##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL Rbowtie
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’
* installing *source* package ‘Rbowtie’ ...
** using staged installation
** libs
g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -Wl,--hash-style=both -g -O2 -g -O2 \"" -Wl,--hash-style=both -g -O2 -g -O2 \
-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2023-05-08T21:26:01\"" -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 \
-I third_party \
-o bowtie-build-s ebwt_build.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp bowtie_build_main.cpp \
-L/usr/local/lib -lz -lpthread
In file included from ebwt_build.cpp:8:
In member function ‘void EList<T, S>::push_back(const T&) [with T = QSortRange; int S = 128]’,
inlined from ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = S2bDnaString]’ at multikey_qsort.h:584:31:
ds.h:497:17: warning: ‘tmp2’ may be used uninitialized [-Wmaybe-uninitialized]
497 | list_[cur_++] = el;
| ^~~~~
In file included from diff_sample.h:14,
from blockwise_sa.h:17,
from ebwt.h:25,
from ebwt_build.cpp:10:
multikey_qsort.h: In function ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = S2bDnaString]’:
multikey_qsort.h:583:36: note: ‘tmp2’ declared here
583 | QSortRange tmp2;
| ^~~~
In file included from ebwt_build.cpp:8:
In member function ‘void EList<T, S>::push_back(const T&) [with T = QSortRange; int S = 128]’,
inlined from ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = S2bDnaString]’ at multikey_qsort.h:593:31:
ds.h:497:17: warning: ‘tmp3’ may be used uninitialized [-Wmaybe-uninitialized]
497 | list_[cur_++] = el;
| ^~~~~
In file included from diff_sample.h:14,
from blockwise_sa.h:17,
from ebwt.h:25,
from ebwt_build.cpp:10:
multikey_qsort.h: In function ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = S2bDnaString]’:
multikey_qsort.h:592:36: note: ‘tmp3’ declared here
592 | QSortRange tmp3;
| ^~~~
In file included from ebwt_build.cpp:8:
In member function ‘void EList<T, S>::push_back(const T&) [with T = QSortRange; int S = 128]’,
inlined from ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = S2bDnaString]’ at multikey_qsort.h:601:31:
ds.h:497:17: warning: ‘tmp4’ may be used uninitialized [-Wmaybe-uninitialized]
497 | list_[cur_++] = el;
| ^~~~~
In file included from diff_sample.h:14,
from blockwise_sa.h:17,
from ebwt.h:25,
from ebwt_build.cpp:10:
multikey_qsort.h: In function ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = S2bDnaString]’:
multikey_qsort.h:600:36: note: ‘tmp4’ declared here
600 | QSortRange tmp4;
| ^~~~
In file included from ebwt_build.cpp:8:
In member function ‘void EList<T, S>::push_back(const T&) [with T = QSortRange; int S = 128]’,
inlined from ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = SString<char>]’ at multikey_qsort.h:584:31:
ds.h:497:17: warning: ‘tmp2’ may be used uninitialized [-Wmaybe-uninitialized]
497 | list_[cur_++] = el;
| ^~~~~
In file included from diff_sample.h:14,
from blockwise_sa.h:17,
from ebwt.h:25,
from ebwt_build.cpp:10:
multikey_qsort.h: In function ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = SString<char>]’:
multikey_qsort.h:583:36: note: ‘tmp2’ declared here
583 | QSortRange tmp2;
| ^~~~
In file included from ebwt_build.cpp:8:
In member function ‘void EList<T, S>::push_back(const T&) [with T = QSortRange; int S = 128]’,
inlined from ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = SString<char>]’ at multikey_qsort.h:593:31:
ds.h:497:17: warning: ‘tmp3’ may be used uninitialized [-Wmaybe-uninitialized]
497 | list_[cur_++] = el;
| ^~~~~
In file included from diff_sample.h:14,
from blockwise_sa.h:17,
from ebwt.h:25,
from ebwt_build.cpp:10:
multikey_qsort.h: In function ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = SString<char>]’:
multikey_qsort.h:592:36: note: ‘tmp3’ declared here
592 | QSortRange tmp3;
| ^~~~
In file included from ebwt_build.cpp:8:
In member function ‘void EList<T, S>::push_back(const T&) [with T = QSortRange; int S = 128]’,
inlined from ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = SString<char>]’ at multikey_qsort.h:601:31:
ds.h:497:17: warning: ‘tmp4’ may be used uninitialized [-Wmaybe-uninitialized]
497 | list_[cur_++] = el;
| ^~~~~
In file included from diff_sample.h:14,
from blockwise_sa.h:17,
from ebwt.h:25,
from ebwt_build.cpp:10:
multikey_qsort.h: In function ‘void mkeyQSortSuf2(const T&, size_t, TIndexOffU*, size_t, TIndexOffU*, int, size_t, size_t, size_t, size_t, EList<long unsigned int>*) [with T = SString<char>]’:
multikey_qsort.h:600:36: note: ‘tmp4’ declared here
600 | QSortRange tmp4;
| ^~~~
g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -Wl,--hash-style=both -g -O2 -g -O2 \"" -Wl,--hash-style=both -g -O2 -g -O2 \
-fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2023-05-08T21:26:25\"" -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 \
-I third_party \
-o bowtie-align-s ebwt_search.cpp \
ccnt_lut.cpp ref_read.cpp alphabet.cpp shmem.cpp edit.cpp ebwt.cpp bt2_locks.cpp tinythread.cpp qual.cpp pat.cpp ebwt_search_util.cpp ref_aligner.cpp log.cpp hit_set.cpp sam.cpp hit.cpp bowtie_main.cpp \
-L/usr/local/lib -lz -lpthread
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-3.17-bioc/meat/Rbowtie/src/SpliceMap'
`"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/bin/R" CMD config CXXFLAGS` -c SpliceMap_utils_QuasR.cpp
`"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/bin/R" CMD config CXXFLAGS` -c params.cpp
`"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/bin/R" CMD config CXXFLAGS` -c cfgfile.cpp
`"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/bin/R" CMD config LDFLAGS` `"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/bin/R" CMD config CXXFLAGS` -o runSpliceMap_QuasR SpliceMap_utils_QuasR.o cfgfile.o runSpliceMap_QuasR.cpp params.o
`"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/bin/R" CMD config LDFLAGS` `"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/bin/R" CMD config CXXFLAGS` -o sortsam sortsam.cpp SpliceMap_utils_QuasR.o params.o
`"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/bin/R" CMD config LDFLAGS` `"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/bin/R" CMD config CXXFLAGS` -o amalgamateSAM amalgamateSAM.cpp SpliceMap_utils_QuasR.o params.o
`"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/bin/R" CMD config LDFLAGS` `"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/bin/R" CMD config CXXFLAGS` -o getSpliceMapUnmapped getSpliceMapUnmapped.cpp
`"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/bin/R" CMD config LDFLAGS` `"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/bin/R" CMD config CXXFLAGS` -o fuseReorder fuseReorder.cpp
`"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/bin/R" CMD config LDFLAGS` `"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/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-3.17-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)