Back to Multiple platform build/check report for BioC 3.7 |
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This page was generated on 2018-10-17 08:34:35 -0400 (Wed, 17 Oct 2018).
Package 1227/1561 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
rGADEM 2.28.0 Arnaud Droit
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: rGADEM |
Version: 2.28.0 |
Command: C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rGADEM.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings rGADEM_2.28.0.tar.gz |
StartedAt: 2018-10-17 04:22:42 -0400 (Wed, 17 Oct 2018) |
EndedAt: 2018-10-17 04:30:11 -0400 (Wed, 17 Oct 2018) |
EllapsedTime: 449.0 seconds |
RetCode: 0 |
Status: OK |
CheckDir: rGADEM.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:rGADEM.install-out.txt --library=C:\Users\biocbuild\bbs-3.7-bioc\R\library --no-vignettes --timings rGADEM_2.28.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.7-bioc/meat/rGADEM.Rcheck' * using R version 3.5.1 Patched (2018-07-24 r75005) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'rGADEM/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'rGADEM' version '2.28.0' * 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 ... OK * 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' 'IRanges' '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 R files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * loading checks for arch 'i386' ** 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 * loading checks for arch 'x64' ** 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 dependencies in R code ... NOTE 'library' or 'require' call to 'methods' which was already attached by Depends. Please remove these calls from your code. * 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'. 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 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 compiled code ... NOTE Note: information on .o files for i386 is not available Note: information on .o files for x64 is not available File 'C:/Users/biocbuild/bbs-3.7-bioc/R/library/rGADEM/libs/i386/rGADEM.dll': 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. 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 files in 'vignettes' ... OK * checking examples ... ** running examples for arch 'i386' ... OK Examples with CPU or elapsed time > 5s user system elapsed GADEM 100.64 3.54 104.23 ** running examples for arch 'x64' ... OK Examples with CPU or elapsed time > 5s user system elapsed GADEM 91.26 0.47 91.77 * checking for unstated dependencies in vignettes ... OK * checking package vignettes in 'inst/doc' ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 5 NOTEs See 'C:/Users/biocbuild/bbs-3.7-bioc/meat/rGADEM.Rcheck/00check.log' for details.
rGADEM.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/rGADEM_2.28.0.tar.gz && rm -rf rGADEM.buildbin-libdir && mkdir rGADEM.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=rGADEM.buildbin-libdir rGADEM_2.28.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL rGADEM_2.28.0.zip && rm rGADEM_2.28.0.tar.gz rGADEM_2.28.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 121k 100 121k 0 0 2089k 0 --:--:-- --:--:-- --:--:-- 2341k install for i386 * installing *source* package 'rGADEM' ... configure.win... ** libs C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c Gadem_Analysis.c -o Gadem_Analysis.o Gadem_Analysis.c: In function 'GADEM_Analysis': 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:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c align_sites.c -o align_sites.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c alloc.c -o alloc.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c background.c -o background.o 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:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c base_frequency.c -o base_frequency.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c check_convergence.c -o check_convergence.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c check_pwm_dist.c -o check_pwm_dist.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c consensus.c -o consensus.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c construct_pwm.c -o construct_pwm.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c copy_pwm.c -o copy_pwm.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c crossover.c -o crossover.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c effect_seq_len.c -o effect_seq_len.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c evalue_meme.c -o evalue_meme.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c extend_alignment.c -o extend_alignment.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c initial_population.c -o initial_population.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c mask_sites.c -o mask_sites.o mask_sites.c: In function 'mask_repetitive': 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:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c mutation.c -o mutation.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c normalization.c -o normalization.o normalization.c: In function 'range': normalization.c:124:3: warning: implicit declaration of function 'Rprintf' [-Wimplicit-function-declaration] if(i==20) Rprintf("score is smaller than 10e-20\n"); ^ C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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: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:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c pwm_score_distr.c -o pwm_score_distr.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -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:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c read_pwm0.c -o read_pwm0.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c read_seq.c -o read_seq.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c reverse_seq.c -o reverse_seq.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c sample_wo_replacement.c -o sample_wo_replacement.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c scan_sites.c -o scan_sites.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c score_subsequence.c -o score_subsequence.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c selection.c -o selection.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c sort.c -o sort.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c top_kmers.c -o top_kmers.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c transform_pwm.c -o transform_pwm.o C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=generic -c weights.c -o weights.o C:/Rtools/mingw_32/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˜1.7-B/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/rGADEM.buildbin-libdir/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 In R CMD INSTALL install for x64 * installing *source* package 'rGADEM' ... configure.win... ** libs C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c Gadem_Analysis.c -o Gadem_Analysis.o Gadem_Analysis.c: In function 'GADEM_Analysis': 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:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c align_sites.c -o align_sites.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c alloc.c -o alloc.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c background.c -o background.o 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:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c base_frequency.c -o base_frequency.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c check_convergence.c -o check_convergence.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c check_pwm_dist.c -o check_pwm_dist.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c consensus.c -o consensus.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c construct_pwm.c -o construct_pwm.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c copy_pwm.c -o copy_pwm.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c crossover.c -o crossover.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c effect_seq_len.c -o effect_seq_len.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c evalue_meme.c -o evalue_meme.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c extend_alignment.c -o extend_alignment.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c initial_population.c -o initial_population.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c mask_sites.c -o mask_sites.o mask_sites.c: In function 'mask_repetitive': 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:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c mutation.c -o mutation.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c normalization.c -o normalization.o normalization.c: In function 'range': normalization.c:124:3: warning: implicit declaration of function 'Rprintf' [-Wimplicit-function-declaration] if(i==20) Rprintf("score is smaller than 10e-20\n"); ^ C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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: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:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c pwm_score_distr.c -o pwm_score_distr.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -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:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c read_pwm0.c -o read_pwm0.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c read_seq.c -o read_seq.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c reverse_seq.c -o reverse_seq.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c sample_wo_replacement.c -o sample_wo_replacement.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c scan_sites.c -o scan_sites.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c score_subsequence.c -o score_subsequence.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c selection.c -o selection.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c sort.c -o sort.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c top_kmers.c -o top_kmers.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c transform_pwm.c -o transform_pwm.o C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG -Ifusion_sdk -D_USE_MEM_MAPPING_ -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=generic -c weights.c -o weights.o C:/Rtools/mingw_64/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˜1.7-B/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/rGADEM.buildbin-libdir/rGADEM/libs/x64 ** testing if installed package can be loaded * MD5 sums packaged installation of 'rGADEM' as rGADEM_2.28.0.zip * DONE (rGADEM) In R CMD INSTALL In R CMD INSTALL * installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library' package 'rGADEM' successfully unpacked and MD5 sums checked In R CMD INSTALL
rGADEM.Rcheck/examples_i386/rGADEM-Ex.timings
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rGADEM.Rcheck/examples_x64/rGADEM-Ex.timings
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