##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rGADEM.install-out.txt --library=C:\Users\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings rGADEM_2.53.0.tar.gz
###
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##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.20-bioc/meat/rGADEM.Rcheck'
* using R version 4.4.1 (2024-06-14 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'rGADEM/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rGADEM' version '2.53.0'
* 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 ... WARNING
Found the following significant warnings:
  Gadem_Analysis.c:1415:16: warning: zero-length gnu_printf format string [-Wformat-zero-length]
  evalue_meme.h:153:11: warning: zero-length gnu_printf format string [-Wformat-zero-length]
See 'C:/Users/biocbuild/bbs-3.20-bioc/meat/rGADEM.Rcheck/00install.out' for details.
* used C compiler: 'gcc.exe (GCC) 13.2.0'
* 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* 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 whether startup messages can be suppressed ... 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 use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.20-bioc/R/library/rGADEM/libs/x64/rGADEM.dll':
  Found '_exit', possibly from '_exit' (C)
  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 nor [v]sprintf. 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 sizes of PDF files under 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
       user system elapsed
GADEM 81.28   0.93   82.79
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.20-bioc/meat/rGADEM.Rcheck/00check.log'
for details.

##############################################################################
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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL rGADEM
###
##############################################################################
##############################################################################


* installing to library 'C:/Users/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'rGADEM' ...
** using staged installation
  configure.win...
** libs
using C compiler: 'gcc.exe (GCC) 13.2.0'
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c Gadem_Analysis.c -o Gadem_Analysis.o
Gadem_Analysis.c: In function 'GADEM_Analysis':
Gadem_Analysis.c:274:3: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
  274 |   for (i=0; i<numSeq; i++) aveSeqLen +=seqLen[i]; aveSeqLen /=(double)numSeq;
      |   ^~~
Gadem_Analysis.c:274:51: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
  274 |   for (i=0; i<numSeq; i++) aveSeqLen +=seqLen[i]; aveSeqLen /=(double)numSeq;
      |                                                   ^~~~~~~~~
Gadem_Analysis.c:182:59: warning: variable 'totalSitesInput' set but not used [-Wunused-but-set-variable]
  182 |   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]
  174 |   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]
  113 |   double **logepwm;                      // log(em-optimized PWM)
      |            ^~~~~~~
Gadem_Analysis.c: In function 'read_background':
Gadem_Analysis.c:1415:16: warning: zero-length gnu_printf format string [-Wformat-zero-length]
 1415 |          error("");
      |                ^~
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c align_sites.c -o align_sites.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c alloc.c -o alloc.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c background.c -o background.o
background.c: In function 'count_nucleotides':
background.c:818:10: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
  818 |          for (k=0; k<wordLen; k++) s1[k]=seq[i][j+k]; s1[k]='\0';
      |          ^~~
background.c:818:55: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
  818 |          for (k=0; k<wordLen; k++) s1[k]=seq[i][j+k]; s1[k]='\0';
      |                                                       ^~
background.c:826:10: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
  826 |          for (k=0; k<wordLen; k++) s1[k]=rseq[i][j+k]; s1[k]='\0';
      |          ^~~
background.c:826:56: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
  826 |          for (k=0; k<wordLen; k++) s1[k]=rseq[i][j+k]; s1[k]='\0';
      |                                                        ^~
background.c: In function 'll_score_backg_model':
background.c:1104:10: warning: variable 's1' set but not used [-Wunused-but-set-variable]
 1104 |    char *s1;
      |          ^~
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c base_frequency.c -o base_frequency.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c check_convergence.c -o check_convergence.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c check_pwm_dist.c -o check_pwm_dist.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c consensus.c -o consensus.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c construct_pwm.c -o construct_pwm.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c copy_pwm.c -o copy_pwm.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c crossover.c -o crossover.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c effect_seq_len.c -o effect_seq_len.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c evalue_meme.c -o evalue_meme.o
In file included from evalue_meme.c:61:
