##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL rGADEM
###
##############################################################################
##############################################################################


* installing to library 'D:/biocbuild/bbs-3.15-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

"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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]
   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'
   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]
   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:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c align_sites.c -o align_sites.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c alloc.c -o alloc.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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]
          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'
          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]
          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'
          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]
    char *s1;
          ^~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c base_frequency.c -o base_frequency.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c check_convergence.c -o check_convergence.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c check_pwm_dist.c -o check_pwm_dist.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c consensus.c -o consensus.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c construct_pwm.c -o construct_pwm.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c copy_pwm.c -o copy_pwm.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c crossover.c -o crossover.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c effect_seq_len.c -o effect_seq_len.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c evalue_meme.c -o evalue_meme.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c extend_alignment.c -o extend_alignment.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c initial_population.c -o initial_population.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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]
       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'
       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]
          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'
          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]
                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'
                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]
          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'
          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]
                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'
                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]
          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'
          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]
                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'
                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]
    int maxNumKmer,maxKmerLen,klen,numKmer,pos,id,cn;
                                                  ^~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c mutation.c -o mutation.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c normalization.c -o normalization.o
normalization.c: In function 'range':
normalization.c:124:13: warning: implicit declaration of function 'Rprintf'; did you mean 'wprintf'? [-Wimplicit-function-declaration]
   if(i==20) Rprintf("score is smaller than 10e-20\n");
             ^~~~~~~
             wprintf
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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:257:10: warning: this 'for' clause does not guard... [-Wmisleading-indentation]
          for (j=site[i].pos+pwmLen; j<min(site[i].pos+pwmLen+FLANKING_BASES,seqLen[site[i].seq]); j++)
          ^~~
output.c:260:4: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the 'for'
    INTEGER(SeqIden)[increment_sequence]=site[i].seq+1;
    ^~~~~~~
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:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c pwm_score_distr.c -o pwm_score_distr.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c read_pwm0.c -o read_pwm0.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c read_seq.c -o read_seq.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c reverse_seq.c -o reverse_seq.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c sample_wo_replacement.c -o sample_wo_replacement.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c scan_sites.c -o scan_sites.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c score_subsequence.c -o score_subsequence.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c selection.c -o selection.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c sort.c -o sort.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -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]
          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'
          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]
          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'
          for (k=0; k<kmerLen; k++)  s2[k]=rseq[i][seqLen[i]-kmerLen-j+k];  s2[k]='\0';
                                                                            ^~
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c transform_pwm.c -o transform_pwm.o
"C:/rtools40/mingw64/bin/"gcc  -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_     -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c weights.c -o weights.o
C:/rtools40/mingw64/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 -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-rGADEM/00new/rGADEM/libs/x64
** 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  
REDIRECT:topic	 Previous alias or file overwritten by alias: D:/biocbuild/bbs-3.15-bioc/R/library/00LOCK-rGADEM/00new/rGADEM/help/gadem.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
* DONE (rGADEM)
Making 'packages.html' ...Warning in packageDescription(i, lib.loc = lib, fields = "Title", encoding = "UTF-8") :
  DESCRIPTION file of package 'Motif2Site' is missing or broken
 done