613452 in Rf_eval (e=0x192a9f0, rho=0x544aa8) at >> eval.c:461 >> #12 0x0000002a956317e8 in Rf_ReplIteration (rho=0x544aa8, savestack=0, >> ? browselevel=Variable "browselevel" is not available. >> ) at main.c:257 >> #13 0x0000002a95631920 in R_ReplConsole (rho=0x544aa8, savestack=0, >> ? browselevel=0) at main.c:306 >> #14 0x0000002a95631c20 in run_Rmainloop () at main.c:966 >> #15 0x00000000004008ab in main () >> (gdb) >> >>> sessionInfo() >> >> R version 2.8.1 (2008-12-22) >> x86_64-redhat-linux-gnu >> >> locale: >> >> LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en _US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;L C_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDE NTIFICATION=C >> >> attached base packages: >> [1] stats ? ? graphics ?grDevices utils ? ? datasets ?methods ? base >> >> other attached packages: >> [1] affxparser_1.16.0 >> >> So this is for the development version of affxparser, but I get the >> same result with the BioC 2.3 version (1.14.2) as well. Moreover, this >> is not the only file that fails, so probably the file is not corrupt. >> >> Any help is appreciated, Best Regards, >> Gabor >> >> -- >> Gabor Csardi <gabor.csardi at="" unil.ch=""> ? ? UNIL DGM >> >> _______________________________________________ >> 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 > > -- Gabor Csardi <gabor.csardi at="" unil.ch=""> UNIL DGM