[Bioc-devel] affxparser: Core dump with R 2.14.0 on OSX
Henrik Bengtsson
hb at biostat.ucsf.edu
Fri Dec 16 00:09:54 CET 2011
Hi.
On Thu, Dec 15, 2011 at 2:06 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
> 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.
I don't have access to the OSX so I cannot do this myself, by as far
as I have understood, the problem occurs on some of the OSX releases
on R v2.14.0. Until this have been resolved, maybe we share such
"manual" builds online. It appears that Snow Leopard, Leopard, and
Lion are the most common. If you're on one of those and end up
building affxparser, could you please verify that it works with the
below, mail the the binary to me and I can make them available online.
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"
hdr <- readCdfHeader(pathname);
str(hdr);
Thanks
/Henrik
PS. The original post of this thread is available at
https://stat.ethz.ch/pipermail/bioc-devel/2011-November/002969.html
(also more readable than the below).
> 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*>>>**>>**>>* _______!
>> ________________________________________*>>* Bioc-devel at r-project.o
>> rg <https://stat.ethz.ch/mailman/listinfo/bioc-devel> mailing list*>>* https://stat.ethz.ch/mailman/listinfo/bioc-devel*>>**>**
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