Jiri Hon
| Snapshot Date: 2025-10-13 13:40 -0400 (Mon, 13 Oct 2025) |
| git_url: https://git.bioconductor.org/packages/triplex |
| git_branch: RELEASE_3_21 |
| git_last_commit: 8434ffd |
| git_last_commit_date: 2025-04-15 10:23:57 -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 11:38 -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 2246/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| triplex 1.48.0 (landing page) Jiri Hon
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| merida1 | macOS 12.7.6 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.7.5 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | NA | ||||||||||
|
To the developers/maintainers of the triplex package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/triplex.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: triplex |
| Version: 1.48.0 |
| Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL triplex |
| StartedAt: 2025-10-15 15:36:04 -0400 (Wed, 15 Oct 2025) |
| EndedAt: 2025-10-15 15:36:20 -0400 (Wed, 15 Oct 2025) |
| EllapsedTime: 15.6 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL triplex
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* installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’
* installing *source* package ‘triplex’ ...
** this is package ‘triplex’ version ‘1.48.0’
** using staged installation
** libs
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c IRanges_stubs.c -o IRanges_stubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c R_init_triplex.c -o R_init_triplex.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c XVector_stubs.c -o XVector_stubs.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c align.c -o align.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c align_interface.c -o align_interface.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c dl_list.c -o dl_list.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c interval.c -o interval.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c libtriplex.c -o libtriplex.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c progress.c -o progress.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c search.c -o search.o
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.21-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/S4Vectors/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/IRanges/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/XVector/include' -I'/home/biocbuild/bbs-3.21-bioc/R/site-library/Biostrings/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c search_interface.c -o search_interface.o
search_interface.c: In function ‘decode_DNAString’:
search_interface.c:371:84: warning: pointer used after ‘free’ [-Wuse-after-free]
371 | error("Unsupported symbol '%c' in input sequence.", dna.seq[i]);
| ^
search_interface.c:370:25: note: call to ‘free’ here
370 | free(dna.seq);
| ^~~~~~~~~~~~~
gcc -std=gnu2x -shared -L/home/biocbuild/bbs-3.21-bioc/R/lib -L/usr/local/lib -o triplex.so Biostrings_stubs.o IRanges_stubs.o R_init_triplex.o XVector_stubs.o align.o align_interface.o dl_list.o interval.o libtriplex.o progress.o search.o search_interface.o -L/home/biocbuild/bbs-3.21-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.21-bioc/R/site-library/00LOCK-triplex/00new/triplex/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘grid::pattern’ by ‘Biostrings::pattern’ when loading ‘triplex’
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘grid::pattern’ by ‘Biostrings::pattern’ when loading ‘triplex’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘grid::pattern’ by ‘Biostrings::pattern’ when loading ‘triplex’
** testing if installed package keeps a record of temporary installation path
* DONE (triplex)