rGADEM 2.7.0
Arnaud Droit
| Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rGADEM | | Last Changed Rev: 70052 / Revision: 72575 | | Last Changed Date: 2012-10-01 15:43:56 -0700 (Mon, 01 Oct 2012) |
| george2 | Linux (Ubuntu 12.04.1 LTS) / x86_64 | OK | WARNINGS | |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | [ ERROR ] | skipped | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* checking for file ‘rGADEM/DESCRIPTION’ ... OK
* preparing ‘rGADEM’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to re-build vignettes
* creating vignettes ...sh: line 1: 31243 Aborted '/home/biocbuild/bbs-2.12-bioc/R/bin/Rscript' --vanilla --default-packages= -e "tools::buildVignettes(dir = '.')" > '/tmp/RtmpwZ9em4/xshell771f465c6a20' 2>&1
ERROR
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel
Attaching package: ‘BiocGenerics’
The following objects are masked from ‘package:parallel’:
clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB
The following object is masked from ‘package:stats’:
xtabs
The following objects are masked from ‘package:base’:
Filter, Find, Map, Position, Reduce, anyDuplicated, as.data.frame,
cbind, colnames, duplicated, eval, get, intersect, lapply, mapply,
match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
rbind, rep.int, rownames, sapply, setdiff, sort, table, tapply,
union, unique, unlist
Loading required package: IRanges
Loading required package: BSgenome
Loading required package: GenomicRanges
Loading required package: seqLogo
Loading required package: grid
*** glibc detected *** /home/biocbuild/bbs-2.12-bioc/R/bin/exec/R: realloc(): invalid old size: 0x00007f65a51bbb20 ***
======= Backtrace: =========
/lib64/libc.so.6(+0x733b6)[0x7f65bf4ca3b6]
/lib64/libc.so.6(+0x76ccc)[0x7f65bf4cdccc]
/lib64/libc.so.6(realloc+0x102)[0x7f65bf4cf452]
/tmp/RtmpwZ9em4/Rinst771f38468bc4/rGADEM/libs/rGADEM.so(get_llr_pv+0x1b5)[0x7f65b9a1ed65]
/tmp/RtmpwZ9em4/Rinst771f38468bc4/rGADEM/libs/rGADEM.so(E_value+0x133)[0x7f65b9a1f8b3]
/tmp/RtmpwZ9em4/Rinst771f38468bc4/rGADEM/libs/rGADEM.so(populationCalculation+0x47b)[0x7f65b9a11acb]
/tmp/RtmpwZ9em4/Rinst771f38468bc4/rGADEM/libs/rGADEM.so(+0x5347)[0x7f65b9a12347]
/usr/lib64/libgomp.so.1(+0x87d2)[0x7f65bf9e97d2]
/lib64/libpthread.so.0(+0x6a3f)[0x7f65bf7caa3f]
/lib64/libc.so.6(clone+0x6d)[0x7f65bf52a71d]
======= Memory map: ========
00400000-00401000 r-xp 00000000 08:03 1463916 /loc/home/biocbuild/bbs-2.12-bioc/R/bin/exec/R
00600000-00601000 r--p 00000000 08:03 1463916 /loc/home/biocbuild/bbs-2.12-bioc/R/bin/exec/R
00601000-00602000 rw-p 00001000 08:03 1463916 /loc/home/biocbuild/bbs-2.12-bioc/R/bin/exec/R
00602000-095d4000 rw-p 00000000 00:00 0 [heap]
7f659c000000-7f659c291000 rw-p 00000000 00:00 0
7f659c291000-7f65a0000000 ---p 00000000 00:00 0
7f65a4000000-7f65a5456000 rw-p 00000000 00:00 0
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7f65a831d000-7f65a8332000 r-xp 00000000 08:02 261782 /lib64/libgcc_s.so.1
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7f65a8532000-7f65a8533000 rw-p 00015000 08:02 261782 /lib64/libgcc_s.so.1
7f65a8533000-7f65a8534000 ---p 00000000 00:00 0
7f65a8534000-7f65a8d34000 rw-p 00000000 00:00 0
7f65a8d34000-7f65a8d35000 ---p 00000000 00:00 0
7f65a8d35000-7f65a9535000 rw-p 00000000 00:00 0
7f65a9535000-7f65a9536000 ---p 00000000 00:00 0
7f65a9536000-7f65b9a0d000 rw-p 00000000 00:00 0
7f65b9a0d000-7f65b9a2c000 r-xp 00000000 08:02 1186863 /tmp/RtmpwZ9em4/Rinst771f38468bc4/rGADEM/libs/rGADEM.so
7f65b9a2c000-7f65b9c2b000 ---p 0001f000 08:02 1186863 /tmp/RtmpwZ9em4/Rinst771f38468bc4/rGADEM/libs/rGADEM.so
7f65b9c2b000-7f65b9c2c000 r--p 0001e000 08:02 1186863 /tmp/RtmpwZ9em4/Rinst771f38468bc4/rGADEM/libs/rGADEM.so
7f65b9c2c000-7f65b9c2d000 rw-p 0001f000 08:02 1186863 /tmp/RtmpwZ9em4/Rinst771f38468bc4/rGADEM/libs/rGADEM.so
