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BioC 3.1: INSTALL report for rGADEM on moscato2

This page was generated on 2015-10-09 09:28:43 -0700 (Fri, 09 Oct 2015).

Package 813/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rGADEM 2.16.0
Arnaud Droit
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/rGADEM
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: rGADEM
Version: 2.16.0
Command: C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.1/bioc/src/contrib/rGADEM_2.16.0.tar.gz && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch rGADEM_2.16.0.tar.gz && rm rGADEM_2.16.0.tar.gz
StartedAt: 2015-10-08 18:58:08 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 18:59:31 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 83.2 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://zin2/BBS/3.1/bioc/src/contrib/rGADEM_2.16.0.tar.gz && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch rGADEM_2.16.0.tar.gz && rm rGADEM_2.16.0.tar.gz
###
##############################################################################
##############################################################################




install for i386

* installing to library 'E:/biocbld/bbs-3.1-bioc/R/library'
* installing *source* package 'rGADEM' ...
  configure.win...
** libs
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c Gadem_Analysis.c -o Gadem_Analysis.o
Gadem_Analysis.c: In function 'GADEM_Analysis':
Gadem_Analysis.c:182:59: warning: variable 'totalSitesInput' set but not used [-Wunused-but-set-variable]
Gadem_Analysis.c:174:7: warning: variable 'generationNoMotif' set but not used [-Wunused-but-set-variable]
Gadem_Analysis.c:113:12: warning: variable 'logepwm' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c align_sites.c -o align_sites.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c alloc.c -o alloc.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c background.c -o background.o
background.c: In function 'll_score_backg_model':
background.c:1104:10: warning: variable 's1' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c base_frequency.c -o base_frequency.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c check_convergence.c -o check_convergence.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c check_pwm_dist.c -o check_pwm_dist.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c consensus.c -o consensus.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c construct_pwm.c -o construct_pwm.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c copy_pwm.c -o copy_pwm.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c crossover.c -o crossover.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c effect_seq_len.c -o effect_seq_len.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c evalue_meme.c -o evalue_meme.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c extend_alignment.c -o extend_alignment.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c initial_population.c -o initial_population.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c mask_sites.c -o mask_sites.o
mask_sites.c: In function 'mask_repetitive':
mask_sites.c:34:50: warning: variable 'cn' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c mutation.c -o mutation.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c normalization.c -o normalization.o
normalization.c: In function 'range':
normalization.c:124:3: warning: implicit declaration of function 'Rprintf' [-Wimplicit-function-declaration]
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c output.c -o output.o
output.c: In function 'print_bed':
output.c:11:10: warning: unused variable 'f1' [-Wunused-variable]
output.c: In function 'print_result_R':
output.c:326:13: warning: unused variable 'number' [-Wunused-variable]
output.c:324:15: warning: unused variable 'base' [-Wunused-variable]
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c pwm_score_distr.c -o pwm_score_distr.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c read_matrix.c -o read_matrix.o
read_matrix.c: In function 'read_initial_pwm':
read_matrix.c:22:8: warning: variable 'checkfscanf' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c read_pwm0.c -o read_pwm0.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c read_seq.c -o read_seq.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c reverse_seq.c -o reverse_seq.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c sample_wo_replacement.c -o sample_wo_replacement.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c scan_sites.c -o scan_sites.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c score_subsequence.c -o score_subsequence.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c selection.c -o selection.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c sort.c -o sort.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c top_kmers.c -o top_kmers.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c transform_pwm.c -o transform_pwm.o
gcc -m32 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c weights.c -o weights.o
gcc -m32 -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:/RCompile/r-compiling/local/local320/lib/i386 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/i386 -lR
installing to E:/biocbld/bbs-3.1-bioc/R/library/rGADEM/libs/i386
** R
** inst
** preparing package for lazy loading
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
** help
*** installing help indices
** building package indices
** installing vignettes
   'rGADEM.Rnw' 
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'

install for x64

* installing to library 'E:/biocbld/bbs-3.1-bioc/R/library'
* installing *source* package 'rGADEM' ...
  configure.win...
** libs
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c Gadem_Analysis.c -o Gadem_Analysis.o
Gadem_Analysis.c: In function 'GADEM_Analysis':
Gadem_Analysis.c:182:59: warning: variable 'totalSitesInput' set but not used [-Wunused-but-set-variable]
Gadem_Analysis.c:174:7: warning: variable 'generationNoMotif' set but not used [-Wunused-but-set-variable]
Gadem_Analysis.c:113:12: warning: variable 'logepwm' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c align_sites.c -o align_sites.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c alloc.c -o alloc.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c background.c -o background.o
background.c: In function 'll_score_backg_model':
background.c:1104:10: warning: variable 's1' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c base_frequency.c -o base_frequency.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c check_convergence.c -o check_convergence.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c check_pwm_dist.c -o check_pwm_dist.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c consensus.c -o consensus.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c construct_pwm.c -o construct_pwm.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c copy_pwm.c -o copy_pwm.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c crossover.c -o crossover.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c effect_seq_len.c -o effect_seq_len.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c evalue_meme.c -o evalue_meme.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c extend_alignment.c -o extend_alignment.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c initial_population.c -o initial_population.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c mask_sites.c -o mask_sites.o
mask_sites.c: In function 'mask_repetitive':
mask_sites.c:34:50: warning: variable 'cn' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c mutation.c -o mutation.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c normalization.c -o normalization.o
normalization.c: In function 'range':
normalization.c:124:3: warning: implicit declaration of function 'Rprintf' [-Wimplicit-function-declaration]
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c output.c -o output.o
output.c: In function 'print_bed':
output.c:11:10: warning: unused variable 'f1' [-Wunused-variable]
output.c: In function 'print_result_R':
output.c:326:13: warning: unused variable 'number' [-Wunused-variable]
output.c:324:15: warning: unused variable 'base' [-Wunused-variable]
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c pwm_score_distr.c -o pwm_score_distr.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c read_matrix.c -o read_matrix.o
read_matrix.c: In function 'read_initial_pwm':
read_matrix.c:22:8: warning: variable 'checkfscanf' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c read_pwm0.c -o read_pwm0.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c read_seq.c -o read_seq.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c reverse_seq.c -o reverse_seq.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c sample_wo_replacement.c -o sample_wo_replacement.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c scan_sites.c -o scan_sites.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c score_subsequence.c -o score_subsequence.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c selection.c -o selection.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c sort.c -o sort.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c top_kmers.c -o top_kmers.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c transform_pwm.c -o transform_pwm.o
gcc -m64 -I"E:/biocbld/BBS-3˜1.1-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/r-compiling/local/local320/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c weights.c -o weights.o
gcc -m64 -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:/RCompile/r-compiling/local/local320/lib/x64 -Ld:/RCompile/r-compiling/local/local320/lib -LE:/biocbld/BBS-3˜1.1-B/R/bin/x64 -lR
installing to E:/biocbld/bbs-3.1-bioc/R/library/rGADEM/libs/x64
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
* DONE (rGADEM)