Back to Multiple platform build/check report for BioC 3.20: simplified long |
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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
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 1732/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
rGADEM 2.54.0 (landing page) Arnaud Droit
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | |||||||||
palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | WARNINGS | OK | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | |||||||||
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. |
Package: rGADEM |
Version: 2.54.0 |
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rGADEM.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings rGADEM_2.54.0.tar.gz |
StartedAt: 2024-12-20 05:13:00 -0500 (Fri, 20 Dec 2024) |
EndedAt: 2024-12-20 05:18:29 -0500 (Fri, 20 Dec 2024) |
EllapsedTime: 328.6 seconds |
RetCode: 0 |
Status: WARNINGS |
CheckDir: rGADEM.Rcheck |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:rGADEM.install-out.txt --library=F:\biocbuild\bbs-3.20-bioc\R\library --no-vignettes --timings rGADEM_2.54.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.20-bioc/meat/rGADEM.Rcheck' * using R version 4.4.2 (2024-10-31 ucrt) * using platform: x86_64-w64-mingw32 * R was compiled by gcc.exe (GCC) 13.3.0 GNU Fortran (GCC) 13.3.0 * running under: Windows Server 2022 x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'rGADEM/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'rGADEM' version '2.54.0' * 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 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 'F:/biocbuild/bbs-3.20-bioc/meat/rGADEM.Rcheck/00install.out' for details. * used C compiler: 'gcc.exe (GCC) 13.3.0' * 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 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 for x64 is not available File 'F:/biocbuild/bbs-3.20-bioc/R/library/rGADEM/libs/x64/rGADEM.dll': Found '_exit', possibly from '_exit' (C) Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran) Compiled code should not call entry points which might terminate R nor write to stdout/stderr instead of to the console, nor use Fortran I/O nor system RNGs nor [v]sprintf. The detected symbols are linked into the code but might come from libraries and not actually be called. See 'Writing portable packages' in the 'Writing R Extensions' manual. * checking sizes of PDF files under 'inst/doc' ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed GADEM 80.06 0.05 80.11 * 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 'F:/biocbuild/bbs-3.20-bioc/meat/rGADEM.Rcheck/00check.log' for details.
rGADEM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL rGADEM ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library' * installing *source* package 'rGADEM' ... ** using staged installation configure.win... ** libs using C compiler: 'gcc.exe (GCC) 13.3.0' gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -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] 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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c align_sites.c -o align_sites.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c alloc.c -o alloc.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -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] 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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c base_frequency.c -o base_frequency.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c check_convergence.c -o check_convergence.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c check_pwm_dist.c -o check_pwm_dist.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c consensus.c -o consensus.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c construct_pwm.c -o construct_pwm.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c copy_pwm.c -o copy_pwm.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c crossover.c -o crossover.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c effect_seq_len.c -o effect_seq_len.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c extend_alignment.c -o extend_alignment.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c initial_population.c -o initial_population.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -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] 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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c mutation.c -o mutation.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c normalization.c -o normalization.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -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] 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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c pwm_score_distr.c -o pwm_score_distr.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -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] 22 | int checkfscanf; | ^~~~~~~~~~~ gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_pwm0.c -o read_pwm0.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c read_seq.c -o read_seq.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c reverse_seq.c -o reverse_seq.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sample_wo_replacement.c -o sample_wo_replacement.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c scan_sites.c -o scan_sites.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c score_subsequence.c -o score_subsequence.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c selection.c -o selection.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c sort.c -o sort.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -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] 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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c transform_pwm.c -o transform_pwm.o gcc -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c weights.c -o weights.o 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:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-rGADEM/00new/rGADEM/libs/x64 ** 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 ** 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 | 80.06 | 0.05 | 80.11 | |
align-class | 0 | 0 | 0 | |
gadem-class | 0 | 0 | 0 | |
motif-class | 0 | 0 | 0 | |
parameters-class | 0 | 0 | 0 | |
readPWMfile | 0.02 | 0.00 | 0.05 | |