rGADEM 2.36.0
Arnaud Droit
| Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020) |
| URL: https://git.bioconductor.org/packages/rGADEM |
| Branch: RELEASE_3_11 |
| Last Commit: 828a40a |
| Last Changed Date: 2020-04-27 14:21:07 -0400 (Mon, 27 Apr 2020) |
| malbec2 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | |
| machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/rGADEM_2.36.0.tar.gz && rm -rf rGADEM.buildbin-libdir && mkdir rGADEM.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rGADEM.buildbin-libdir rGADEM_2.36.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL rGADEM_2.36.0.zip && rm rGADEM_2.36.0.tar.gz rGADEM_2.36.0.zip
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install for i386
* installing *source* package 'rGADEM' ...
** using staged installation
configure.win...
** libs
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/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]
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/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c align_sites.c -o align_sites.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c alloc.c -o alloc.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/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]
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/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c base_frequency.c -o base_frequency.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c check_convergence.c -o check_convergence.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c check_pwm_dist.c -o check_pwm_dist.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c consensus.c -o consensus.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c construct_pwm.c -o construct_pwm.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c copy_pwm.c -o copy_pwm.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c crossover.c -o crossover.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c effect_seq_len.c -o effect_seq_len.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c evalue_meme.c -o evalue_meme.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c extend_alignment.c -o extend_alignment.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c initial_population.c -o initial_population.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/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]
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/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mutation.c -o mutation.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/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]
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/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c pwm_score_distr.c -o pwm_score_distr.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/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]
int checkfscanf;
^~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read_pwm0.c -o read_pwm0.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read_seq.c -o read_seq.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c reverse_seq.c -o reverse_seq.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sample_wo_replacement.c -o sample_wo_replacement.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c scan_sites.c -o scan_sites.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c score_subsequence.c -o score_subsequence.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c selection.c -o selection.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sort.c -o sort.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/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]
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/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c transform_pwm.c -o transform_pwm.o
"C:/rtools40/mingw32/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c weights.c -o weights.o
C:/rtools40/mingw32/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-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-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:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/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]
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"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c align_sites.c -o align_sites.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c alloc.c -o alloc.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/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]
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"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c base_frequency.c -o base_frequency.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c check_convergence.c -o check_convergence.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c check_pwm_dist.c -o check_pwm_dist.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c consensus.c -o consensus.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c construct_pwm.c -o construct_pwm.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c copy_pwm.c -o copy_pwm.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c crossover.c -o crossover.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c effect_seq_len.c -o effect_seq_len.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c evalue_meme.c -o evalue_meme.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c extend_alignment.c -o extend_alignment.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c initial_population.c -o initial_population.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/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]
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"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c mutation.c -o mutation.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/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]
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"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c pwm_score_distr.c -o pwm_score_distr.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/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]
int checkfscanf;
^~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read_pwm0.c -o read_pwm0.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c read_seq.c -o read_seq.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c reverse_seq.c -o reverse_seq.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sample_wo_replacement.c -o sample_wo_replacement.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c scan_sites.c -o scan_sites.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c score_subsequence.c -o score_subsequence.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c selection.c -o selection.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c sort.c -o sort.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/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]
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"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c transform_pwm.c -o transform_pwm.o
"C:/rtools40/mingw64/bin/"gcc -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -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 -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/rGADEM.buildbin-libdir/rGADEM/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rGADEM' as rGADEM_2.36.0.zip
* DONE (rGADEM)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'rGADEM' successfully unpacked and MD5 sums checked