[BioC] makecdfenv crashes

Wed Dec 3 13:27:49 CET 2008

Either that or have a look at aroma.affymetrix.

Regards,

Benjamin

-----Ursprüngliche Nachricht-----
Von: bioconductor-bounces at stat.math.ethz.ch
[mailto:bioconductor-bounces at stat.math.ethz.ch] Im Auftrag von James W.
MacDonald
Gesendet: 02 December 2008 22:31
An: Skewes,Aaron
Cc: bioconductor at stat.math.ethz.ch
Betreff: Re: [BioC] makecdfenv crashes

Hi Aaron,

Skewes,Aaron wrote:
> Hi,
> 
> I am attempting to make a CDF package for Affy GenomeWideSNP 6.0 platform
using makecdfenv, and it crashes. Any suggestions?

Yes. Don't do that ;-D

You want to use oligo for the analysis of the SNP6.0 data. This package 
doesn't use a cdf package - instead it uses a pdInfoPackage, which you 
can get via biocLite("pd.genomewidesnp.6").

Best,

Jim

> 
> Thanks,
> Aaron
> 
>> library("makecdfenv")
> Loading required package: Biobase
> Loading required package: tools
> 
> Welcome to Bioconductor
> 
>   Vignettes contain introductory material. To view, type
>   'openVignette()'. To cite Bioconductor, see
>   'citation("Biobase")' and for packages 'citation(pkgname)'.
> 
> Loading required package: affy
> Loading required package: affyio
> Loading required package: preprocessCore
>> make.cdf.package("GenomeWideSNP_6.Full.cdf", species = "Human")
> *** glibc detected *** /usr/local/lib64/R/bin/exec/R: malloc(): memory
corruption: 0x0000000001149120 ***
> ======= Backtrace: =========
> /lib64/libc.so.6[0x36c0a71cd1]
> /lib64/libc.so.6(__libc_malloc+0x7d)[0x36c0a72e8d]
> /usr/local/lib64/R/bin/exec/R(Rf_allocVector+0x5de)[0x41a26e]
> /usr/local/lib64/R/bin/exec/R(Rf_allocMatrix+0x6e)[0x4cc47e]
>
/home/askewes/R/x86_64-unknown-linux-gnu-library/2.7/affyio/libs/affyio.so(R
eadCDFFile+0x1cb)[0x2b9550e4cb8b]
> /usr/local/lib64/R/bin/exec/R[0x51a286]
> /usr/local/lib64/R/bin/exec/R(Rf_eval+0x5b1)[0x5409d1]
> /usr/local/lib64/R/bin/exec/R[0x544672]
> /usr/local/lib64/R/bin/exec/R(Rf_eval+0x3de)[0x5407fe]
> /usr/local/lib64/R/bin/exec/R[0x541430]
> /usr/local/lib64/R/bin/exec/R(Rf_eval+0x3de)[0x5407fe]
> /usr/local/lib64/R/bin/exec/R(Rf_eval+0x3de)[0x5407fe]
> /usr/local/lib64/R/bin/exec/R[0x541430]
> /usr/local/lib64/R/bin/exec/R(Rf_eval+0x3de)[0x5407fe]
> /usr/local/lib64/R/bin/exec/R(Rf_applyClosure+0x270)[0x542990]
> /usr/local/lib64/R/bin/exec/R(Rf_eval+0x2c9)[0x5406e9]
> /usr/local/lib64/R/bin/exec/R[0x544672]
> /usr/local/lib64/R/bin/exec/R(Rf_eval+0x3de)[0x5407fe]
> /usr/local/lib64/R/bin/exec/R[0x541430]
> /usr/local/lib64/R/bin/exec/R(Rf_eval+0x3de)[0x5407fe]
> /usr/local/lib64/R/bin/exec/R(Rf_applyClosure+0x270)[0x542990]
> /usr/local/lib64/R/bin/exec/R(Rf_eval+0x2c9)[0x5406e9]
> /usr/local/lib64/R/bin/exec/R(Rf_ReplIteration+0x16e)[0x4144ce]
> /usr/local/lib64/R/bin/exec/R(tan+0x30f0)[0x4147c8]
> /usr/local/lib64/R/bin/exec/R(run_Rmainloop+0x40)[0x414a90]
> /usr/local/lib64/R/bin/exec/R(main+0x18)[0x412578]
