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This page was generated on 2023-06-06 11:00:39 -0000 (Tue, 06 Jun 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.3.0 (2023-04-21) -- "Already Tomorrow" | 4366 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
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To the developers/maintainers of the Rbowtie package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rbowtie.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 1614/2199 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rbowtie 1.41.0 (landing page) Michael Stadler
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | |||||||||
| Package: Rbowtie |
| Version: 1.41.0 |
| Command: /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL Rbowtie |
| StartedAt: 2023-06-05 08:13:03 -0000 (Mon, 05 Jun 2023) |
| EndedAt: 2023-06-05 08:15:15 -0000 (Mon, 05 Jun 2023) |
| EllapsedTime: 132.1 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/R/R-4.3.0/bin/R CMD INSTALL Rbowtie
###
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* installing to library ‘/home/biocbuild/R/R-4.3.0/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="\"2023-06-05T08:13:03\"" -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
/bin/sh: line 1: hostname: command not found
In file included from ebwt_build.cpp:8:
ds.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]’:
ds.h:497:3: warning: ‘tmp2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
497 | list_[cur_++] = el;
| ^~~~~
ds.h:497:3: warning: ‘tmp3’ may be used uninitialized in this function [-Wmaybe-uninitialized]
497 | list_[cur_++] = el;
| ^~~~~
ds.h:497:3: warning: ‘tmp4’ may be used uninitialized in this function [-Wmaybe-uninitialized]
497 | list_[cur_++] = el;
| ^~~~~
ds.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>]’:
ds.h:497:3: warning: ‘tmp2’ may be used uninitialized in this function [-Wmaybe-uninitialized]
497 | list_[cur_++] = el;
| ^~~~~
ds.h:497:3: warning: ‘tmp3’ may be used uninitialized in this function [-Wmaybe-uninitialized]
497 | list_[cur_++] = el;
| ^~~~~
ds.h:497:3: warning: ‘tmp4’ may be used uninitialized in this function [-Wmaybe-uninitialized]
497 | list_[cur_++] = el;
| ^~~~~
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="\"2023-06-05T08:13:27\"" -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
/bin/sh: line 1: hostname: command not found
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-3.18-bioc/meat/Rbowtie/src/SpliceMap'
`"/home/biocbuild/R/R-4.3.0/bin/R" CMD config CXX` `"/home/biocbuild/R/R-4.3.0/bin/R" CMD config CXXFLAGS` -c SpliceMap_utils_QuasR.cpp
`"/home/biocbuild/R/R-4.3.0/bin/R" CMD config CXX` `"/home/biocbuild/R/R-4.3.0/bin/R" CMD config CXXFLAGS` -c params.cpp
`"/home/biocbuild/R/R-4.3.0/bin/R" CMD config CXX` `"/home/biocbuild/R/R-4.3.0/bin/R" CMD config CXXFLAGS` -c cfgfile.cpp
`"/home/biocbuild/R/R-4.3.0/bin/R" CMD config CXX` `"/home/biocbuild/R/R-4.3.0/bin/R" CMD config LDFLAGS` `"/home/biocbuild/R/R-4.3.0/bin/R" CMD config CXXFLAGS` -o runSpliceMap_QuasR SpliceMap_utils_QuasR.o cfgfile.o runSpliceMap_QuasR.cpp params.o
`"/home/biocbuild/R/R-4.3.0/bin/R" CMD config CXX` `"/home/biocbuild/R/R-4.3.0/bin/R" CMD config LDFLAGS` `"/home/biocbuild/R/R-4.3.0/bin/R" CMD config CXXFLAGS` -o sortsam sortsam.cpp SpliceMap_utils_QuasR.o params.o
`"/home/biocbuild/R/R-4.3.0/bin/R" CMD config CXX` `"/home/biocbuild/R/R-4.3.0/bin/R" CMD config LDFLAGS` `"/home/biocbuild/R/R-4.3.0/bin/R" CMD config CXXFLAGS` -o amalgamateSAM amalgamateSAM.cpp SpliceMap_utils_QuasR.o params.o
`"/home/biocbuild/R/R-4.3.0/bin/R" CMD config CXX` `"/home/biocbuild/R/R-4.3.0/bin/R" CMD config LDFLAGS` `"/home/biocbuild/R/R-4.3.0/bin/R" CMD config CXXFLAGS` -o getSpliceMapUnmapped getSpliceMapUnmapped.cpp
`"/home/biocbuild/R/R-4.3.0/bin/R" CMD config CXX` `"/home/biocbuild/R/R-4.3.0/bin/R" CMD config LDFLAGS` `"/home/biocbuild/R/R-4.3.0/bin/R" CMD config CXXFLAGS` -o fuseReorder fuseReorder.cpp
`"/home/biocbuild/R/R-4.3.0/bin/R" CMD config CXX` `"/home/biocbuild/R/R-4.3.0/bin/R" CMD config LDFLAGS` `"/home/biocbuild/R/R-4.3.0/bin/R" CMD config CXXFLAGS` -o SpliceMap main.cpp SpliceMap_utils_QuasR.o params.o cfgfile.o
make[1]: Leaving directory '/home/biocbuild/bbs-3.18-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)