Michael Stadler
| Snapshot Date: 2025-02-03 13:40 -0500 (Mon, 03 Feb 2025) |
| git_url: https://git.bioconductor.org/packages/Rbowtie |
| git_branch: devel |
| git_last_commit: 4dc6fb5 |
| git_last_commit_date: 2025-01-06 07:06:33 -0500 (Mon, 06 Jan 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-02-04 11:40 -0500 (Tue, 04 Feb 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4716 |
| palomino7 | Windows Server 2022 Datacenter | x64 | R Under development (unstable) (2025-01-21 r87610 ucrt) -- "Unsuffered Consequences" | 4478 |
| lconway | macOS 12.7.1 Monterey | x86_64 | R Under development (unstable) (2025-01-22 r87618) -- "Unsuffered Consequences" | 4489 |
| kjohnson3 | macOS 13.7.1 Ventura | arm64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 4442 |
| 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 1676/2295 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rbowtie 1.47.0 (landing page) Michael Stadler
| nebbiolo1 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.1 Ventura / arm64 | OK | OK | WARNINGS | 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: 1.47.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL Rbowtie |
| StartedAt: 2025-02-03 15:14:33 -0500 (Mon, 03 Feb 2025) |
| EndedAt: 2025-02-03 15:16:27 -0500 (Mon, 03 Feb 2025) |
| EllapsedTime: 114.5 seconds |
| RetCode: 0 |
| Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL Rbowtie ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘Rbowtie’ ... ** this is package ‘Rbowtie’ version ‘1.47.0’ ** using staged installation ** libs g++ -O3 -DCOMPILER_OPTIONS="\"-O3 -Wl,--hash-style=both -DPOPCNT_CAPABILITY -g -O2 -g -O2 \"" -Wl,--hash-style=both -DPOPCNT_CAPABILITY -g -O2 -g -O2 \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2025-02-03T15:14:33\"" -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 -g -O2 \"" -Wl,--hash-style=both -DPOPCNT_CAPABILITY -g -O2 -g -O2 \ -fno-strict-aliasing -DBOWTIE_VERSION="\"`cat VERSION`\"" -DBUILD_HOST="\"`hostname`\"" -DBUILD_TIME="\"2025-02-03T15:14:50\"" -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-3.21-bioc/meat/Rbowtie/src/SpliceMap' `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXXFLAGS` -c SpliceMap_utils_QuasR.cpp `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXXFLAGS` -c params.cpp `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXXFLAGS` -c cfgfile.cpp `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config LDFLAGS` `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXXFLAGS` -o runSpliceMap_QuasR SpliceMap_utils_QuasR.o cfgfile.o runSpliceMap_QuasR.cpp params.o `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config LDFLAGS` `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXXFLAGS` -o sortsam sortsam.cpp SpliceMap_utils_QuasR.o params.o `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config LDFLAGS` `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXXFLAGS` -o amalgamateSAM amalgamateSAM.cpp SpliceMap_utils_QuasR.o params.o `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config LDFLAGS` `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXXFLAGS` -o getSpliceMapUnmapped getSpliceMapUnmapped.cpp `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config LDFLAGS` `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXXFLAGS` -o fuseReorder fuseReorder.cpp `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config CXX` `"/home/biocbuild/bbs-3.21-bioc/R/bin/R" CMD config LDFLAGS` `"/home/biocbuild/bbs-3.21-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-3.21-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)