Michael Stadler
| Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019) |
| URL: https://git.bioconductor.org/packages/Rbowtie |
| Branch: RELEASE_3_9 |
| Last Commit: 512cdaa |
| Last Changed Date: 2019-05-02 11:53:40 -0400 (Thu, 02 May 2019) |
| Back to Multiple platform build/check report for BioC 3.9 |
|
This page was generated on 2019-10-16 12:27:22 -0400 (Wed, 16 Oct 2019).
| Package 1319/1741 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Rbowtie 1.24.0 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 | |
| Package: Rbowtie |
| Version: 1.24.0 |
| Command: rm -rf Rbowtie.buildbin-libdir && mkdir Rbowtie.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch --build --library=Rbowtie.buildbin-libdir Rbowtie_1.24.0.tar.gz |
| StartedAt: 2019-10-16 10:01:02 -0400 (Wed, 16 Oct 2019) |
| EndedAt: 2019-10-16 10:03:10 -0400 (Wed, 16 Oct 2019) |
| EllapsedTime: 127.6 seconds |
| RetCode: 0 |
| Status: OK |
| PackageFile: Rbowtie_1.24.0.zip |
| PackageFileSize: 3.845 MiB |
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### Running command:
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### rm -rf Rbowtie.buildbin-libdir && mkdir Rbowtie.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe --arch x64 CMD INSTALL --no-multiarch --build --library=Rbowtie.buildbin-libdir Rbowtie_1.24.0.tar.gz
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* installing *source* package 'Rbowtie' ...
** using staged installation
** 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::nextSuffix() [with TStr = seqan::String, seqan::Alloc >; 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::nextSuffix() [with TStr = seqan::String, 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 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::map > >&, 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
* MD5 sums
packaged installation of 'Rbowtie' as Rbowtie_1.24.0.zip
* DONE (Rbowtie)