Hervé Pagès
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/pwalign |
| git_branch: RELEASE_3_21 |
| git_last_commit: 9842dde |
| git_last_commit_date: 2025-04-15 13:32:59 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-10-16 11:41 -0400 (Thu, 16 Oct 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
| merida1 | macOS 12.7.6 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
| kjohnson1 | macOS 13.7.5 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
| 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 1652/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| pwalign 1.4.0 (landing page) Hervé Pagès
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the pwalign package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pwalign.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: pwalign |
| Version: 1.4.0 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL pwalign |
| StartedAt: 2025-10-13 21:06:43 -0000 (Mon, 13 Oct 2025) |
| EndedAt: 2025-10-13 21:07:05 -0000 (Mon, 13 Oct 2025) |
| EllapsedTime: 22.6 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/R/R/bin/R CMD INSTALL pwalign
###
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* installing to library ‘/home/biocbuild/R/R-devel_2025-02-19/site-library’
* installing *source* package ‘pwalign’ ...
** this is package ‘pwalign’ version ‘1.4.0’
** using staged installation
** libs
using C compiler: ‘aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c Biostrings_stubs.c -o Biostrings_stubs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c IRanges_stubs.c -o IRanges_stubs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c R_init_pairwiseAlignment.c -o R_init_pairwiseAlignment.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c S4Vectors_stubs.c -o S4Vectors_stubs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c XVector_stubs.c -o XVector_stubs.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/S4Vectors/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/IRanges/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/XVector/include' -I'/home/biocbuild/R/R-devel_2025-02-19/site-library/Biostrings/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c align_utils.c -o align_utils.o
align_utils.c: In function ‘PairwiseAlignmentsSingleSubject_align_aligned’:
align_utils.c:234:78: warning: ‘indelStartPattern’ may be used uninitialized [-Wmaybe-uninitialized]
234 | if ((numberOfIndelPattern == 0) || (jPattern < indelStartPattern)) {
| ~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
align_utils.c:223:21: note: ‘indelStartPattern’ was declared here
223 | int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject;
| ^~~~~~~~~~~~~~~~~
align_utils.c:240:55: warning: ‘indelWidthPattern’ may be used uninitialized [-Wmaybe-uninitialized]
240 | for (k = 0; k < indelWidthPattern; k++) {
| ~~^~~~~~~~~~~~~~~~~~~
align_utils.c:223:40: note: ‘indelWidthPattern’ was declared here
223 | int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject;
| ^~~~~~~~~~~~~~~~~
align_utils.c:233:63: warning: ‘indelStartSubject’ may be used uninitialized [-Wmaybe-uninitialized]
233 | if ((numberOfIndelSubject == 0) || (j < indelStartSubject)) {
| ~~~^~~~~~~~~~~~~~~~~~~~
align_utils.c:223:59: note: ‘indelStartSubject’ was declared here
223 | int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject;
| ^~~~~~~~~~~~~~~~~
align_utils.c:252:42: warning: ‘indelWidthSubject’ may be used uninitialized [-Wmaybe-uninitialized]
252 | jPattern += indelWidthSubject;
| ~~~~~~~~~^~~~~~~~~~~~~~~~~~~~
align_utils.c:223:78: note: ‘indelWidthSubject’ was declared here
223 | int indelStartPattern, indelWidthPattern, indelStartSubject, indelWidthSubject;
| ^~~~~~~~~~~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-gcc -std=gnu23 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o pwalign.so Biostrings_stubs.o IRanges_stubs.o R_init_pairwiseAlignment.o S4Vectors_stubs.o XVector_stubs.o align_pairwiseAlignment.o align_utils.o -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-devel_2025-02-19/site-library/00LOCK-pwalign/00new/pwalign/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Creating a new generic function for ‘insertion’ in package ‘pwalign’
Creating a new generic function for ‘deletion’ in package ‘pwalign’
Creating a new generic function for ‘unaligned’ in package ‘pwalign’
Creating a new generic function for ‘aligned’ in package ‘pwalign’
Creating a new generic function for ‘indel’ in package ‘pwalign’
Creating a new generic function for ‘nindel’ in package ‘pwalign’
Creating a new generic function for ‘PairwiseAlignments’ in package ‘pwalign’
Creating a new generic function for ‘pattern’ in package ‘pwalign’
Creating a new generic function for ‘alignedPattern’ in package ‘pwalign’
Creating a new generic function for ‘alignedSubject’ in package ‘pwalign’
Creating a new generic function for ‘PairwiseAlignmentsSingleSubject’ in package ‘pwalign’
Creating a new generic function for ‘nedit’ in package ‘pwalign’
Creating a new generic function for ‘mismatchTable’ in package ‘pwalign’
Creating a new generic function for ‘mismatchSummary’ in package ‘pwalign’
Creating a new generic function for ‘compareStrings’ in package ‘pwalign’
Creating a new generic function for ‘pid’ in package ‘pwalign’
Creating a new generic function for ‘pairwiseAlignment’ in package ‘pwalign’
Creating a new generic function for ‘stringDist’ in package ‘pwalign’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (pwalign)