Rbowtie 1.24.0
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) |
| 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 | |
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###
### Running command:
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### /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL Rbowtie
###
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘Rbowtie’ ...
** using staged installation
** libs
** arch -
g++ -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64 -Wl,--hash-style=both -DPOPCNT_CAPABILITY -g -O2 -Wall -g -O2 -Wall \"" -Wl,--hash-style=both -DPOPCNT_CAPABILITY -g -O2 -Wall -g -O2 -Wall \
-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -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 \
-L/usr/local/lib -lz -lpthread
In file included from blockwise_sa.h:19:0,
from ebwt.h:27,
from ebwt_build.cpp:11:
diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
diff_sample.h:162:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if(!diffs[d1]) diffCnt++; diffs[d1] = true;
^~
diff_sample.h:162:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
if(!diffs[d1]) diffCnt++; diffs[d1] = true;
^~~~~
diff_sample.h:163:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if(!diffs[d2]) diffCnt++; diffs[d2] = true;
^~
diff_sample.h:163:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
if(!diffs[d2]) diffCnt++; diffs[d2] = true;
^~~~~
In file included from ebwt.h:27:0,
from ebwt_build.cpp:11:
blockwise_sa.h: In destructor ‘KarkkainenBlockwiseSA::~KarkkainenBlockwiseSA()’:
blockwise_sa.h:212:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample
^~
blockwise_sa.h:212:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample
^~~
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_build.cpp:11:0:
ebwt.h: In destructor ‘Ebwt::~Ebwt()’:
ebwt.h:825:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if(_fchr != NULL) delete[] _fchr; _fchr = NULL;
^~
ebwt.h:825:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
if(_fchr != NULL) delete[] _fchr; _fchr = NULL;
^~~~~
ebwt.h:826:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if(_ftab != NULL) delete[] _ftab; _ftab = NULL;
^~
ebwt.h:826:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
if(_ftab != NULL) delete[] _ftab; _ftab = NULL;
^~~~~
ebwt.h:827:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if(_eftab != NULL) delete[] _eftab; _eftab = NULL;
^~
ebwt.h:827:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
if(_eftab != NULL) delete[] _eftab; _eftab = NULL;
^~~~~~
ebwt.h:833:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if(_isa != NULL) delete[] _isa; _isa = NULL;
^~
ebwt.h:833:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
if(_isa != NULL) delete[] _isa; _isa = NULL;
^~~~
ebwt.h:834:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if(_plen != NULL) delete[] _plen; _plen = NULL;
^~
ebwt.h:834:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
if(_plen != NULL) delete[] _plen; _plen = NULL;
^~~~~
ebwt.h:835:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL;
^~
ebwt.h:835:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL;
^~~~~~~~
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]
g++ -O3 -m64 -DCOMPILER_OPTIONS="\"-O3 -m64 -Wl,--hash-style=both -DPOPCNT_CAPABILITY -g -O2 -Wall -g -O2 -Wall \"" -Wl,--hash-style=both -DPOPCNT_CAPABILITY -g -O2 -Wall -g -O2 -Wall \
-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"`date`\"" -DCOMPILER_VERSION="\"`g++ -v 2>&1 | tail -1`\"" -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_GNU_SOURCE -DPREFETCH_LOCALITY=2 -DBOWTIE_MM -DBOWTIE_SHARED_MEM -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 \
-L/usr/local/lib -lz -lpthread
In file included from blockwise_sa.h:19:0,
from ebwt.h:27,
from ebwt_search.cpp:21:
diff_sample.h: In function ‘void calcExhaustiveDC(T, bool, bool)’:
diff_sample.h:162:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if(!diffs[d1]) diffCnt++; diffs[d1] = true;
^~
diff_sample.h:162:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
if(!diffs[d1]) diffCnt++; diffs[d1] = true;
^~~~~
diff_sample.h:163:6: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if(!diffs[d2]) diffCnt++; diffs[d2] = true;
^~
diff_sample.h:163:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
if(!diffs[d2]) diffCnt++; diffs[d2] = true;
