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 'E:/biocbld/bbs-2.9-bioc/meat/rGADEM.Rcheck'
* using R version 2.14.0 Under development (unstable) (2011-06-03 r56036)
* using platform: i386-pc-mingw32 (32-bit)
* using session charset: ISO8859-1
* 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 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 ... WARNING
Found the following significant warnings:
Warning: Using XStringViews() on a character vector is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK
WARNING: There was 1 warning, see
'E:/biocbld/bbs-2.9-bioc/meat/rGADEM.Rcheck/00check.log'
for details
* installing *source* package 'rGADEM' ...
configure.win...
** libs
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -O3 -Wall -std=gnu99 -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 -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -O3 -Wall -std=gnu99 -c align_sites.c -o align_sites.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -O3 -Wall -std=gnu99 -c alloc.c -o alloc.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -O3 -Wall -std=gnu99 -c background.c -o background.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -O3 -Wall -std=gnu99 -c base_frequency.c -o base_frequency.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -O3 -Wall -std=gnu99 -c check_convergence.c -o check_convergence.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -O3 -Wall -std=gnu99 -c check_pwm_dist.c -o check_pwm_dist.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -O3 -Wall -std=gnu99 -c consensus.c -o consensus.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -O3 -Wall -std=gnu99 -c construct_pwm.c -o construct_pwm.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -O3 -Wall -std=gnu99 -c copy_pwm.c -o copy_pwm.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -O3 -Wall -std=gnu99 -c crossover.c -o crossover.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -O3 -Wall -std=gnu99 -c effect_seq_len.c -o effect_seq_len.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -O3 -Wall -std=gnu99 -c evalue_meme.c -o evalue_meme.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -O3 -Wall -std=gnu99 -c extend_alignment.c -o extend_alignment.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -O3 -Wall -std=gnu99 -c initial_population.c -o initial_population.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -O3 -Wall -std=gnu99 -c mask_sites.c -o mask_sites.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -O3 -Wall -std=gnu99 -c mutation.c -o mutation.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -O3 -Wall -std=gnu99 -c normalization.c -o normalization.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -O3 -Wall -std=gnu99 -c output.c -o output.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -O3 -Wall -std=gnu99 -c pwm_score_distr.c -o pwm_score_distr.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -O3 -Wall -std=gnu99 -c read_matrix.c -o read_matrix.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -O3 -Wall -std=gnu99 -c read_pwm0.c -o read_pwm0.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -O3 -Wall -std=gnu99 -c read_seq.c -o read_seq.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -O3 -Wall -std=gnu99 -c reverse_seq.c -o reverse_seq.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -O3 -Wall -std=gnu99 -c sample_wo_replacement.c -o sample_wo_replacement.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -O3 -Wall -std=gnu99 -c scan_sites.c -o scan_sites.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -O3 -Wall -std=gnu99 -c score_subsequence.c -o score_subsequence.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -O3 -Wall -std=gnu99 -c selection.c -o selection.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -O3 -Wall -std=gnu99 -c sort.c -o sort.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -O3 -Wall -std=gnu99 -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 -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -O3 -Wall -std=gnu99 -c transform_pwm.c -o transform_pwm.o
gcc -I"E:/biocbld/BBS-2˜1.9-B/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -O3 -Wall -std=gnu99 -c weights.c -o weights.o
gcc -shared -s -static-libgcc -o rGADEM.dll tmp.def 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 -lws2_32 -LE:/biocbld/BBS-2˜1.9-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-2.9-bioc/meat/rGADEM.Rcheck/rGADEM/libs/i386
** 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)