BioC 3.5: CHECK report for rGADEM on tokay2

Package: rGADEM

Version: 2.24.0

Command: rm -rf rGADEM.buildbin-libdir rGADEM.Rcheck && mkdir rGADEM.buildbin-libdir rGADEM.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rGADEM.buildbin-libdir rGADEM_2.24.0.tar.gz >rGADEM.Rcheck\00install.out 2>&1 && cp rGADEM.Rcheck\00install.out rGADEM-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=rGADEM.buildbin-libdir --install="check:rGADEM-install.out" --force-multiarch --no-vignettes --timings rGADEM_2.24.0.tar.gz

StartedAt: 2017-08-16 02:24:08 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 02:31:50 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 462.0 seconds

RetCode: 0

Status:  OK

CheckDir: rGADEM.Rcheck

Warnings: 0

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###
### Running command:
###
###   rm -rf rGADEM.buildbin-libdir rGADEM.Rcheck && mkdir rGADEM.buildbin-libdir rGADEM.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rGADEM.buildbin-libdir rGADEM_2.24.0.tar.gz >rGADEM.Rcheck\00install.out 2>&1 && cp rGADEM.Rcheck\00install.out rGADEM-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=rGADEM.buildbin-libdir --install="check:rGADEM-install.out" --force-multiarch --no-vignettes --timings rGADEM_2.24.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/rGADEM.Rcheck'
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-w64-mingw32 (64-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 '2.24.0'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'rGADEM' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'Biostrings' 'IRanges' 'methods' 'seqLogo'
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
'library' or 'require' call to 'methods' which was already attached by Depends.
  Please remove these calls from your code.
* 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'.

readGademPWMFile: no visible global function definition for 'read.csv'
readPWMfile: no visible global function definition for 'read.table'
readTransfacFile: no visible global function definition for
  'read.table'
[,gadem-ANY-ANY-ANY: no visible binding for global variable 'ANY'
[,gadem-ANY-ANY-ANY : <anonymous>: no visible binding for global
  variable 'gadem'
plot,gadem-ANY : <anonymous>: no visible global function definition for
  'makePWM'
plot,motif-ANY: no visible global function definition for 'makePWM'
Undefined global functions or variables:
  ANY gadem makePWM read.csv read.table
Consider adding
  importFrom("utils", "read.csv", "read.table")
to your NAMESPACE file.
* 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 compilation flags in Makevars ... NOTE
Package has both 'src/Makevars.in' and 'src/Makevars'.
Installation with --no-configure' is unlikely to work.  If you intended
'src/Makevars' to be used on Windows, rename it to 'src/Makevars.win'
otherwise remove it.  If 'configure' created 'src/Makevars', you need a
'cleanup' script.
* checking for GNU extensions in Makefiles ... 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 'C:/Users/biocbuild/bbs-3.5-bioc/meat/rGADEM.buildbin-libdir/rGADEM/libs/i386/rGADEM.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
       user system elapsed
GADEM 92.73   2.26   95.04
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
       user system elapsed
GADEM 80.74   0.45   81.19
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/rGADEM.Rcheck/00check.log'
for details.

install for i386

* installing *source* package 'rGADEM' ...
  configure.win...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/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]
   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˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c align_sites.c -o align_sites.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c alloc.c -o alloc.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/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]
    char *s1; 
          ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c base_frequency.c -o base_frequency.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c check_convergence.c -o check_convergence.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c check_pwm_dist.c -o check_pwm_dist.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c consensus.c -o consensus.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c construct_pwm.c -o construct_pwm.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c copy_pwm.c -o copy_pwm.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c crossover.c -o crossover.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c effect_seq_len.c -o effect_seq_len.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c evalue_meme.c -o evalue_meme.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c extend_alignment.c -o extend_alignment.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c initial_population.c -o initial_population.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/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]
    int maxNumKmer,maxKmerLen,klen,numKmer,pos,id,cn;
                                                  ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c mutation.c -o mutation.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/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]
   if(i==20) Rprintf("score is smaller than 10e-20\n");
   ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/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]
    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˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c pwm_score_distr.c -o pwm_score_distr.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/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]
    int checkfscanf;
        ^
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c read_pwm0.c -o read_pwm0.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c read_seq.c -o read_seq.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c reverse_seq.c -o reverse_seq.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c sample_wo_replacement.c -o sample_wo_replacement.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c scan_sites.c -o scan_sites.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c score_subsequence.c -o score_subsequence.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c selection.c -o selection.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c sort.c -o sort.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c top_kmers.c -o top_kmers.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -c transform_pwm.c -o transform_pwm.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O3 -Wall  -std=gnu99 -mtune=core2 -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:/local323/lib/i386 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/rGADEM.buildbin-libdir/rGADEM/libs/i386
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'rGADEM' ...
  configure.win...
** libs
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/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]
   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˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c align_sites.c -o align_sites.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c alloc.c -o alloc.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/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]
    char *s1; 
          ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c base_frequency.c -o base_frequency.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c check_convergence.c -o check_convergence.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c check_pwm_dist.c -o check_pwm_dist.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c consensus.c -o consensus.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c construct_pwm.c -o construct_pwm.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c copy_pwm.c -o copy_pwm.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c crossover.c -o crossover.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c effect_seq_len.c -o effect_seq_len.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c evalue_meme.c -o evalue_meme.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c extend_alignment.c -o extend_alignment.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c initial_population.c -o initial_population.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/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]
    int maxNumKmer,maxKmerLen,klen,numKmer,pos,id,cn;
                                                  ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c mutation.c -o mutation.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/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]
   if(i==20) Rprintf("score is smaller than 10e-20\n");
   ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/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]
    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˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c pwm_score_distr.c -o pwm_score_distr.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/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]
    int checkfscanf;
        ^
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c read_pwm0.c -o read_pwm0.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c read_seq.c -o read_seq.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c reverse_seq.c -o reverse_seq.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c sample_wo_replacement.c -o sample_wo_replacement.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c scan_sites.c -o scan_sites.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c score_subsequence.c -o score_subsequence.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c selection.c -o selection.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c sort.c -o sort.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c top_kmers.c -o top_kmers.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -c transform_pwm.c -o transform_pwm.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/local323/include"     -O2 -Wall  -std=gnu99 -mtune=core2 -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:/local323/lib/x64 -LC:/local323/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.5-bioc/meat/rGADEM.buildbin-libdir/rGADEM/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rGADEM' as rGADEM_2.24.0.zip
* DONE (rGADEM)

name	user	system	elapsed
GADEM	92.73	2.26	95.04
align-class	0	0	0
gadem-class	0	0	0
motif-class	0	0	0
parameters-class	0	0	0
readPWMfile	0.02	0.00	0.02

name	user	system	elapsed
GADEM	80.74	0.45	81.19
align-class	0	0	0
gadem-class	0.02	0.00	0.01
motif-class	0	0	0
parameters-class	0	0	0
readPWMfile	0.01	0.00	0.02