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CHECK report for rGADEM on tokay1

This page was generated on 2020-04-15 12:19:06 -0400 (Wed, 15 Apr 2020).

Package 1419/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
rGADEM 2.34.1
Arnaud Droit
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/rGADEM
Branch: RELEASE_3_10
Last Commit: 803317f
Last Changed Date: 2019-12-16 09:19:31 -0400 (Mon, 16 Dec 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: rGADEM
Version: 2.34.1
Command: C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rGADEM.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings rGADEM_2.34.1.tar.gz
StartedAt: 2020-04-15 05:59:41 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 06:08:43 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 541.6 seconds
RetCode: 0
Status:  OK  
CheckDir: rGADEM.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rGADEM.install-out.txt --library=C:\Users\biocbuild\bbs-3.10-bioc\R\library --no-vignettes --timings rGADEM_2.34.1.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.10-bioc/meat/rGADEM.Rcheck'
* using R version 3.6.3 (2020-02-29)
* 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 '2.34.1'
* 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' '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.
Namespace in Imports field not imported from: 'GenomicRanges'
  All declared Imports should be used.
* 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'.

GADEM: no visible global function definition for 'seqlevels'
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 seqlevels
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 shell scripts ... 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-3.10-bioc/R/library/rGADEM/libs/i386/rGADEM.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'C:/Users/biocbuild/bbs-3.10-bioc/R/library/rGADEM/libs/x64/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 use Fortran I/O
nor system RNGs. 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
GADEM       85.6   2.29  134.19
readPWMfile  0.0   0.00   29.39
** running examples for arch 'x64' ... OK
Examples with CPU or elapsed time > 5s
      user system elapsed
GADEM 83.3    0.5    83.8
* 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-3.10-bioc/meat/rGADEM.Rcheck/00check.log'
for details.



Installation output

rGADEM.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/rGADEM_2.34.1.tar.gz && rm -rf rGADEM.buildbin-libdir && mkdir rGADEM.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rGADEM.buildbin-libdir rGADEM_2.34.1.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL rGADEM_2.34.1.zip && rm rGADEM_2.34.1.tar.gz rGADEM_2.34.1.zip
###
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  % 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   687k      0 --:--:-- --:--:-- --:--:--  704k

install for i386

* installing *source* package 'rGADEM' ...
** using staged installation
  configure.win...
** libs
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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-3~1.10-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/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:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/rGADEM.buildbin-libdir/rGADEM/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rGADEM' as rGADEM_2.34.1.zip
* DONE (rGADEM)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'rGADEM' successfully unpacked and MD5 sums checked

Tests output


Example timings

rGADEM.Rcheck/examples_i386/rGADEM-Ex.timings

nameusersystemelapsed
GADEM 85.60 2.29134.19
align-class000
gadem-class000
motif-class000
parameters-class000
readPWMfile 0.00 0.0029.39

rGADEM.Rcheck/examples_x64/rGADEM-Ex.timings

nameusersystemelapsed
GADEM83.3 0.583.8
align-class000
gadem-class000
motif-class000
parameters-class000
readPWMfile0.010.000.02