Michael Stadler
| Snapshot Date: 2024-03-27 14:00:18 -0400 (Wed, 27 Mar 2024) |
| git_url: https://git.bioconductor.org/packages/Rbowtie |
| git_branch: devel |
| git_last_commit: 8e83209 |
| git_last_commit_date: 2023-10-24 09:52:24 -0400 (Tue, 24 Oct 2023) |
| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-03-28 11:36:57 -0400 (Thu, 28 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4708 |
| palomino3 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2024-03-16 r86144 ucrt) -- "Unsuffered Consequences" | 4446 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2024-03-18 r86148) -- "Unsuffered Consequences" | 4471 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | R Under development (unstable) (2024-03-19 r86153) -- "Unsuffered Consequences" | 4426 |
| 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 | ||||
| Package 1668/2270 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rbowtie 1.43.0 (landing page) Michael Stadler
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino3 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
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. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: Rbowtie |
| Version: 1.43.0 |
| Command: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL Rbowtie |
| StartedAt: 2024-03-27 15:15:15 -0400 (Wed, 27 Mar 2024) |
| EndedAt: 2024-03-27 15:16:36 -0400 (Wed, 27 Mar 2024) |
| EllapsedTime: 81.0 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL Rbowtie
###
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* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘Rbowtie’ ...
** using staged installation
** libs
g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -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="\"2024-03-27T15:15:16\"" -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 -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
g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -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="\"2024-03-27T15:15:31\"" -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 -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-3.19-bioc/meat/Rbowtie/src/SpliceMap'
`"/home/biocbuild/bbs-3.19-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.19-bioc/R/bin/R" CMD config CXXFLAGS` -c SpliceMap_utils_QuasR.cpp
`"/home/biocbuild/bbs-3.19-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.19-bioc/R/bin/R" CMD config CXXFLAGS` -c params.cpp
`"/home/biocbuild/bbs-3.19-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.19-bioc/R/bin/R" CMD config CXXFLAGS` -c cfgfile.cpp
`"/home/biocbuild/bbs-3.19-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.19-bioc/R/bin/R" CMD config LDFLAGS` `"/home/biocbuild/bbs-3.19-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:108:38: warning: variable ‘chr_file_list_it’ set but not used [-Wunused-but-set-variable]
108 | vector<string>::iterator chr_file_list_it = chr_file_list.begin();
| ^~~~~~~~~~~~~~~~
runSpliceMap_QuasR.cpp:537:47: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
537 | if (line.length() > head_clip_length) {
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
runSpliceMap_QuasR.cpp:595:47: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
595 | if (line.length() > head_clip_length) {
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
runSpliceMap_QuasR.cpp:716:47: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
716 | if (line.length() > head_clip_length) {
| ~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~
runSpliceMap_QuasR.cpp:841:43: warning: comparison of integer expressions of different signedness: ‘std::__cxx11::basic_string<char>::size_type’ {aka ‘long unsigned int’} and ‘int’ [-Wsign-compare]
841 | 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]
1327 | int min_mismatch;
| ^~~~~~~~~~~~
`"/home/biocbuild/bbs-3.19-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.19-bioc/R/bin/R" CMD config LDFLAGS` `"/home/biocbuild/bbs-3.19-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:189:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare]
189 | if (nmloc == string::npos) { // unaligned, no NM tag
| ~~~~~~^~~~~~~~~~~~~~~
sortsam.cpp:194:32: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare]
194 | if (nmloc2 == string::npos) {
| ~~~~~~~^~~~~~~~~~~~~~~
sortsam.cpp:231:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare]
231 | if (nmloc == string::npos) { // unaligned, no NM tag
| ~~~~~~^~~~~~~~~~~~~~~
sortsam.cpp:236:40: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare]
236 | if (nmloc2 == string::npos) {
| ~~~~~~~^~~~~~~~~~~~~~~
`"/home/biocbuild/bbs-3.19-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.19-bioc/R/bin/R" CMD config LDFLAGS` `"/home/biocbuild/bbs-3.19-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 of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare]
19 | if(start_pos != string::npos && end_pos != string::npos)
| ~~~~~~~~~~^~~~~~~~~~~~~~~
amalgamateSAM.cpp:19:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare]
19 | if(start_pos != string::npos && end_pos != string::npos)
| ~~~~~~~~^~~~~~~~~~~~~~~
amalgamateSAM.cpp: In function ‘void update_jun_coverage(std::map<std::__cxx11::basic_string<char>, std::map<int, std::map<int, jun_store_ij> > >&, std::string, bool)’:
amalgamateSAM.cpp:695:31: warning: variable ‘front_clip’ set but not used [-Wunused-but-set-variable]
695 | uint_fast32_t front_clip = 0;
| ^~~~~~~~~~
`"/home/biocbuild/bbs-3.19-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.19-bioc/R/bin/R" CMD config LDFLAGS` `"/home/biocbuild/bbs-3.19-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 of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare]
88 | if(start_pos != string::npos && end_pos != string::npos)
| ~~~~~~~~~~^~~~~~~~~~~~~~~
getSpliceMapUnmapped.cpp:88:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const size_type’ {aka ‘const long unsigned int’} [-Wsign-compare]
88 | if(start_pos != string::npos && end_pos != string::npos)
| ~~~~~~~~^~~~~~~~~~~~~~~
`"/home/biocbuild/bbs-3.19-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.19-bioc/R/bin/R" CMD config LDFLAGS` `"/home/biocbuild/bbs-3.19-bioc/R/bin/R" CMD config CXXFLAGS` -o fuseReorder fuseReorder.cpp
`"/home/biocbuild/bbs-3.19-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.19-bioc/R/bin/R" CMD config LDFLAGS` `"/home/biocbuild/bbs-3.19-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-3.19-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)