7f65b9c2d000-7f65b9e30000 rw-p 00000000 00:00 0
7f65b9e30000-7f65b9e4d000 r-xp 00000000 08:03 1842494 /loc/home/biocbuild/bbs-2.12-bioc/R/library/grid/libs/grid.so
7f65b9e4d000-7f65ba04d000 ---p 0001d000 08:03 1842494 /loc/home/biocbuild/bbs-2.12-bioc/R/library/grid/libs/grid.so
7f65ba04d000-7f65ba04e000 r--p 0001d000 08:03 1842494 /loc/home/biocbuild/bbs-2.12-bioc/R/library/grid/libs/grid.so
7f65ba04e000-7f65ba04f000 rw-p 0001e000 08:03 1842494 /loc/home/biocbuild/bbs-2.12-bioc/R/library/grid/libs/grid.so
7f65ba04f000-7f65ba05c000 r-xp 00000000 08:03 11167605 /loc/home/biocbuild/bbs-2.12-bioc/R/library/GenomicRanges/libs/GenomicRanges.so
7f65ba05c000-7f65ba25c000 ---p 0000d000 08:03 11167605 /loc/home/biocbuild/bbs-2.12-bioc/R/library/GenomicRanges/libs/GenomicRanges.so
7f65ba25c000-7f65ba25d000 r--p 0000d000 08:03 11167605 /loc/home/biocbuild/bbs-2.12-bioc/R/library/GenomicRanges/libs/GenomicRanges.so
7f65ba25d000-7f65ba25e000 rw-p 0000e000 08:03 11167605 /loc/home/biocbuild/bbs-2.12-bioc/R/library/GenomicRanges/libs/GenomicRanges.so
7f65ba25e000-7f65ba293000 r-xp 00000000 08:03 10905953 /loc/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/libs/Biostrings.so
7f65ba293000-7f65ba492000 ---p 00035000 08:03 10905953 /loc/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/libs/Biostrings.so
7f65ba492000-7f65ba493000 r--p 00034000 08:03 10905953 /loc/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/libs/Biostrings.so
7f65ba493000-7f65ba494000 rw-p 00035000 08:03 10905953 /loc/home/biocbuild/bbs-2.12-bioc/R/library/Biostrings/libs/Biostrings.so
7f65ba494000-7f65bcabd000 rw-p 00000000 00:00 0
7f65bcabd000-7f65bcafe000 r-xp 00000000 08:03 10905885 /loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/libs/IRanges.so
7f65bcafe000-7f65bccfd000 ---p 00041000 08:03 10905885 /loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/libs/IRanges.so
7f65bccfd000-7f65bccff000 r--p 00040000 08:03 10905885 /loc/home/biocbuild/bbs-2.12-bioc/R/library/IRanges/libs/IRanges.so
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7f65bcd00000-7f65bcebe000 rw-p 00000000 00:00 0
7f65bcebe000-7f65bcec2000 r-xp 00000000 08:03 1866663 /loc/home/biocbuild/bbs-2.12-bioc/R/library/parallel/libs/parallel.so
7f65bcec2000-7f65bd0c1000 ---p 00004000 08:03 1866663 /loc/home/biocbuild/bbs-2.12-bioc/R/library/parallel/libs/parallel.so
7f65bd0c1000-7f65bd0c2000 r--p 00003000 08:03 1866663 /loc/home/biocbuild/bbs-2.12-bioc/R/library/parallel/libs/parallel.so
7f65bd0c2000-7f65bd0c3000 rw-p 00004000 08:03 1866663 /loc/home/biocbuild/bbs-2.12-bioc/R/library/parallel/libs/parallel.so
7f65bd0c3000-7f65bd0d6000 r-xp 00000000 08:03 1730786 /loc/home/biocbuild/bbs-2.12-bioc/R/library/tools/libs/tools.so
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7f65c05f3000-7f65c05f4000 rw-p 00000000 00:00 0
7fffaea79000-7fffaeab0000 rw-p 00000000 00:00 0 [stack]
7fffaebc9000-7fffaebca000 r-xp 00000000 00:00 0 [vdso]
ffffffffff600000-ffffffffff601000 r-xp 00000000 00:00 0 [vsyscall]
==============================================================================================
input sequence file:
number of sequences and average length: 50 202.0
Use pgf method to approximate llr null distribution
parameters estimated from sequences in:
number of GA generations & population size: 5 100
PWM score p-value cutoff for binding site declaration: 2.000000e-04
ln(E-value) cutoff for motif declaration: 0.000000
number of EM steps: 40
minimal no. sites considered for a motif: 2
[a,c,g,t] frequencies in input data: 0.264031 0.235969 0.235969 0.264031
==============================================================================================
*** Running an unseeded analysis ***
GADEM cycle 1: enumerate and count k-mers... top 3 4, 5-mers: 10 26 46
Done.
Initializing GA... Done.