Back to Multiple platform build/check report for BioC 3.9 |
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This page was generated on 2019-04-09 12:01:36 -0400 (Tue, 09 Apr 2019).
Package 1293/1703 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
Rbowtie 1.23.3 Michael Stadler
| malbec2 | Linux (Ubuntu 18.04.2 LTS) / x86_64 | OK | OK | OK | |||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |||||||
celaya2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |||||||
merida2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK |
Package: Rbowtie |
Version: 1.23.3 |
Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:Rbowtie.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Rbowtie_1.23.3.tar.gz |
StartedAt: 2019-04-09 05:15:22 -0400 (Tue, 09 Apr 2019) |
EndedAt: 2019-04-09 05:16:02 -0400 (Tue, 09 Apr 2019) |
EllapsedTime: 39.2 seconds |
RetCode: 0 |
Status: OK |
CheckDir: Rbowtie.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe --arch x64 CMD check --no-multiarch --install=check:Rbowtie.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings Rbowtie_1.23.3.tar.gz ### ############################################################################## ############################################################################## * using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/Rbowtie.Rcheck' * using R Under development (unstable) (2019-03-09 r76216) * using platform: x86_64-w64-mingw32 (64-bit) * using session charset: ISO8859-1 * using option '--no-vignettes' * checking for file 'Rbowtie/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'Rbowtie' version '1.23.3' * 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 'Rbowtie' can be installed ... OK * checking installed package size ... NOTE installed size is 15.0Mb * checking package directory ... OK * checking 'build' directory ... OK * checking DESCRIPTION meta-information ... OK * 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 * 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 ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * 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 C/C++/Fortran sources/headers ... OK * checking line endings in Makefiles ... OK * checking for GNU extensions in Makefiles ... NOTE GNU make is a SystemRequirements. * checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK * checking include directives in Makefiles ... OK * checking compiled code ... OK * checking files in 'vignettes' ... OK * checking examples ... OK Examples with CPU or elapsed time > 5s user system elapsed SpliceMap 0.05 0.06 8.77 * 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: 2 NOTEs See 'C:/Users/biocbuild/bbs-3.9-bioc/meat/Rbowtie.Rcheck/00check.log' for details.
Rbowtie.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch Rbowtie ### ############################################################################## ############################################################################## * installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library' * installing *source* package 'Rbowtie' ... ** libs running 'src/Makefile.win' ... C:/Rtools/mingw_64/bin//g++ -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64 -static-libgcc -static-libstdc++ -DPOPCNT_CAPABILITY \"" -static-libgcc -static-libstdc++ -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`R CMD config CXX -v 2>&1 | grep \" version \"`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DNDEBUG -Wall -Wno-unused-parameter -Wno-reorder -Wno-unused-local-typedefs \ -isystem ./SeqAn-1.1 -I third_party -I third_party \ -o bowtie-build-s ebwt_build.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp bowtie_build_main.cpp \ -lz In file included from ebwt.h:31:0, from ebwt_build.cpp:11: hit.h: In member function 'void HitSink::maybeFlush(size_t)': hit.h:580:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(ptCounts_[threadId] >= perThreadBufSize_) { ^ In file included from ebwt.h:39:0, from ebwt_build.cpp:11: reference.h: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const': reference.h:534:13: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^ In file included from ebwt.h:27:0, from ebwt_build.cpp:11: blockwise_sa.h: In instantiation of 'TIndexOffU KarkkainenBlockwiseSA<TStr>::nextSuffix() [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Alloc<void> >; TIndexOffU = unsigned int]': ebwt_build.cpp:673:1: required from here blockwise_sa.h:305:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for (int i = 0; i < length(_sampleSuffs) + 1; i++) { ^ blockwise_sa.h: In instantiation of 'TIndexOffU KarkkainenBlockwiseSA<TStr>::nextSuffix() [with TStr = seqan::String<seqan::SimpleType<unsigned char, seqan::_Dna>, seqan::Packed<> >; TIndexOffU = unsigned int]': ebwt_build.cpp:673:1: required from here blockwise_sa.h:305:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] C:/Rtools/mingw_64/bin//g++ -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64 -static-libgcc -static-libstdc++ -DPOPCNT_CAPABILITY \"" -static-libgcc -static-libstdc++ -DPOPCNT_CAPABILITY \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`R CMD config CXX -v 2>&1 | grep \" version \"`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DNDEBUG -Wall -Wno-unused-parameter -Wno-reorder -Wno-unused-local-typedefs \ -isystem ./SeqAn-1.1 -I third_party -I third_party \ -o bowtie-align-s ebwt_search.cpp \ ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp sam.cpp color.cpp color_dec.cpp hit.cpp bowtie_main.cpp \ -lz In file included from ebwt.h:31:0, from ebwt_search.cpp:21: hit.h: In member function 'void HitSink::maybeFlush(size_t)': hit.h:580:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(ptCounts_[threadId] >= perThreadBufSize_) { ^ In file included from ebwt.h:39:0, from ebwt_search.cpp:21: reference.h: In member function 'int BitPairReference::getStretch(uint32_t*, size_t, size_t, size_t) const': reference.h:534:13: warning: variable 'origBufOff' set but not used [-Wunused-but-set-variable] uint64_t origBufOff = bufOff; ^ pat.cpp: In member function 