rGADEM 1.5.0
Arnaud Droit
| Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/rGADEM | | Last Changed Rev: 54811 / Revision: 56603 | | Last Changed Date: 2011-04-13 18:45:05 -0700 (Wed, 13 Apr 2011) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | [ ERROR ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | WARNINGS | OK |
| moscato1 | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | WARNINGS | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | WARNINGS | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/rGADEM.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-06-15 r56138)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘rGADEM/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘rGADEM’ version ‘1.5.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘rGADEM’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking examples ...sh: line 1: 10170 Segmentation fault LANGUAGE=en '/home/biocbuild/bbs-2.9-bioc/R/bin/R' --vanilla > 'rGADEM-Ex.Rout' 2>&1 < rGADEM-Ex.R
ERROR
Running examples in ‘rGADEM-Ex.R’ failed
The error most likely occurred in:
> assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: GADEM
> ### Title: Motif Analysis with rGADEM
> ### Aliases: GADEM
> ### Keywords: GADEM MOTIFS
>
> ### ** Examples
>
>
> library(BSgenome.Hsapiens.UCSC.hg18)
> pwd<-"" #INPUT FILES- BedFiles, FASTA, etc.
> path<- system.file("extdata","Test_100.bed",package="rGADEM")
> BedFile<-paste(pwd,path,sep="")
> BED<-read.table(BedFile,header=FALSE,sep="\t")
> BED<-data.frame(chr=as.factor(BED[,1]),start=as.numeric(BED[,2]),end=as.numeric(BED[,3]))
> #Create RD files
> rgBED<-IRanges(start=BED[,2],end=BED[,3])
> Sequences<-RangedData(rgBED,space=BED[,1])
>
>
> gadem<-GADEM(Sequences,verbose=1,genome=Hsapiens)
Retrieving sequences... Warning in .local(x, ...) :
Starting with BioC 2.9, the default for getSeq() 'as.character' argument
has changed from TRUE to FALSE. From now you need to specify
getSeq(..., as.character=TRUE)
if you want the result of getSeq() in a character vector.
Warning: Using XStringViews() on a character vector is deprecated.
Please use instead something like:
as(DNAStringSet(x)), "Views")
if you really want views, otherwise just:
DNAStringSet(x)
Done.
*** Start C Programm ***
Estimating background Markov models using input sequences... Done
==============================================================================================
input sequence file:
number of sequences and average length: 50 202.0
Use pgf method to approximate llr null distribution
background Markov order: 0th
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: 0.264059 0.235941 0.235941 0.264059
==============================================================================================
*** Running an unseeded analysis ***
GADEM cycle 1: enumerate and count k-mers... Done.
Initializing GA... Done.
*** caught segfault ***
address 0x4, cause 'memory not mapped'
Traceback:
1: .Call("GADEM_Analysis", sequenceFasta, Lengthfasta, accession, as.logical(verbose), numWordGroup, numTop3mer, numTop4mer, numTop5mer, numGeneration, populationSize, pValue, eValue, extTrim, minSpaceWidth, maxSpaceWidth, useChIPscore, numEM, fEM, widthWt, fullScan, userBackgModel, slideWinPWM, stopCriterion, MarkovOrder, userMarkovOrder, numBackgSets, weightType, pgf, startPWMfound, bOrder, bFileName, Spwm, minSites, fixSeeded)
2: GADEM(Sequences, verbose = 1, genome = Hsapiens)
aborting ...
*** caught segfault ***
address (nil), cause 'unknown'
Traceback:
1: .Call("GADEM_Analysis", sequenceFasta, Lengthfasta, accession, as.logical(verbose), numWordGroup, numTop3mer, numTop4mer, numTop5mer, numGeneration, populationSize, pValue, eValue, extTrim, minSpaceWidth, maxSpaceWidth, useChIPscore, numEM, fEM, widthWt, fullScan, userBackgModel, slideWinPWM, stopCriterion, MarkovOrder, userMarkovOrder, numBackgSets, weightType, pgf, startPWMfound, bOrder, bFileName, Spwm, minSites, fixSeeded)
2: GADEM(Sequences, verbose = 1, genome = Hsapiens)
aborting ...
* installing *source* package ‘rGADEM’ ...
checking for gcc... gcc -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for gcc -std=gnu99 option to support OpenMP... -fopenmp
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dispatch/dispatch.h usability... no
checking dispatch/dispatch.h presence... no
checking for dispatch/dispatch.h... no
checking whether OpenMP will work in a package... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/config.h
config.status: src/config.h is unchanged
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c Gadem_Analysis.c -o Gadem_Analysis.o
Gadem_Analysis.c: In function ‘GADEM_Analysis’:
Gadem_Analysis.c:123:7: warning: unused variable ‘nsitesEM’
Gadem_Analysis.c:109:7: warning: ‘llrDim’ may be used uninitialized in this function
Gadem_Analysis.c:112:7: warning: ‘empDim’ may be used uninitialized in this function
Gadem_Analysis.c:118:10: warning: ‘llrCutoff’ may be used uninitialized in this function
Gadem_Analysis.c:143:7: warning: ‘numTopWmerInB’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c align_sites.c -o align_sites.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c alloc.c -o alloc.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c background.c -o background.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c base_frequency.c -o base_frequency.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c check_convergence.c -o check_convergence.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c check_pwm_dist.c -o check_pwm_dist.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c consensus.c -o consensus.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c construct_pwm.c -o construct_pwm.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c copy_pwm.c -o copy_pwm.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c crossover.c -o crossover.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c effect_seq_len.c -o effect_seq_len.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c evalue_meme.c -o evalue_meme.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c extend_alignment.c -o extend_alignment.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c initial_population.c -o initial_population.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c mask_sites.c -o mask_sites.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c mutation.c -o mutation.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c normalization.c -o normalization.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c output.c -o output.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c pwm_score_distr.c -o pwm_score_distr.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c read_matrix.c -o read_matrix.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c read_pwm0.c -o read_pwm0.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c read_seq.c -o read_seq.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c reverse_seq.c -o reverse_seq.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c sample_wo_replacement.c -o sample_wo_replacement.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c scan_sites.c -o scan_sites.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c score_subsequence.c -o score_subsequence.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c selection.c -o selection.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c sort.c -o sort.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c top_kmers.c -o top_kmers.o
top_kmers.c: In function ‘top_kmer’:
top_kmers.c:154:8: warning: ‘numAvailableTopKmer’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c transform_pwm.c -o transform_pwm.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c weights.c -o weights.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o rGADEM.so Gadem_Analysis.o align_sites.o alloc.o background.o base_frequency.o check_convergence.o check_pwm_dist.o consensus.o construct_pwm.o copy_pwm.o crossover.o effect_seq_len.o evalue_meme.o extend_alignment.o initial_population.o mask_sites.o mutation.o normalization.o output.o pwm_score_distr.o read_matrix.o read_pwm0.o read_seq.o reverse_seq.o sample_wo_replacement.o scan_sites.o score_subsequence.o selection.o sort.o top_kmers.o transform_pwm.o weights.o -fopenmp -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/rGADEM.Rcheck/rGADEM/libs
** R
** inst
** preparing package for lazy loading
Loading required package: IRanges
Attaching package: ‘IRanges’
The following object(s) are masked from ‘package:base’:
Map, cbind, eval, intersect, mapply, order, paste, pmax, pmax.int,
pmin, pmin.int, rbind, rep.int, setdiff, table, union
Loading required package: GenomicRanges
Loading required package: grid
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
‘rGADEM.Rnw’
** testing if installed package can be loaded
* DONE (rGADEM)