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###
### Running command:
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###   F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD INSTALL rGADEM
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* installing to library 'F:/biocbuild/bbs-3.17-bioc/R/library'
* installing *source* package 'rGADEM' ...
** using staged installation
  configure.win...
** libs
Warning: this package has a non-empty 'configure.win' file,
so building only the main architecture

using C compiler: 'gcc.exe (GCC) 12.2.0'
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -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)
      |            ^~~~~~~
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c align_sites.c -o align_sites.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c alloc.c -o alloc.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -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"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c base_frequency.c -o base_frequency.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c check_convergence.c -o check_convergence.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c check_pwm_dist.c -o check_pwm_dist.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c consensus.c -o consensus.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c construct_pwm.c -o construct_pwm.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c copy_pwm.c -o copy_pwm.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c crossover.c -o crossover.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c effect_seq_len.c -o effect_seq_len.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c evalue_meme.c -o evalue_meme.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c extend_alignment.c -o extend_alignment.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c initial_population.c -o initial_population.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -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"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c mutation.c -o mutation.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c normalization.c -o normalization.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -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"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c pwm_score_distr.c -o pwm_score_distr.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -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"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c read_pwm0.c -o read_pwm0.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c read_seq.c -o read_seq.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c reverse_seq.c -o reverse_seq.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c sample_wo_replacement.c -o sample_wo_replacement.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c scan_sites.c -o scan_sites.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c score_subsequence.c -o score_subsequence.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c selection.c -o selection.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c sort.c -o sort.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -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"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign  -c transform_pwm.c -o transform_pwm.o
gcc  -I"F:/biocbuild/bbs-3.17-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"c:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -std=gnu99 -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:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -Lc:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.17-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.17-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)