[Bioc-devel] affxparser: Core dump with R 2.14.0 on OSX
Dan Tenenbaum
dtenenba at fhcrc.org
Thu Dec 15 23:06:56 CET 2011
Hi Lin,
On Wed, Dec 14, 2011 at 7:01 AM, Lin Guey <lin.t.guey at gmail.com> wrote:
> Hi,
>
> I am getting the same error as Dan on my Mac Lion:
>
>> library("affxparser");
>> library("digest");
>> pathname <- "annotationData/chipTypes/HG-U133_Plus_2/HG-U133_Plus_2.cdf";
>> fi <- file.info(pathname);
>> rownames(fi) <- NULL;
>> print(fi);
> size isdir mode mtime ctime
> 1 26251783 FALSE 644 2008-07-30 20:20:31 2011-12-13 16:42:43
> atime uid gid uname grname
> 1 2011-12-14 09:35:25 501 20 Lin staff
>> print(digest(file=pathname));
> [1] "fee66da06031332d311d355684291e2b"
>> print(sessionInfo());
> R version 2.14.0 (2011-10-31)
> Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] aroma.affymetrix_2.3.0 affxparser_1.26.2 aroma.apd_0.2.0
> [4] R.huge_0.3.0 aroma.core_2.3.2 aroma.light_1.22.0
> [7] matrixStats_0.4.0 R.rsp_0.7.0 R.cache_0.5.2
> [10] R.filesets_1.1.3 digest_0.5.1 R.utils_1.9.6
> [13] R.oo_1.8.3 R.methodsS3_1.2.1
>> hdr <- readCdfHeader(pathname);
> Abort trap: 6
>
>
> Any suggestions would be greatly appreciated.
Until this issue is definitively resolved, I know that installing
affxparser as follows will work:
source("http://bioconductor.org/biocLite.R")
biocLite("affxparser", type="source")
This requires that you have Xcode installed on your Mac.
Dan
> Lin
>
>
> On Tue, Nov 8, 2011 at 12:21 PM, Kasper Daniel Hansen
> <kasperdanielhansen at gmail.com
> <https://stat.ethz.ch/mailman/listinfo/bioc-devel>> wrote:
>>* Reading Dan's error I realize I did something else: he points to the zip archive*>* pathname <- "~/Downloads/250k_nsp_libraryfile_rev4.zip"*>* whereas I unzip the archive, and point it directly to the cdf file*>* inside some subdirectory of the unpacked zip file.*>**>* We do not expect that readCdfHeader on a zip archive works. We are*>* aware that reading "wrong" files may lead to a core dump which is*>* rather bad and we should try to fix this.*
> Seems like there is stil a problem on Lion.
> I unzipped the zip file and then:
>
>>* hdr <- readCdfHeader("CD_Mapping250K_Nsp_rev4/Full/Mapping250K_Nsp/LibFiles/Mapping250K_Nsp.cdf")*Abort trap: 6
>
> It works on Leopard, though.
>
> Dan
>
>>**>* Kasper*>**>**>* On Tue, Nov 8, 2011 at 3:04 PM, Dan Tenenbaum <dtenenba at fhcrc.org <https://stat.ethz.ch/mailman/listinfo/bioc-devel>> wrote:*>>* Hi Henrik,*>>**>>* On Mon, Nov 7, 2011 at 2:41 PM, Henrik Bengtsson <hb at biostat.ucsf.edu <https://stat.ethz.ch/mailman/listinfo/bioc-devel>> wrote:*>>>* Hi,*>>>**>>>* over at the aroma.affymetrix mailing list, a user (cc:ed) reports that*>>>* affxparser v1.26.1 core dumps when trying to read a CDF file. I'm*>>>* moving it to BioC-devel, and asks if others can reproduce this. I*>>>* don't have access to R v2.14.0 on OSX. It does not core dump on*>>>* Windows 7 with the same setup and versions. The OP says he got the*>>>* problems after updated to R v2.14.0. The CDF file*>>>* (Mapping250K_Nsp.cdf) is available in (34Mb download after login):*>>>**>>>* http://www.affymetrix.com/Auth/support/downloads/library_files/250k_nsp_libraryfile_rev4.zip*>>>**>>**>>* I am able to reproduce the problem:*>>**>>>* library(digest)*>!