> /lib64/libc.so.6(__libc_start_main+0xf4)[0x36c0a1d8b4]
> /usr/local/lib64/R/bin/exec/R(sinh+0x61)[0x412479]
> ======= Memory map: ========
> 00400000-0065c000 r-xp 00000000 68:02 9428372
/usr/local/lib64/R/bin/exec/R
> 0085c000-0086b000 rw-p 0025c000 68:02 9428372
/usr/local/lib64/R/bin/exec/R
> 0086b000-00902000 rw-p 0086b000 00:00 0
> 00eaa000-267cf000 rw-p 00eaa000 00:00 0
> 36a4000000-36a4035000 r-xp 00000000 68:02 6580119
/usr/lib64/libreadline.so.5.1
> 36a4035000-36a4234000 ---p 00035000 68:02 6580119
/usr/lib64/libreadline.so.5.1
> 36a4234000-36a423c000 rw-p 00034000 68:02 6580119
/usr/lib64/libreadline.so.5.1
> 36a423c000-36a423d000 rw-p 36a423c000 00:00 0
> 36a8000000-36a804f000 r-xp 00000000 68:02 6580023
/usr/lib64/libncurses.so.5.5
> 36a804f000-36a824e000 ---p 0004f000 68:02 6580023
/usr/lib64/libncurses.so.5.5
> 36a824e000-36a825c000 rw-p 0004e000 68:02 6580023
/usr/lib64/libncurses.so.5.5
> 36a825c000-36a825d000 rw-p 36a825c000 00:00 0
> 36c0600000-36c061a000 r-xp 00000000 68:02 1735295
/lib64/ld-2.5.so
> 36c081a000-36c081b000 r--p 0001a000 68:02 1735295
/lib64/ld-2.5.so
> 36c081b000-36c081c000 rw-p 0001b000 68:02 1735295
/lib64/ld-2.5.so
> 36c0a00000-36c0b4a000 r-xp 00000000 68:02 1735296
/lib64/libc-2.5.so
> 36c0b4a000-36c0d49000 ---p 0014a000 68:02 1735296
/lib64/libc-2.5.so
> 36c0d49000-36c0d4d000 r--p 00149000 68:02 1735296
/lib64/libc-2.5.so
> 36c0d4d000-36c0d4e000 rw-p 0014d000 68:02 1735296
/lib64/libc-2.5.so
> 36c0d4e000-36c0d53000 rw-p 36c0d4e000 00:00 0
> 36c0e00000-36c0e02000 r-xp 00000000 68:02 1735298
/lib64/libdl-2.5.so
> 36c0e02000-36c1002000 ---p 00002000 68:02 1735298
/lib64/libdl-2.5.so
> 36c1002000-36c1003000 r--p 00002000 68:02 1735298
/lib64/libdl-2.5.so
> 36c1003000-36c1004000 rw-p 00003000 68:02 1735298
/lib64/libdl-2.5.so
> 36c1200000-36c1282000 r-xp 00000000 68:02 1735306
/lib64/libm-2.5.so
> 36c1282000-36c1481000 ---p 00082000 68:02 1735306
/lib64/libm-2.5.so
> 36c1481000-36c1482000 r--p 00081000 68:02 1735306
/lib64/libm-2.5.so
> 36c1482000-36c1483000 rw-p 00082000 68:02 1735306
/lib64/libm-2.5.so
> 36c1600000-36c1615000 r-xp 00000000 68:02 1735297
/lib64/libpthread-2.5.so
> 36c1615000-36c1814000 ---p 00015000 68:02 1735297
/lib64/libpthread-2.5.so
> 36c1814000-36c1815000 r--p 00014000 68:02 1735297
/lib64/libpthread-2.5.so
> 36c1815000-36c1816000 rw-p 00015000 68:02 1735297
/lib64/libpthread-2.5.so
> 36c1816000-36c181a000 rw-p 36c1816000 00:00 0
> 36c1a00000-36c1a14000 r-xp 00000000 68:02 7405522
/usr/lib64/libz.so.1.2.3
> 36c1a14000-36c1c13000 ---p 00014000 68:02 7405522
/usr/lib64/libz.so.1.2.3
> 36c1c13000-36c1c14000 rw-p 00013000 68:02 7405522
/usr/lib64/libz.so.1.2.3
> 36c5e00000-36c5e0d000 r-xp 00000000 68:02 1735307
/lib64/libgcc_s-4.1.2-20080102.so.1
> 36c5e0d000-36c600d000 ---p 0000d000 68:02 1735307
/lib64/libgcc_s-4.1.2-20080102.so.1
> 36c600d000-36c600e000 rw-p 0000d000 68:02 1735307
/lib64/libgcc_s-4.1.2-20080102.so.1
