Package: rGADEM

Version: 2.6.0

Command: rm -rf rGADEM.buildbin-libdir && mkdir rGADEM.buildbin-libdir && D:\biocbld\bbs-2.11-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rGADEM.buildbin-libdir rGADEM_2.6.0.tar.gz >rGADEM-install.out 2>&1 && D:\biocbld\bbs-2.11-bioc\R\bin\R.exe CMD check --library=rGADEM.buildbin-libdir --install="check:rGADEM-install.out" --force-multiarch --no-vignettes --timings rGADEM_2.6.0.tar.gz && mv rGADEM.buildbin-libdir/* rGADEM.Rcheck/ && rmdir rGADEM.buildbin-libdir

StartedAt: 2013-03-25 02:50:48 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:57:16 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 388.4 seconds

RetCode: 0

Status:  OK

CheckDir: rGADEM.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.11-bioc/meat/rGADEM.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-w64-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 '2.6.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... 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 for left-over 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
* loading checks for arch 'i386'
** 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 namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** 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 namespace can be loaded with stated dependencies ... OK
** checking whether the namespace 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 ... NOTE
File 'rGADEM/R/zzz.R':
  .onLoad calls:
    require(methods)

Package startup functions should not change the search path.
See section 'Good practice' in ?.onAttach.

* 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 compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'D:/biocbld/bbs-2.11-bioc/meat/rGADEM.buildbin-libdir/rGADEM/libs/i386/rGADEM.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'putchar', possibly from 'putchar' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
File 'D:/biocbld/bbs-2.11-bioc/meat/rGADEM.buildbin-libdir/rGADEM/libs/x64/rGADEM.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
  Found 'putchar', possibly from 'putchar' (C)
  Found 'puts', possibly from 'printf' (C), 'puts' (C)

Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console.  The detected symbols
are linked into the code but might come from libraries and not actually
be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking installed files from 'inst/doc' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
        user system elapsed
GADEM 112.14   0.47  112.61
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
       user system elapsed
GADEM 101.8   0.46  102.26
* 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

NOTE: There were 2 notes.
See
  'D:/biocbld/bbs-2.11-bioc/meat/rGADEM.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'rGADEM' ...
  configure.win...
** libs
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c align_sites.c -o align_sites.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c alloc.c -o alloc.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c background.c -o background.o
background.c: In function 'll_score_backg_model':
background.c:1094:10: warning: variable 's1' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c base_frequency.c -o base_frequency.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c check_convergence.c -o check_convergence.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c check_pwm_dist.c -o check_pwm_dist.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c consensus.c -o consensus.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c construct_pwm.c -o construct_pwm.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c copy_pwm.c -o copy_pwm.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c crossover.c -o crossover.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c effect_seq_len.c -o effect_seq_len.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c evalue_meme.c -o evalue_meme.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c extend_alignment.c -o extend_alignment.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c initial_population.c -o initial_population.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c mutation.c -o mutation.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c normalization.c -o normalization.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c output.c -o output.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c pwm_score_distr.c -o pwm_score_distr.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/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:21:8: warning: variable 'checkfscanf' set but not used [-Wunused-but-set-variable]
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c read_pwm0.c -o read_pwm0.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c read_seq.c -o read_seq.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c reverse_seq.c -o reverse_seq.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c sample_wo_replacement.c -o sample_wo_replacement.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c scan_sites.c -o scan_sites.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c score_subsequence.c -o score_subsequence.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c selection.c -o selection.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c sort.c -o sort.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c top_kmers.c -o top_kmers.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c transform_pwm.c -o transform_pwm.o
gcc -m32 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/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/CRANpkg/extralibs64/local/lib/i386 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.11-/R/bin/i386 -lR
installing to D:/biocbld/bbs-2.11-bioc/meat/rGADEM.buildbin-libdir/rGADEM/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'rGADEM.Rnw' 
** testing if installed package can be loaded

install for x64

* installing *source* package 'rGADEM' ...
  configure.win...
** libs
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c align_sites.c -o align_sites.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c alloc.c -o alloc.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c background.c -o background.o
background.c: In function 'll_score_backg_model':
background.c:1094:10: warning: variable 's1' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c base_frequency.c -o base_frequency.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c check_convergence.c -o check_convergence.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c check_pwm_dist.c -o check_pwm_dist.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c consensus.c -o consensus.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c construct_pwm.c -o construct_pwm.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c copy_pwm.c -o copy_pwm.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c crossover.c -o crossover.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c effect_seq_len.c -o effect_seq_len.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c evalue_meme.c -o evalue_meme.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c extend_alignment.c -o extend_alignment.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c initial_population.c -o initial_population.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/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"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c mutation.c -o mutation.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c normalization.c -o normalization.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c output.c -o output.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c pwm_score_distr.c -o pwm_score_distr.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/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:21:8: warning: variable 'checkfscanf' set but not used [-Wunused-but-set-variable]
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c read_pwm0.c -o read_pwm0.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c read_seq.c -o read_seq.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c reverse_seq.c -o reverse_seq.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c sample_wo_replacement.c -o sample_wo_replacement.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c scan_sites.c -o scan_sites.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c score_subsequence.c -o score_subsequence.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c selection.c -o selection.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c sort.c -o sort.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c top_kmers.c -o top_kmers.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c transform_pwm.c -o transform_pwm.o
gcc -m64 -I"D:/biocbld/BBS-2˜1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"d:/RCompile/CRANpkg/extralibs64/local/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/CRANpkg/extralibs64/local/lib/x64 -Ld:/RCompile/CRANpkg/extralibs64/local/lib -LD:/biocbld/BBS-2˜1.11-/R/bin/x64 -lR
installing to D:/biocbld/bbs-2.11-bioc/meat/rGADEM.buildbin-libdir/rGADEM/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rGADEM' as rGADEM_2.6.0.zip

* DONE (rGADEM)