> >>* library(affxparser)*>>>* pathname <- "~/Downloads/250k_nsp_libraryfile_rev4.zip"*>>>* fi <- file.info(pathname)*>>>* rownames(fi) <- NULL*>>>* print(fi)*>>* size isdir mode mtime ctime*>>* 1 45043262 FALSE 644 2011-11-08 11:48:45 2011-11-08 11:48:45*>>* atime uid gid uname grname*>>* 1 2011-11-08 11:54:09 502 20 dtenenba staff*>>>* print(digest(file=pathname))*>>* [1] "cf10a53b36108315542276875d43c24a"*>>>* print(sessionInfo())*>>* R version 2.14.0 (2011-10-31)*>>* Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)*>>**>>* locale:*>>* [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8*>>**>>* attached base packages:*>>* [1] stats graphics grDevices utils datasets methods base*>>**>>* other attached packages:*>>* [1] affxparser_1.26.1 digest_0.5.1 BiocInstaller_1.2.0*>>**>>* loaded via a namespace (and not attached):*>>* [1] tools_2.14.0*>>>* hdr <- readCdfHeader(pathname)*>>* Abort!
> trap: 6*>>**>>* It happens in 32-bit R as well.*>>**>>* That's on a L
> ion machine. On Leopard, I get a different error:*>>**>>>* library(affxparser)*>>>* pathname <- "~/Downloads/250k_nsp_libraryfile_rev4.zip"*>>>* hdr <- readCdfHeader(pathname)*>>* Failed to read the CDF file header for:*>>* /Users/biocbuild/Downloads/250k_nsp_libraryfile_rev4.zip*>>* Error in basename(res$chiptype) : a character vector argument expected*>>>* sessionInfo()*>>* R version 2.14.0 (2011-10-31)*>>* Platform: i386-apple-darwin9.8.0/i386 (32-bit)*>>**>>* locale:*>>* [1] en_US.US-ASCII/en_US.US-ASCII/en_US.US-ASCII/C/en_US.US-ASCII/en_US.US-ASCII*>>**>>* attached base packages:*>>* [1] stats graphics grDevices utils datasets methods base*>>**>>* other attached packages:*>>* [1] affxparser_1.26.1 BiocInstaller_1.2.0*>>**>>* loaded via a namespace (and not attached):*>>* [1] tools_2.14.0*>>>* library(digest)*>>>* fi <- file.info(pathname)*>>>* rownames(fi) <- NULL*>>>* fi*>>* size isdir mode mtime ctime*>>* 1 45043262 FALS!
> E 644 2011-11-08 11:58:53 2011-11-08 11:58:53*>>* atime uid gid uname grname*>>* 1 2011-11-08 12:01:17 502 20 biocbuild staff*>>>* digest(file=pathname)*>>* [1] "cf10a53b36108315542276875d43c24a"*>>**>>**>>* Dan*>>**>>**>>**>>>* More details below.*>>>**>>>* BTW, Peter, could you please check if you have issues with any other*>>>* CDF files, such as the Mapping10K_Xba142.cdf?*>>>**>>>* /Henrik*>>>**>>>* On Mon, Nov 7, 2011 at 2:27 PM, Peter Kang wrote:*>>>>* Henrik,*>>>>* Thanks for your advice. This is what I get:*>>>>>* library("affxparser");*>>>>>* library("digest");*>>>>>**>>>>>* pathname <-*>>>>>* "annotationData/chipTypes/Mapping250K_Nsp/Mapping250K_Nsp.cdf";*>>>>>* fi <- file.info (pathname);*>>>>>* rownames(fi) <- NULL;*>>>>>* print(fi);*>>>>* size isdir mode mtime ctime*>>>>* 1 194455495 FALSE 755 2005-08-24 16:01:42 2011-11-07 09:53:41*>>>>* atime uid gid uname grname*>>>>* 1 2011-11-07 11:!
> 47:58 503 20 hpkang staff*>>>>>* print(digest(file=pathname));*>>>>*
> [1] "59ae263311a2cf63b8d1b9b4cc7d663b"*>>>>>**>>>>>* print(sessionInfo());*>>>>* R version 2.14.0 (2011-10-31)*>>>>* Platform: x86_64-apple-darwin9.8.0/x86_64 (64-bit)*>>>>* locale:*>>>>* [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8*>>>>* attached base packages:*>>>>* [1] stats graphics grDevices utils datasets methods base*>>>>* other attached packages:*>>>>* [1] digest_0.5.1 affxparser_1.26.1*>>>>>* hdr <- readCdfHeader(pathname);*>>>>* zsh: abort (core dumped) R*>>>**>>>* [...]*>>>**>>>>* On Mon, Nov 7, 2011 at 12:35 PM, Henrik Bengtsson wrote:*>>>>>**>>>>>* Hi,*>>>>>**>>>>>* you can still do sessionInfo() just before you call the core-dumping*>>>>>* method; sessionInfo() is so key to solving problems, especially core*>>>>>* dumps so we cannot be without them. What do you get when you do:*>>>>>**>>>>>* library("affxparser");*>>>>>* library("digest");*>>>>>**>>>>>* pathname <-*>>>>>* "annotationData/chipTypes/Mapping250K_Nsp/Mapping!
