Jiri Hon
| Snapshot Date: 2025-01-02 13:00 -0500 (Thu, 02 Jan 2025) |
| git_url: https://git.bioconductor.org/packages/pqsfinder |
| git_branch: RELEASE_3_20 |
| git_last_commit: 7baec2f |
| git_last_commit_date: 2024-10-29 10:10:06 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2025-01-09 12:11 -0500 (Thu, 09 Jan 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4744 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4487 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4515 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4467 |
| taishan | Linux (openEuler 24.03 LTS) | aarch64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4358 |
| 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 1584/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| pqsfinder 2.22.0 (landing page) Jiri Hon
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | WARNINGS | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | WARNINGS | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | WARNINGS | OK | | ||||||||
| taishan | Linux (openEuler 24.03 LTS) / aarch64 | OK | ERROR | skipped | ||||||||||
|
To the developers/maintainers of the pqsfinder package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/pqsfinder.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: pqsfinder |
| Version: 2.22.0 |
| Command: /home/biocbuild/R/R/bin/R CMD INSTALL pqsfinder |
| StartedAt: 2025-01-08 20:01:37 -0000 (Wed, 08 Jan 2025) |
| EndedAt: 2025-01-08 20:02:34 -0000 (Wed, 08 Jan 2025) |
| EllapsedTime: 57.2 seconds |
| RetCode: 0 |
| Status: OK |
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###
### Running command:
###
### /home/biocbuild/R/R/bin/R CMD INSTALL pqsfinder
###
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* installing to library ‘/home/biocbuild/R/R-4.4.2/site-library’
* installing *source* package ‘pqsfinder’ ...
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
using C++11
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c pqsfinder.cpp -o pqsfinder.o
pqsfinder.cpp: In function ‘void find_all_runs(SEXP, int, std::__cxx11::basic_string<char>::const_iterator, std::__cxx11::basic_string<char>::const_iterator, run_match*, const boost::regex&, const opts_t&, const scoring&, const std::__cxx11::basic_string<char>::const_iterator&, size_t, storage&, int&, results&, bool, std::chrono::_V2::system_clock::time_point, int, int, int, int&, bool)’:
pqsfinder.cpp:582:22: warning: ‘loop_len’ may be used uninitialized [-Wmaybe-uninitialized]
582 | find_all_runs(
| ~~~~~~~~~~~~~^
583 | subject, i+1, e, end, m, run_re_c, opts, sc, ref, len,
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
584 | pqs_storage, int_cnt, res, (loop_len == 0 ? true : zero_loop),
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
585 | s_time, next_tetrad_count, next_defect_count, next_loop_sum, fn_call_count, show_progress
| ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
586 | );
| ~
pqsfinder.cpp:489:14: note: ‘loop_len’ was declared here
489 | int score, loop_len;
| ^~~~~~~~
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c boost_regex/posix_api.cpp -o boost_regex/posix_api.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c boost_regex/regex.cpp -o boost_regex/regex.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c boost_regex/regex_debug.cpp -o boost_regex/regex_debug.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c boost_regex/static_mutex.cpp -o boost_regex/static_mutex.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -I"/home/biocbuild/R/R/include" -DNDEBUG -I'/home/biocbuild/R/R-4.4.2/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.2/site-library/BH/include' -I/usr/local/include -fPIC -g -O2 -Wall -Werror=format-security -c boost_regex/wide_posix_api.cpp -o boost_regex/wide_posix_api.o
mkdir -p "/home/biocbuild/R/R-4.4.2/site-library/00LOCK-pqsfinder/00new/pqsfinder/lib"
ar rs "/home/biocbuild/R/R-4.4.2/site-library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a" boost_regex/posix_api.o boost_regex/regex.o boost_regex/regex_debug.o boost_regex/static_mutex.o boost_regex/wide_posix_api.o
ar: creating /home/biocbuild/R/R-4.4.2/site-library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++11 -shared -L/home/biocbuild/R/R/lib -L/usr/local/lib -o pqsfinder.so RcppExports.o pqsfinder.o /home/biocbuild/R/R-4.4.2/site-library/00LOCK-pqsfinder/00new/pqsfinder/lib/libboost_regex.a -L/home/biocbuild/R/R/lib -lR
installing to /home/biocbuild/R/R-4.4.2/site-library/00LOCK-pqsfinder/00new/pqsfinder/libs
** 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
** 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 (pqsfinder)