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This page was generated on 2019-04-09 11:57:49 -0400 (Tue, 09 Apr 2019).
Package 1335/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
rGADEM 2.31.0 Arnaud Droit
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: rGADEM |
Version: 2.31.0 |
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/rGADEM_2.31.0.tar.gz && rm -rf rGADEM.buildbin-libdir && mkdir rGADEM.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rGADEM.buildbin-libdir rGADEM_2.31.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL rGADEM_2.31.0.zip && rm rGADEM_2.31.0.tar.gz rGADEM_2.31.0.zip |
StartedAt: 2019-04-08 20:08:51 -0400 (Mon, 08 Apr 2019) |
EndedAt: 2019-04-08 20:10:13 -0400 (Mon, 08 Apr 2019) |
EllapsedTime: 81.6 seconds |
RetCode: 0 |
Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/rGADEM_2.31.0.tar.gz && rm -rf rGADEM.buildbin-libdir && mkdir rGADEM.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rGADEM.buildbin-libdir rGADEM_2.31.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL rGADEM_2.31.0.zip && rm rGADEM_2.31.0.tar.gz rGADEM_2.31.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 121k 100 121k 0 0 2037k 0 --:--:-- --:--:-- --:--:-- 2297k install for i386 * installing *source* package 'rGADEM' ... configure.win... ** libs C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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] int cn[4],bcn[4],*seqCn,*bseqCn,avebnsites,avebnsiteSeq,totalSitesInput; ^ Gadem_Analysis.c:174:7: warning: variable 'generationNoMotif' set but not used [-Wunused-but-set-variable] int generationNoMotif; // maximal number of GA generations in a GADEM cycle resulted in no motifs ^ Gadem_Analysis.c:113:12: warning: variable 'logepwm' set but not used [-Wunused-but-set-variable] double **logepwm; // log(em-optimized PWM) ^ C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c align_sites.c -o align_sites.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c alloc.c -o alloc.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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] char *s1; ^ C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c base_frequency.c -o base_frequency.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c check_convergence.c -o check_convergence.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c check_pwm_dist.c -o check_pwm_dist.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c consensus.c -o consensus.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c construct_pwm.c -o construct_pwm.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c copy_pwm.c -o copy_pwm.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c crossover.c -o crossover.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c effect_seq_len.c -o effect_seq_len.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c evalue_meme.c -o evalue_meme.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c extend_alignment.c -o extend_alignment.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c initial_population.c -o initial_population.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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] int maxNumKmer,maxKmerLen,klen,numKmer,pos,id,cn; ^ C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c mutation.c -o mutation.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c normalization.c -o normalization.o normalization.c: In function 'range': normalization.c:124:3: warning: implicit declaration of function 'Rprintf' [-Wimplicit-function-declaration] if(i==20) Rprintf("score is smaller than 10e-20\n"); ^ C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c output.c -o output.o output.c: In function 'print_bed': output.c:11:10: warning: unused variable 'f1' [-Wunused-variable] FILE *f1; ^ output.c: In function 'print_result_R': output.c:326:13: warning: unused variable 'number' [-Wunused-variable] int number = id; ^ output.c:324:15: warning: unused variable 'base' [-Wunused-variable] const char base[] = "m"; ^ C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c pwm_score_distr.c -o pwm_score_distr.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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] int checkfscanf; ^ C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c read_pwm0.c -o read_pwm0.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c read_seq.c -o read_seq.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c reverse_seq.c -o reverse_seq.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c sample_wo_replacement.c -o sample_wo_replacement.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c scan_sites.c -o scan_sites.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c score_subsequence.c -o score_subsequence.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c selection.c -o selection.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c sort.c -o sort.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c top_kmers.c -o top_kmers.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c transform_pwm.c -o transform_pwm.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c weights.c -o weights.o C:/Rtools/mingw_32/bin/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 -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/rGADEM.buildbin-libdir/00LOCK-rGADEM/00new/rGADEM/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'rGADEM' finding HTML links ... done GADEM html align-class html gadem-class html motif-class html parameters-class html readPWMfile html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'rGADEM' ... configure.win... ** libs C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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] int cn[4],bcn[4],*seqCn,*bseqCn,avebnsites,avebnsiteSeq,totalSitesInput; ^ Gadem_Analysis.c:174:7: warning: variable 'generationNoMotif' set but not used [-Wunused-but-set-variable] int generationNoMotif; // maximal number of GA generations in a GADEM cycle resulted in no motifs ^ Gadem_Analysis.c:113:12: warning: variable 'logepwm' set but not used [-Wunused-but-set-variable] double **logepwm; // log(em-optimized PWM) ^ C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c align_sites.c -o align_sites.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c alloc.c -o alloc.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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] char *s1; ^ C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c base_frequency.c -o base_frequency.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c check_convergence.c -o check_convergence.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c check_pwm_dist.c -o check_pwm_dist.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c consensus.c -o consensus.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c construct_pwm.c -o construct_pwm.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c copy_pwm.c -o copy_pwm.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c crossover.c -o crossover.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c effect_seq_len.c -o effect_seq_len.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c evalue_meme.c -o evalue_meme.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c extend_alignment.c -o extend_alignment.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c initial_population.c -o initial_population.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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] int maxNumKmer,maxKmerLen,klen,numKmer,pos,id,cn; ^ C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c mutation.c -o mutation.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c normalization.c -o normalization.o normalization.c: In function 'range': normalization.c:124:3: warning: implicit declaration of function 'Rprintf' [-Wimplicit-function-declaration] if(i==20) Rprintf("score is smaller than 10e-20\n"); ^ C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c output.c -o output.o output.c: In function 'print_bed': output.c:11:10: warning: unused variable 'f1' [-Wunused-variable] FILE *f1; ^ output.c: In function 'print_result_R': output.c:326:13: warning: unused variable 'number' [-Wunused-variable] int number = id; ^ output.c:324:15: warning: unused variable 'base' [-Wunused-variable] const char base[] = "m"; ^ C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c pwm_score_distr.c -o pwm_score_distr.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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] int checkfscanf; ^ C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c read_pwm0.c -o read_pwm0.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c read_seq.c -o read_seq.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c reverse_seq.c -o reverse_seq.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c sample_wo_replacement.c -o sample_wo_replacement.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c scan_sites.c -o scan_sites.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c score_subsequence.c -o score_subsequence.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c selection.c -o selection.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c sort.c -o sort.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c top_kmers.c -o top_kmers.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c transform_pwm.c -o transform_pwm.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c weights.c -o weights.o C:/Rtools/mingw_64/bin/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 -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/rGADEM.buildbin-libdir/rGADEM/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'rGADEM' as rGADEM_2.31.0.zip * DONE (rGADEM) * installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library' package 'rGADEM' successfully unpacked and MD5 sums checked