> 250K_Nsp.cdf";*>>>>>* fi <- file.info(pathname);*>>>>>* rownames(fi) <- NULL;*>>>>>* print(fi);*>>>>>* print(digest(file=pathname));*>>>>>**>>>>>* print(sessionInfo());*>>>>>* hdr <- readCdfHeader(pathname);*>>>>>* str(hdr);*>>>>>**>>>>>* Also, if you get some core dump messages, what are they?*>>>>>**>>>>>* After you reply here, I'm most likely going to move this to the*>>>>>* Bioconductor devel mailing list, because that is most likely where the*>>>>>* real help will come from.*>>>>>**>>>>>* /Henrik*>>>>>**>>>>>* On Mon, Nov 7, 2011 at 11:54 AM, Peter Kang wrote:*>>>>>* > Sorry, I couldn't do sessionInfo() or traceback() because of the core*>>>>>* > dump.*>>>>>* > The core dump was with all of the latest packages in R 2.14.0. The funny*>>>>>* > thing is it worked perfectly well before I upgraded R and reinstalled*>>>>>* > aroma.*>>>>>* > I tried Henrik's suggestion, and get the 'core dumped' error after*>>>>>* > hdr <- readCdfHeader(pathname);*>>>>>* > I also redownloaded!
> the cdf files from the Affy website, no difference.*>>>>>* > Thank yo
> u.*>>>>>* >*>>>>>* > On Mon, Nov 7, 2011 at 11:19 AM, Henrik Bengtsson*>>>>>* > <henrik.bengtsson at aroma-project.org <https://stat.ethz.ch/mailman/listinfo/bioc-devel>> wrote:*>>>>>* >>*>>>>>* >> On Mon, Nov 7, 2011 at 9:35 AM, Pierre Neuvial wrote:*>>>>>* >> > What is your sessionInfo() ?*>>>>>* >> >*>>>>>* >> > Perhaps you need to upgrade aroma.affymetrix instead, although I*>>>>>* >> > don't*>>>>>* >> > see why you would get this core dump.*>>>>>* >>*>>>>>* >> Yes, sessionInfo() and showing that you've tried with the latest*>>>>>* >> version speeds up troubleshooting and response time.*>>>>>* >>*>>>>>* >> I the past, basically all core dumps have been attributed to the*>>>>>* >> affxparser package *and* almost all of those have been due to corrupt*>>>>>* >> Affymetrix files. I suspect that affxparser is the player here to,*>>>>>* >> and maybe even a corrupt file. So, in a fresh R session try with:*>>>>>* >>*>>>>>* >> library("affxparser");*>>>>>* >> pathname <-*>>>>>!
> * >> "annotationData/chipTypes/Mapping250K_Nsp/Mapping250K_Nsp.cdf";*>>>>>* >> hdr <- readCdfHeader(pathname);*>>>>>* >> str(hdr);*>>>>>* >> cdfList <- readCdf(pathname);*>>>>>* >> str(cdfList);*>>>>>* >>*>>>>>* >> Core dump?*>>>>>* >>*>>>>>* >> /Henrik*>>>>>* >>*>>>>>* >> >*>>>>>* >> > Pierre*>>>>>* >> >*>>>>>* >> > On Mon, Nov 7, 2011 at 6:20 PM, Peter Kang wrote:*>>>>>* >> >> I just upgraded to 2.14.0 (Mac OSX), and I'm getting a 'core dumped'*>>>>>* >> >> error when trying to access the cdf file.*>>>>>* >> >>*>>>>>* >> >>> cdf <- AffymetrixCdfFile$byChipType("Mapping250K_Nsp")*>>>>>* >> >>> print(cdf)*>>>>>* >> >> zsh: abort (core dumped) R*>>>>>* >> >>*>>>>>* >> >> Do I need to downgrade R?*>>>>>* >> >>*>>>>>* >> >> Thank you.*>>>**>>>* [...]*>>>**>>>* _______________________________________________*>>>* Bioc-devel at r-project.org <https://stat.ethz.ch/mailman/listinfo/bioc-devel> mailing list*>>>* https://stat.ethz.ch/mailman/listinfo/bioc-devel*>>>**>>**>>* _______!
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