evalue_meme.c: In function 'llr_distr':
evalue_meme.h:153:11: warning: zero-length gnu_printf format string [-Wformat-zero-length]
  153 |     error("");                                                          \
      |           ^~
evalue_meme.c:155:3: note: in expansion of macro 'Resize'
  155 |   Resize(minI, N+1, int);
      |   ^~~~~~
evalue_meme.h:153:11: warning: zero-length gnu_printf format string [-Wformat-zero-length]
  153 |     error("");                                                          \
      |           ^~
evalue_meme.c:156:3: note: in expansion of macro 'Resize'
  156 |   Resize(maxI, N+1, int);
      |   ^~~~~~
evalue_meme.h:153:11: warning: zero-length gnu_printf format string [-Wformat-zero-length]
  153 |     error("");                                                          \
      |           ^~
evalue_meme.c:250:3: note: in expansion of macro 'Resize'
  250 |   Resize(prob, *range+2, double);
      |   ^~~~~~
evalue_meme.c: In function 'sum_distr':
evalue_meme.h:153:11: warning: zero-length gnu_printf format string [-Wformat-zero-length]
  153 |     error("");                                                          \
      |           ^~
evalue_meme.c:286:3: note: in expansion of macro 'Resize'
  286 |   Resize(d_sum, range+1, double);       /* space for distribution */
      |   ^~~~~~
evalue_meme.c: In function 'cdf':
evalue_meme.h:153:11: warning: zero-length gnu_printf format string [-Wformat-zero-length]
  153 |     error("");                                                          \
      |           ^~
evalue_meme.c:325:3: note: in expansion of macro 'Resize'
  325 |   Resize(cdf, r+1, double);
      |   ^~~~~~
evalue_meme.c: In function 'get_llr_pv':
evalue_meme.h:153:11: warning: zero-length gnu_printf format string [-Wformat-zero-length]
  153 |     error("");                                                          \
      |           ^~
evalue_meme.c:393:5: note: in expansion of macro 'Resize'
  393 |     Resize(distrs, N+1, DISTR);         /* create array of distributions */
      |     ^~~~~~
evalue_meme.h:153:11: warning: zero-length gnu_printf format string [-Wformat-zero-length]
  153 |     error("");                                                          \
      |           ^~
evalue_meme.c:410:5: note: in expansion of macro 'Resize'
  410 |     Resize(distrs[N].d, w+1, double *);
      |     ^~~~~~
evalue_meme.h:153:11: warning: zero-length gnu_printf format string [-Wformat-zero-length]
  153 |     error("");                                                          \
      |           ^~
evalue_meme.c:411:5: note: in expansion of macro 'Resize'
  411 |     Resize(distrs[N].cdf, w+1, double *);
      |     ^~~~~~
evalue_meme.h:153:11: warning: zero-length gnu_printf format string [-Wformat-zero-length]
  153 |     error("");                                                          \
      |           ^~
evalue_meme.c:412:5: note: in expansion of macro 'Resize'
  412 |     Resize(distrs[N].offset, w+1, int);
      |     ^~~~~~
evalue_meme.h:153:11: warning: zero-length gnu_printf format string [-Wformat-zero-length]
  153 |     error("");                                                          \
      |           ^~
evalue_meme.c:413:5: note: in expansion of macro 'Resize'
  413 |     Resize(distrs[N].range, w+1, int);
      |     ^~~~~~
evalue_meme.c: In function 'get_log_nalign':
evalue_meme.h:153:11: warning: zero-length gnu_printf format string [-Wformat-zero-length]
  153 |     error("");                                                          \
      |           ^~
evalue_meme.c:520:5: note: in expansion of macro 'Resize'
  520 |     Resize(len, nseqs, int);
      |     ^~~~~~
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c extend_alignment.c -o extend_alignment.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c initial_population.c -o initial_population.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c mask_sites.c -o mask_sites.o
mask_sites.c: In function 'mask_repetitive':
mask_sites.c:61:7: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
   61 |       for (k=0,i=id+1; i<strlen(fileName); i++,k++) maskedFileName[k]=fileName[i]; maskedFileName[k]='\0';
      |       ^~~
mask_sites.c:61:84: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
   61 |       for (k=0,i=id+1; i<strlen(fileName); i++,k++) maskedFileName[k]=fileName[i]; maskedFileName[k]='\0';
      |                                                                                    ^~~~~~~~~~~~~~
mask_sites.c:69:10: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
   69 |          for (k=0; k<klen; k++) s1[k]=seq[i][j+k]; s1[k]='\0';
      |          ^~~
mask_sites.c:69:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
   69 |          for (k=0; k<klen; k++) s1[k]=seq[i][j+k]; s1[k]='\0';
      |                                                    ^~
mask_sites.c:82:16: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
   82 |                for (k=0; k<klen; k++) s1[k]=seq[i][j+k+pos]; s1[k]='\0';
      |                ^~~
mask_sites.c:82:62: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
   82 |                for (k=0; k<klen; k++) s1[k]=seq[i][j+k+pos]; s1[k]='\0';
      |                                                              ^~
