Jean-Philippe Fortin
| Snapshot Date: 2025-10-22 13:45 -0400 (Wed, 22 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/Rbwa |
| git_branch: devel |
| git_last_commit: cb640b6 |
| git_last_commit_date: 2025-04-15 12:47:04 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.22: simplified long |
|
This page was generated on 2025-10-23 12:07 -0400 (Thu, 23 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" | 4894 |
| lconway | macOS 12.7.6 Monterey | x86_64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4684 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | 4.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" | 4629 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.5.0 (2025-04-11) -- "How About a Twenty-Six" | 4642 |
| 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 1719/2355 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| Rbwa 1.13.0 (landing page) Jean-Philippe Fortin
| nebbiolo2 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| lconway | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | NA | ||||||||||
|
To the developers/maintainers of the Rbwa package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Rbwa.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. - See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host. |
| Package: Rbwa |
| Version: 1.13.0 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL Rbwa |
| StartedAt: 2025-10-20 20:08:47 -0000 (Mon, 20 Oct 2025) |
| EndedAt: 2025-10-20 20:09:17 -0000 (Mon, 20 Oct 2025) |
| EllapsedTime: 29.9 seconds |
| RetCode: 0 |
| Status: OK |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD INSTALL Rbwa
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘Rbwa’ ...
** this is package ‘Rbwa’ version ‘1.13.0’
** using staged installation
** libs
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c utils.c -o utils.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c kthread.c -o kthread.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c kstring.c -o kstring.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c ksw.c -o ksw.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwt.c -o bwt.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bntseq.c -o bntseq.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwa.c -o bwa.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwamem.c -o bwamem.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwamem_pair.c -o bwamem_pair.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwamem_extra.c -o bwamem_extra.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c malloc_wrap.c -o malloc_wrap.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c QSufSort.c -o QSufSort.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwt_gen.c -o bwt_gen.o
bwt_gen.c: In function ‘BWTIncBuildRelativeRank’:
bwt_gen.c:879:17: warning: variable ‘oldInverseSa0RelativeRank’ set but not used [-Wunused-but-set-variable]
879 | bgint_t oldInverseSa0RelativeRank = 0;
| ^~~~~~~~~~~~~~~~~~~~~~~~~
bwt_gen.c: In function ‘BWTIncMergeBwt’:
bwt_gen.c:953:22: warning: variable ‘bitsInWordMinusBitPerChar’ set but not used [-Wunused-but-set-variable]
953 | unsigned int bitsInWordMinusBitPerChar;
| ^~~~~~~~~~~~~~~~~~~~~~~~~
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c rope.c -o rope.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c rle.c -o rle.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c is.c -o is.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwtindex.c -o bwtindex.o
ar -csru libbwa.a utils.o kthread.o kstring.o ksw.o bwt.o bntseq.o bwa.o bwamem.o bwamem_pair.o bwamem_extra.o malloc_wrap.o QSufSort.o bwt_gen.o rope.o rle.o is.o bwtindex.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwashm.c -o bwashm.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwase.c -o bwase.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwaseqio.c -o bwaseqio.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwtgap.c -o bwtgap.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwtaln.c -o bwtaln.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bamlite.c -o bamlite.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwape.c -o bwape.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c kopen.c -o kopen.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c pemerge.c -o pemerge.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c maxk.c -o maxk.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwtsw2_core.c -o bwtsw2_core.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwtsw2_main.c -o bwtsw2_main.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwtsw2_aux.c -o bwtsw2_aux.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwt_lite.c -o bwt_lite.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwtsw2_chain.c -o bwtsw2_chain.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c fastmap.c -o fastmap.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c bwtsw2_pair.c -o bwtsw2_pair.o
gcc -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG -I/usr/local/include -fPIC -g -Wall -O2 -c main.c -o main.o
gcc -g -Wall -O2 -DHAVE_PTHREAD -DUSE_MALLOC_WRAPPERS bwashm.o bwase.o bwaseqio.o bwtgap.o bwtaln.o bamlite.o bwape.o kopen.o pemerge.o maxk.o bwtsw2_core.o bwtsw2_main.o bwtsw2_aux.o bwt_lite.o bwtsw2_chain.o fastmap.o bwtsw2_pair.o main.o -o bwa -L. -lbwa -lm -lz -lpthread -lrt
mkdir -p ../inst
cp bwa ../inst/bwa
rm -f gmon.out *.o a.out bwa *~ *.a
rm -f bwa
** 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 (Rbwa)