[Bioc-devel] affxparser: Core dump with R 2.14.0 on OSX
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. Kasper
On Tue, Nov 8, 2011 at 3:04 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
Hi Henrik, On Mon, Nov 7, 2011 at 2:41 PM, Henrik Bengtsson <hb at biostat.ucsf.edu> 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 Lion 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 FALSE ?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/Mapping250K_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 you. On Mon, Nov 7, 2011 at 11:19 AM, Henrik Bengtsson <henrik.bengtsson at aroma-project.org> 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.
[...]
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