mask_sites.c:107:10: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
  107 |          for (k=0; k<klen; k++) s1[k]=seq[i][j+k]; s1[k]='\0';
      |          ^~~
mask_sites.c:107:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
  107 |          for (k=0; k<klen; k++) s1[k]=seq[i][j+k]; s1[k]='\0';
      |                                                    ^~
mask_sites.c:125:16: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
  125 |                for (k=0; k<klen; k++) s1[k]=seq[i][j+k+pos]; s1[k]='\0';
      |                ^~~
mask_sites.c:125:62: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
  125 |                for (k=0; k<klen; k++) s1[k]=seq[i][j+k+pos]; s1[k]='\0';
      |                                                              ^~
mask_sites.c:141:10: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
  141 |          for (k=0; k<klen; k++) s1[k]=seq[i][j+k]; s1[k]='\0';
      |          ^~~
mask_sites.c:141:52: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
  141 |          for (k=0; k<klen; k++) s1[k]=seq[i][j+k]; s1[k]='\0';
      |                                                    ^~
mask_sites.c:150:16: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
  150 |                for (k=0; k<klen; k++) s1[k]=seq[i][j+k+pos]; s1[k]='\0';
      |                ^~~
mask_sites.c:150:62: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
  150 |                for (k=0; k<klen; k++) s1[k]=seq[i][j+k+pos]; s1[k]='\0';
      |                                                              ^~
mask_sites.c:34:50: warning: variable 'cn' set but not used [-Wunused-but-set-variable]
   34 |    int maxNumKmer,maxKmerLen,klen,numKmer,pos,id,cn;
      |                                                  ^~
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c mutation.c -o mutation.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c normalization.c -o normalization.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c output.c -o output.o
output.c: In function 'print_bed':
output.c:11:10: warning: unused variable 'f1' [-Wunused-variable]
   11 |    FILE *f1;
      |          ^~
output.c: In function 'print_result_R':
output.c:257:10: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
  257 |          for (j=site[i].pos+pwmLen; j<min(site[i].pos+pwmLen+FLANKING_BASES,seqLen[site[i].seq]); j++)
      |          ^~~
output.c:260:25: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
  260 |                         INTEGER(SeqIden)[increment_sequence]=site[i].seq+1;
      |                         ^~~~~~~
output.c:326:27: warning: unused variable 'number' [-Wunused-variable]
  326 |                       int number = id;
      |                           ^~~~~~
output.c:324:29: warning: unused variable 'base' [-Wunused-variable]
  324 |                  const char base[] = "m";
      |                             ^~~~
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pwm_score_distr.c -o pwm_score_distr.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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]
   22 |    int checkfscanf;
      |        ^~~~~~~~~~~
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c read_pwm0.c -o read_pwm0.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c read_seq.c -o read_seq.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c reverse_seq.c -o reverse_seq.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sample_wo_replacement.c -o sample_wo_replacement.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c scan_sites.c -o scan_sites.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c score_subsequence.c -o score_subsequence.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c selection.c -o selection.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c sort.c -o sort.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c top_kmers.c -o top_kmers.o
top_kmers.c: In function 'count_k_tuples':
top_kmers.c:332:10: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
  332 |          for (k=0; k<kmerLen; k++)  s1[k]=seq[i][j+k];  s1[k]='\0';
      |          ^~~
top_kmers.c:332:57: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
  332 |          for (k=0; k<kmerLen; k++)  s1[k]=seq[i][j+k];  s1[k]='\0';
      |                                                         ^~
top_kmers.c:333:10: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
  333 |          for (k=0; k<kmerLen; k++)  s2[k]=rseq[i][seqLen[i]-kmerLen-j+k];  s2[k]='\0';
      |          ^~~
top_kmers.c:333:76: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
  333 |          for (k=0; k<kmerLen; k++)  s2[k]=rseq[i][seqLen[i]-kmerLen-j+k];  s2[k]='\0';
      |                                                                            ^~
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c transform_pwm.c -o transform_pwm.o
gcc  -I"C:/Users/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c weights.c -o weights.o
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:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LC:/Users/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.20-bioc/R/library/00LOCK-rGADEM/00new/rGADEM/libs/x64
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** 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
* DONE (rGADEM)