Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-08-27 11:47 -0400 (Tue, 27 Aug 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4703 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4440 |
lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4472 |
kjohnson3 | macOS 13.6.5 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4421 |
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4415 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 1710/2255 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
rGADEM 2.53.0 (landing page) Arnaud Droit
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | WARNINGS | ![]() | ||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kjohnson3 | macOS 13.6.5 Ventura / arm64 | OK | OK | WARNINGS | OK | ![]() | ||||||||
kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | WARNINGS | ||||||||||
To the developers/maintainers of the rGADEM package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/rGADEM.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
Package: rGADEM |
Version: 2.53.0 |
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:rGADEM.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings rGADEM_2.53.0.tar.gz |
StartedAt: 2024-08-27 08:20:43 -0000 (Tue, 27 Aug 2024) |
EndedAt: 2024-08-27 08:26:00 -0000 (Tue, 27 Aug 2024) |
EllapsedTime: 316.7 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: rGADEM.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:rGADEM.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings rGADEM_2.53.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/rGADEM.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14) GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘rGADEM/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘rGADEM’ version ‘2.53.0’ * checking package namespace information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘rGADEM’ can be installed ... WARNING Found the following significant warnings: Gadem_Analysis.c:1415:16: warning: zero-length gnu_printf format string [-Wformat-zero-length] evalue_meme.h:153:11: warning: zero-length gnu_printf format string [-Wformat-zero-length] See ‘/home/biocbuild/bbs-3.20-bioc/meat/rGADEM.Rcheck/00install.out’ for details. * used C compiler: ‘gcc (GCC) 10.3.1’ * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... NOTE Packages listed in more than one of Depends, Imports, Suggests, Enhances: ‘Biostrings’ ‘methods’ ‘seqLogo’ A package should be listed in only one of these fields. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... NOTE 'library' or 'require' call to ‘methods’ which was already attached by Depends. Please remove these calls from your code. Namespace in Imports field not imported from: ‘GenomicRanges’ All declared Imports should be used. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE File ‘rGADEM/R/zzz.R’: .onLoad calls: require(methods) Package startup functions should not change the search path. See section ‘Good practice’ in '?.onAttach'. GADEM: no visible global function definition for ‘seqlevels’ readGademPWMFile: no visible global function definition for ‘read.csv’ readPWMfile: no visible global function definition for ‘read.table’ readTransfacFile: no visible global function definition for ‘read.table’ [,gadem-ANY-ANY-ANY: no visible binding for global variable ‘ANY’ [,gadem-ANY-ANY-ANY : <anonymous>: no visible binding for global variable ‘gadem’ plot,gadem-ANY : <anonymous>: no visible global function definition for ‘makePWM’ plot,motif-ANY: no visible global function definition for ‘makePWM’ Undefined global functions or variables: ANY gadem makePWM read.csv read.table seqlevels Consider adding importFrom("utils", "read.csv", "read.table") to your NAMESPACE file. * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking line endings in shell scripts ... OK * checking line endings in C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking compilation flags in Makevars ... NOTE Package has both ‘src/Makevars.in’ and ‘src/Makevars’. Installation with --no-configure' is unlikely to work. If you intended ‘src/Makevars’ to be used on Windows, rename it to ‘src/Makevars.win’ otherwise remove it. If ‘configure’ created ‘src/Makevars’, you need a ‘cleanup’ script. * checking for GNU extensions in Makefiles ... OK * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking use of PKG_*FLAGS in Makefiles ... OK * checking compiled code ... NOTE Note: information on .o files is not available * checking files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed GADEM 65.303 0.108 34.908 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 1 WARNING, 5 NOTEs See ‘/home/biocbuild/bbs-3.20-bioc/meat/rGADEM.Rcheck/00check.log’ for details.
rGADEM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD INSTALL rGADEM ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/R/R-4.4.1/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 (GCC) 10.3.1’ gcc -I"/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c align_sites.c -o align_sites.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c alloc.c -o alloc.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -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"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c base_frequency.c -o base_frequency.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c check_convergence.c -o check_convergence.o gcc -I"/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c consensus.c -o consensus.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c construct_pwm.c -o construct_pwm.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c copy_pwm.c -o copy_pwm.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c crossover.c -o crossover.o gcc -I"/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/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/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c extend_alignment.c -o extend_alignment.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c initial_population.c -o initial_population.o gcc -I"/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c mutation.c -o mutation.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c normalization.c -o normalization.o gcc -I"/home/biocbuild/R/R-4.4.1/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:260:4: 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:326:13: warning: unused variable ‘number’ [-Wunused-variable] 326 | int number = id; | ^~~~~~ output.c:324:15: warning: unused variable ‘base’ [-Wunused-variable] 324 | const char base[] = "m"; | ^~~~ gcc -I"/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/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:22:8: warning: variable ‘checkfscanf’ set but not used [-Wunused-but-set-variable] 22 | int checkfscanf; | ^~~~~~~~~~~ gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c read_pwm0.c -o read_pwm0.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c read_seq.c -o read_seq.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c reverse_seq.c -o reverse_seq.o gcc -I"/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c scan_sites.c -o scan_sites.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c score_subsequence.c -o score_subsequence.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c selection.c -o selection.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c sort.c -o sort.o gcc -I"/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c transform_pwm.c -o transform_pwm.o gcc -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -Wall -c weights.c -o weights.o gcc -shared -L/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/lib -lR installing to /home/biocbuild/R/R-4.4.1/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)
rGADEM.Rcheck/rGADEM-Ex.timings
name | user | system | elapsed | |
GADEM | 65.303 | 0.108 | 34.908 | |
align-class | 0.001 | 0.000 | 0.001 | |
gadem-class | 0.001 | 0.000 | 0.000 | |
motif-class | 0.001 | 0.000 | 0.000 | |
parameters-class | 0.001 | 0.000 | 0.000 | |
readPWMfile | 0.009 | 0.004 | 0.013 | |