^~~~~
In file included from ebwt.h:27:0,
from ebwt_search.cpp:21:
blockwise_sa.h: In destructor ‘KarkkainenBlockwiseSA::~KarkkainenBlockwiseSA()’:
blockwise_sa.h:212:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample
^~
blockwise_sa.h:212:32: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
if(_dc != NULL) delete _dc; _dc = NULL; // difference cover sample
^~~
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;
^~~~~~~~~~
In file included from ebwt_search.cpp:21:0:
ebwt.h: In destructor ‘Ebwt::~Ebwt()’:
ebwt.h:825:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if(_fchr != NULL) delete[] _fchr; _fchr = NULL;
^~
ebwt.h:825:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
if(_fchr != NULL) delete[] _fchr; _fchr = NULL;
^~~~~
ebwt.h:826:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if(_ftab != NULL) delete[] _ftab; _ftab = NULL;
^~
ebwt.h:826:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
if(_ftab != NULL) delete[] _ftab; _ftab = NULL;
^~~~~
ebwt.h:827:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if(_eftab != NULL) delete[] _eftab; _eftab = NULL;
^~
ebwt.h:827:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
if(_eftab != NULL) delete[] _eftab; _eftab = NULL;
^~~~~~
ebwt.h:833:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if(_isa != NULL) delete[] _isa; _isa = NULL;
^~
ebwt.h:833:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
if(_isa != NULL) delete[] _isa; _isa = NULL;
^~~~
ebwt.h:834:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if(_plen != NULL) delete[] _plen; _plen = NULL;
^~
ebwt.h:834:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
if(_plen != NULL) delete[] _plen; _plen = NULL;
^~~~~
ebwt.h:835:4: warning: this ‘if’ clause does not guard... [-Wmisleading-indentation]
if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL;
^~
ebwt.h:835:44: note: ...this statement, but the latter is misleadingly indented as if it were guarded by the ‘if’
if(_rstarts != NULL) delete[] _rstarts; _rstarts = NULL;
^~~~~~~~
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; \
echo "MAKE of SpliceMap DONE"
make[1]: Entering directory '/home/biocbuild/bbs-3.9-bioc/meat/Rbowtie/src/SpliceMap'
`"/home/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXXFLAGS` -c SpliceMap_utils_QuasR.cpp
`"/home/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXXFLAGS` -c params.cpp
`"/home/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXXFLAGS` -c cfgfile.cpp
`"/home/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXX` `"/home/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
runSpliceMap_QuasR.cpp: In function ‘int main(int, char* const*)’:
runSpliceMap_QuasR.cpp:108:31: warning: variable ‘chr_file_list_it’ set but not used [-Wunused-but-set-variable]
vector::iterator chr_file_list_it = chr_file_list.begin();
^~~~~~~~~~~~~~~~
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::__cxx11::string&, std::__cxx11::string&)’:
runSpliceMap_QuasR.cpp:1327:9: warning: variable ‘min_mismatch’ set but not used [-Wunused-but-set-variable]
int min_mismatch;
^~~~~~~~~~~~
`"/home/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXXFLAGS` -o sortsam sortsam.cpp SpliceMap_utils_QuasR.o params.o
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) {
~~~~~~~^~~~~~~~~
`"/home/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXXFLAGS` -o amalgamateSAM amalgamateSAM.cpp SpliceMap_utils_QuasR.o params.o
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::__cxx11::string, bool)’:
amalgamateSAM.cpp:695:17: warning: variable ‘front_clip’ set but not used [-Wunused-but-set-variable]
uint_fast32_t front_clip = 0;
^~~~~~~~~~
`"/home/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXXFLAGS` -o getSpliceMapUnmapped getSpliceMapUnmapped.cpp
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)
~~~~~~~~^~~~~~~~~
`"/home/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXXFLAGS` -o fuseReorder fuseReorder.cpp
`"/home/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.9-bioc/R/bin/R" CMD config CXXFLAGS` -o SpliceMap main.cpp SpliceMap_utils_QuasR.o params.o cfgfile.o
make[1]: Leaving directory '/home/biocbuild/bbs-3.9-bioc/meat/Rbowtie/src/SpliceMap'
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
** 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)