rGADEM 1.0.1
Arnaud Droit
| Snapshot Date: 2010-10-04 11:22:20 -0700 (Mon, 04 Oct 2010) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_6/madman/Rpacks/rGADEM | | Last Changed Rev: 48890 / Revision: 49923 | | Last Changed Date: 2010-08-19 09:15:51 -0700 (Thu, 19 Aug 2010) |
| wilson1 | Linux (openSUSE 11.1) / x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | OK | [ OK ] |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* installing *source* package 'rGADEM' ...
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WARNING: this package has a configure script
It probably needs manual configuration
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** libs
making DLL ...
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -O2 -Wall -std=gnu99 -c Gadem_Analysis.c -o Gadem_Analysis.o
Gadem_Analysis.c: In function 'GADEM_Analysis':
Gadem_Analysis.c:138: warning: unused variable 'nsitesEM'
Gadem_Analysis.c:124: warning: 'llrDim' may be used uninitialized in this function
Gadem_Analysis.c:126: warning: 'empDim' may be used uninitialized in this function
Gadem_Analysis.c:132: warning: 'llrCutoff' may be used uninitialized in this function
Gadem_Analysis.c:159: warning: 'numTopWmerInB' may be used uninitialized in this function
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -O2 -Wall -std=gnu99 -c align_sites.c -o align_sites.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -O2 -Wall -std=gnu99 -c alloc.c -o alloc.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -O2 -Wall -std=gnu99 -c background.c -o background.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -O2 -Wall -std=gnu99 -c base_frequency.c -o base_frequency.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -O2 -Wall -std=gnu99 -c check_convergence.c -o check_convergence.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -O2 -Wall -std=gnu99 -c check_pwm_dist.c -o check_pwm_dist.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -O2 -Wall -std=gnu99 -c consensus.c -o consensus.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -O2 -Wall -std=gnu99 -c construct_pwm.c -o construct_pwm.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -O2 -Wall -std=gnu99 -c copy_pwm.c -o copy_pwm.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -O2 -Wall -std=gnu99 -c crossover.c -o crossover.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -O2 -Wall -std=gnu99 -c effect_seq_len.c -o effect_seq_len.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -O2 -Wall -std=gnu99 -c evalue_meme.c -o evalue_meme.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -O2 -Wall -std=gnu99 -c extend_alignment.c -o extend_alignment.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -O2 -Wall -std=gnu99 -c initial_population.c -o initial_population.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -O2 -Wall -std=gnu99 -c mask_sites.c -o mask_sites.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -O2 -Wall -std=gnu99 -c mutation.c -o mutation.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -O2 -Wall -std=gnu99 -c normalization.c -o normalization.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -O2 -Wall -std=gnu99 -c output.c -o output.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -O2 -Wall -std=gnu99 -c pwm_score_distr.c -o pwm_score_distr.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -O2 -Wall -std=gnu99 -c read_matrix.c -o read_matrix.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -O2 -Wall -std=gnu99 -c read_pwm0.c -o read_pwm0.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -O2 -Wall -std=gnu99 -c read_seq.c -o read_seq.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -O2 -Wall -std=gnu99 -c reverse_seq.c -o reverse_seq.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -O2 -Wall -std=gnu99 -c sample_wo_replacement.c -o sample_wo_replacement.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -O2 -Wall -std=gnu99 -c scan_sites.c -o scan_sites.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -O2 -Wall -std=gnu99 -c score_subsequence.c -o score_subsequence.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -O2 -Wall -std=gnu99 -c selection.c -o selection.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -O2 -Wall -std=gnu99 -c sort.c -o sort.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -O2 -Wall -std=gnu99 -c top_kmers.c -o top_kmers.o
top_kmers.c: In function 'top_kmer':
top_kmers.c:154: warning: 'numAvailableTopKmer' may be used uninitialized in this function
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -O2 -Wall -std=gnu99 -c transform_pwm.c -o transform_pwm.o
x86_64-w64-mingw32-gcc -I"D:/biocbld/bbs-2.6-bioc/R/include" -Ifusion_sdk -D_USE_MEM_MAPPING_ -D_MSC_VER -ID:/biocbld/bbs-2.6-bioc/R/src/include -O2 -Wall -std=gnu99 -c weights.c -o weights.o
x86_64-w64-mingw32-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 -LD:/biocbld/bbs-2.6-bioc/R/bin -lR
installing to D:/biocbld/bbs-2.6-bioc/meat/rGADEM.buildbin-libdir/rGADEM/libs/x64
... done
** 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, mapply, order, paste, pmax, pmax.int, pmin, pmin.int,
rbind, rep.int, table
Loading required package: GenomicRanges
Loading required package: grid
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rGADEM' as rGADEM_1.0.1.zip
* DONE (rGADEM)