> 2b954c2f8000-2b954c2fa000 rw-p 2b954c2f8000 00:00 0
> 2b954c2fa000-2b954c326000 r-xp 00000000 68:02 9428369
/usr/local/lib64/R/lib/libRblas.so
> 2b954c326000-2b954c525000 ---p 0002c000 68:02 9428369
/usr/local/lib64/R/lib/libRblas.so
> 2b954c525000-2b954c526000 rw-p 0002b000 68:02 9428369
/usr/local/lib64/R/lib/libRblas.so
> 2b954c54b000-2b954c5e1000 r-xp 00000000 68:02 7422570
/usr/lib64/libgfortran.so.1.0.0
> 2b954c5e1000-2b954c7e0000 ---p 00096000 68:02 7422570
/usr/lib64/libgfortran.so.1.0.0
> 2b954c7e0000-2b954c7e2000 rw-p 00095000 68:02 7422570
/usr/lib64/libgfortran.so.1.0.0
> 2b954c7e2000-2b954c7e5000 rw-p 2b954c7e2000 00:00 0
> 2b954c7e5000-2b954fdb7000 r--p 00000000 68:02 7404270
/usr/lib/locale/locale-archive
> 2b954fdb7000-2b954fe9c000 rw-p 2b954fdb7000 00:00 0
> 2b954fe9e000-2b954fee2000 rw-p 2b954fe9e000 00:00 0
> 2b954fee2000-2b954fee9000 r--s 00000000 68:02 7404775
/usr/lib64/gconv/gconv-modules.cache
> 2b954ff0e000-2b954ff18000 r-xp 00000000 68:02 1735036
/lib64/libnss_files-2.5.so
> 2b954ff18000-2b9550117000 ---p 0000a000 68:02 1735036
/lib64/libnss_files-2.5.so
> 2b9550117000-2b9550118000 r--p 00009000 68:02 1735036
/lib64/libnss_files-2.5.so
> 2b9550118000-2b9550119000 rw-p 0000a000 68:02 1735036
/lib64/libnss_files-2.5.so
> 2b9550119000-2b9550143000 rw-p 2b9550119000 00:00 0
> 2b9550143000-2b9550149000 r-xp 00000000 68:02 9430370
/usr/local/lib64/R/library/methods/libs/methods.so
> 2b9550149000-2b9550348000 ---p 00006000 68:02 9430370
/usr/local/lib64/R/library/methods/libs/methods.so
> 2b9550348000-2b9550349000 rw-p 00005000 68:02 9430370
/usr/local/lib64/R/library/methods/libs/methods.so
> 2b955034a000-2b95503aa000 rw-p 2b955034a000 00:00 0
> 2b95503aa000-2b95503ab000 r--p 00000000 68:02 9463067
/usr/local/lib64/R/share/locale/en/LC_MESSAGES/R.mo
> 2b95503ab000-2b95503ac000 r-xp 00000000 68:02 7404712
/usr/lib64/gconv/ISO8859-1.so
> 2b95503ac000-2b95505ac000 ---p 00001000 68:02 7404712
/usr/lib64/gconv/ISO8859-1.so
> 2b95505ac000-2b95505ae000 rw-p 00001000 68:02 7404712
/usr/lib64/gconv/ISO8859-1.so
> 2b95505ae000-2b95505ca000 r-xp 00000000 68:02 9433566
/usr/local/lib64/R/library/grDevices/libs/grDevices.so
> 2b95505ca000-2b95507ca000 ---p 0001c000 68:02 9433566
/usr/local/lib64/R/library/grDevices/libs/grDevices.so
> 2b95507ca000-2b95507cb000 rw-p 0001c000 68:02 9433566
/usr/local/lib64/R/library/grDevices/libs/grDevices.so
> 2b95507cb000-2b955082c000 r-xp 00000000 68:02 9460776
/usr/local/lib64/R/library/stats/libs/stats.so
> 2b955082c000-2b9550a2b000 ---p 00061000 68:02 9460776
/usr/local/lib64/R/library/stats/libs/stats.so
> 2b9550a2b000-2b9550a2e000 rw-p 00060000 68:02 9460776
/usr/local/lib64/R/library/stats/libs/stats.so
> 2b9550a2e000-2b9550a31000 r-xp 00000000 68:02 9432206
/usr/local/lib64/R/library/tools/libs/tools.so
> 2b9550a31000-2b9550c30000 ---p 00003000 68:02 9432206
/usr/local/lib64/R/library/tools/libs/tools.so
> 2b9550c30000-2b9550c31000 rw-p 00002000 68:02 9432206