'std::pair<bool, bool> PatternSourcePerThread::nextReadPair()': pat.cpp:109:36: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] bool this_is_last = buf_.cur_buf_ == last_batch_size_-1; ^ pat.cpp: In member function 'virtual bool FastaPatternSource::parse(Read&, Read&, TReadId) const': pat.cpp:711:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(size_t i = 0; i < seqoff - trim3; i++) { ^ pat.cpp: In member function 'virtual bool FastaContinuousPatternSource::parse(Read&, Read&, TReadId) const': pat.cpp:888:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] for(size_t i = 0; i < seqoff; i++) { ^ In file included from ebwt_search_util.h:9:0, from ebwt_search_util.cpp:1: hit.h: In member function 'void HitSink::maybeFlush(size_t)': hit.h:580:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(ptCounts_[threadId] >= perThreadBufSize_) { ^ In file included from sam.cpp:12:0: hit.h: In member function 'void HitSink::maybeFlush(size_t)': hit.h:580:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(ptCounts_[threadId] >= perThreadBufSize_) { ^ In file included from hit.cpp:1:0: hit.h: In member function 'void HitSink::maybeFlush(size_t)': hit.h:580:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(ptCounts_[threadId] >= perThreadBufSize_) { ^ mkdir -p ../inst cp bowtie-align-s ../inst/bowtie cp bowtie-build-s ../inst/bowtie-build cd SpliceMap; \ make -f Makefile.win; \ echo "MAKE of SpliceMap DONE" `"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXX` `"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXXFLAGS` -c SpliceMap_utils_QuasR.cpp -static-libgcc `"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXX` `"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXXFLAGS` -c params.cpp -static-libgcc `"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXX` `"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXXFLAGS` -c cfgfile.cpp -static-libgcc `"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXX` `"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXXFLAGS` -o runSpliceMap_QuasR SpliceMap_utils_QuasR.o cfgfile.o runSpliceMap_QuasR.cpp params.o -static-libgcc runSpliceMap_QuasR.cpp: In function 'int main(int, char* const*)': runSpliceMap_QuasR.cpp:537:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (line.length() > head_clip_length) { ^ runSpliceMap_QuasR.cpp:595:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (line.length() > head_clip_length) { ^ runSpliceMap_QuasR.cpp:716:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (line.length() > head_clip_length) { ^ runSpliceMap_QuasR.cpp:841:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (line.length() > head_clip_length) { ^ runSpliceMap_QuasR.cpp: In function 'void processbowtie(std::string&, std::string&)': runSpliceMap_QuasR.cpp:1327:9: warning: variable 'min_mismatch' set but not used [-Wunused-but-set-variable] int min_mismatch; ^ `"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXX` `"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXXFLAGS` -o sortsam sortsam.cpp SpliceMap_utils_QuasR.o params.o -static-libgcc sortsam.cpp: In function 'int main(int, char* const*)': sortsam.cpp:189:13: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (nmloc == string::npos) { // unaligned, no NM tag ^ sortsam.cpp:194:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (nmloc2 == string::npos) { ^ sortsam.cpp:231:14: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (nmloc == string::npos) { // unaligned, no NM tag ^ sortsam.cpp:236:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if (nmloc2 == string::npos) { ^ `"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXX` `"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXXFLAGS` -o amalgamateSAM amalgamateSAM.cpp SpliceMap_utils_QuasR.o params.o -static-libgcc amalgamateSAM.cpp: In function 'int extractId(const string&)': amalgamateSAM.cpp:19:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(start_pos != string::npos && end_pos != string::npos) ^ amalgamateSAM.cpp:19:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(start_pos != string::npos && end_pos != string::npos) ^ amalgamateSAM.cpp: In function 'void update_jun_coverage(std::map<std::basic_string<char>, std::map<int, std::map<int, jun_store_ij> > >&, std::string, bool)': amalgamateSAM.cpp:695:17: warning: variable 'front_clip' set but not used [-Wunused-but-set-variable] uint_fast32_t front_clip = 0; ^ `"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXX` `"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXXFLAGS` -o getSpliceMapUnmapped getSpliceMapUnmapped.cpp -static-libgcc getSpliceMapUnmapped.cpp: In function 'int extractNextId(const string&)': getSpliceMapUnmapped.cpp:88:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(start_pos != string::npos && end_pos != string::npos) ^ getSpliceMapUnmapped.cpp:88:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare] if(start_pos != string::npos && end_pos != string::npos) ^ `"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXX` `"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXXFLAGS` -o fuseReorder fuseReorder.cpp -static-libgcc `"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXX` `"C:/Users/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXXFLAGS` -o SpliceMap main.cpp SpliceMap_utils_QuasR.o params.o cfgfile.o -static-libgcc MAKE of SpliceMap DONE mkdir -p ../inst cp SpliceMap/SpliceMap ../inst/SpliceMap cp SpliceMap/amalgamateSAM ../inst/amalgamateSAM cp SpliceMap/getSpliceMapUnmapped ../inst/getSpliceMapUnmapped cp SpliceMap/fuseReorder ../inst/fuseReorder cp SpliceMap/runSpliceMap_QuasR ../inst/runSpliceMap_QuasR cp SpliceMap/sortsam ../inst/sortsam ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'Rbowtie' finding HTML links ... done Rbowtie-package html Rbowtie html SpliceMap html ** 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 (Rbowtie) Making 'packages.html' ... done
Rbowtie.Rcheck/Rbowtie-Ex.timings
name | user | system | elapsed | |
Rbowtie-package | 0 | 0 | 0 | |
Rbowtie | 0.00 | 0.09 | 2.81 | |
SpliceMap | 0.05 | 0.06 | 8.77 | |