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### Running command:
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### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL rGADEM
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘rGADEM’ ...
** using staged installation
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for gcc option to support OpenMP... -fopenmp
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking dispatch/dispatch.h usability... no
checking dispatch/dispatch.h presence... no
checking for dispatch/dispatch.h... no
checking whether OpenMP will work in a package... yes
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/config.h
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -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"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c align_sites.c -o align_sites.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c alloc.c -o alloc.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c background.c -o background.o
background.c: In function ‘read_userBackgModel’:
background.c:31:7: warning: format not a string literal and no format arguments [-Wformat-security]
31 | error(fileName);
| ^~~~~
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"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c base_frequency.c -o base_frequency.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c check_convergence.c -o check_convergence.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c check_pwm_dist.c -o check_pwm_dist.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c consensus.c -o consensus.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c construct_pwm.c -o construct_pwm.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c copy_pwm.c -o copy_pwm.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c crossover.c -o crossover.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c effect_seq_len.c -o effect_seq_len.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -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"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c extend_alignment.c -o extend_alignment.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c initial_population.c -o initial_population.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -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"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c mutation.c -o mutation.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c normalization.c -o normalization.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -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"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c pwm_score_distr.c -o pwm_score_distr.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c read_matrix.c -o read_matrix.o
read_matrix.c: In function ‘read_initial_pwm’:
read_matrix.c:27:4: warning: format not a string literal and no format arguments [-Wformat-security]
27 | if (!fp) { error(fileName);}
| ^~
read_matrix.c:22:8: warning: variable ‘checkfscanf’ set but not used [-Wunused-but-set-variable]
22 | int checkfscanf;
| ^~~~~~~~~~~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c read_pwm0.c -o read_pwm0.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c read_seq.c -o read_seq.o
read_seq.c: In function ‘read_seq’:
read_seq.c:30:4: warning: format not a string literal and no format arguments [-Wformat-security]
30 | if (!fp) { error(fileName);}
| ^~
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c reverse_seq.c -o reverse_seq.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c sample_wo_replacement.c -o sample_wo_replacement.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c scan_sites.c -o scan_sites.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c score_subsequence.c -o score_subsequence.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c selection.c -o selection.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c sort.c -o sort.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -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"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c transform_pwm.c -o transform_pwm.o
gcc -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -Wall -c weights.c -o weights.o
gcc -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o rGADEM.so 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 -fopenmp -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/site-library/00LOCK-rGADEM/00new/rGADEM/libs
** 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
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rGADEM)