/usr/local/lib64/R/library/tools/libs/tools.so
> 2b9550c31000-2b9550c36000 r-xp 00000000 68:05 5538407
/home/askewes/R/x86_64-unknown-linux-gnu-library/2.7/Biobase/libs/Biobase.so
> 2b9550c36000-2b9550e35000 ---p 00005000 68:05 5538407
/home/askewes/R/x86_64-unknown-linux-gnu-library/2.7/Biobase/libs/Biobase.so
> 2b9550e35000-2b9550e36000 rw-p 00004000 68:05 5538407
/home/askewes/R/x86_64-unknown-linux-gnu-library/2.7/Biobase/libs/Biobase.so
> 2b9550e36000-2b9550e5d000 r-xp 00000000 68:05 5539021
/home/askewes/R/x86_64-unknown-linux-gnu-library/2.7/affyio/libs/affyio.so
> 2b9550e5d000-2b955105c000 ---p 00027000 68:05 5539021
/home/askewes/R/x86_64-unknown-linux-gnu-library/2.7/affyio/libs/affyio.so
> 2b955105c000-2b955105d000 rw-p 00026000 68:05 5539021
/home/askewes/R/x86_64-unknown-linux-gnu-library/2.7/affyio/libs/affyio.so
> 2b955105d000-2b955107d000 r-xp 00000000 68:05 5538942
/home/askewes/R/x86_64-unknown-linux-gnu-library/2.7/preprocessCore/libs/pre
processCore.so
> 2b955107d000-2b955127d000 ---p 00020000 68:05 5538942
/home/askewes/R/x86_64-unknown-linux-gnu-library/2.7/preprocessCore/libs/pre
processCore.so
> 2b955127d000-2b955127e000 rw-p 00020000 68:05 5538942
/home/askewes/R/x86_64-unknown-linux-gnu-library/2.7/preprocessCore/libs/pre
processCore.so
> 2b955127e000-2b95513e4000 r-xp 00000000 68:02 9428377
/usr/local/lib64/R/lib/libRlapack.so
> 2b95513e4000-2b95515e3000 ---p 00166000 68:02 9428377
/usr/local/lib64/R/lib/libRlapack.so
> 2b95515e3000-2b95515e5000 rw-p 00165000 68:02 9428377
/usr/local/lib64/R/lib/libRlapack.so
> 2b95515e5000-2b9551660000 rw-p 2b95515e5000 00:00 0
> 2b9551660000-2b9551668000 r-xp 00000000 68:05 5539060
/home/askewes/R/x86_64-unknown-linux-gnu-library/2.7/affy/libs/affy.so
> 2b9551668000-2b9551868000 ---p 00008000 68:05 5539060
/home/askewes/R/x86_64-unknown-linux-gnu-library/2.7/affy/libs/affy.so
> 2b9551868000-2b9551869000 rw-p 00008000 68:05 5539060
/home/askewes/R/x86_64-unknown-linux-gnu-library/2.7/affy/libs/affy.so
> 2b9551869000-2b955186c000 r-xp 00000000 68:05 5570789
/home/askewes/R/x86_64-unknown-linux-gnu-library/2.7/makecdfenv/libs/makecdf
env.so
> 2b955186c000-2b9551a6b000 ---p 00003000 68:05 5570789
/home/askewes/R/x86_64-unknown-linux-gnu-library/2.7/makecdfenv/libs/makecdf
env.so
> 2b9551a6b000-2b9551a6c000 rw-p 00002000 68:05 5570789
/home/askewes/R/x86_64-unknown-linux-gnu-library/2.7/makecdfenv/libs/makecdf
env.so
> 2b9551a6c000-2b9551a6d000 rw-p 2b9551a6c000 00:00 0
> 2b9551a6e000-2b9558618000 rw-p 2b9551a6e000 00:00 0
> 2b955c000000-2b955c021000 rw-p 2b955c000000 00:00 0
> 2b955c021000-2b9560000000 ---p 2b955c021000 00:00 0
> 7fff5e795000-7fff5e7b2000 rw-p 7fff5e795000 00:00 0
[stack]
> ffffffffff600000-ffffffffffe00000 ---p 00000000 00:00 0
[vdso]
> Aborted
> 
> 
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James W. MacDonald, M.S.
Biostatistician
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