############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL rGADEM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘rGADEM’ ... ** this is package ‘rGADEM’ version ‘2.55.0’ ** 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-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c Gadem_Analysis.c -o Gadem_Analysis.o 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-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c align_sites.c -o align_sites.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c alloc.c -o alloc.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -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); | ^~~~~ gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c base_frequency.c -o base_frequency.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c check_convergence.c -o check_convergence.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c check_pwm_dist.c -o check_pwm_dist.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c consensus.c -o consensus.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c construct_pwm.c -o construct_pwm.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c copy_pwm.c -o copy_pwm.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c crossover.c -o crossover.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c effect_seq_len.c -o effect_seq_len.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -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-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c extend_alignment.c -o extend_alignment.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c initial_population.c -o initial_population.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c mask_sites.c -o mask_sites.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c mutation.c -o mutation.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c normalization.c -o normalization.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c output.c -o output.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c pwm_score_distr.c -o pwm_score_distr.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -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);} | ^~ gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c read_pwm0.c -o read_pwm0.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -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-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c reverse_seq.c -o reverse_seq.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c sample_wo_replacement.c -o sample_wo_replacement.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c scan_sites.c -o scan_sites.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c score_subsequence.c -o score_subsequence.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c selection.c -o selection.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c sort.c -o sort.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c top_kmers.c -o top_kmers.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c transform_pwm.c -o transform_pwm.o gcc -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fpic -g -O2 -c weights.c -o weights.o gcc -shared -L/home/biocbuild/bbs-3.21-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-3.21-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.21-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)