| Back to Build/check report for BioC 3.23: simplified long |
|
This page was generated on 2026-01-30 13:21 -0500 (Fri, 30 Jan 2026).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2026-01-15 r89304) -- "Unsuffered Consequences" | 4852 |
| 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 1999/2347 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| signatureSearch 1.25.1 (landing page) Brendan Gongol
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| See other builds for signatureSearch in R Universe. | ||||||||||||||
|
To the developers/maintainers of the signatureSearch package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/signatureSearch.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: signatureSearch |
| Version: 1.25.1 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL signatureSearch |
| StartedAt: 2026-01-29 15:49:28 -0500 (Thu, 29 Jan 2026) |
| EndedAt: 2026-01-29 15:51:10 -0500 (Thu, 29 Jan 2026) |
| EllapsedTime: 102.1 seconds |
| RetCode: 0 |
| Status: OK |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL signatureSearch
###
##############################################################################
##############################################################################
* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
Warning: SystemRequirements specified C++11: support has been removed
* installing *source* package ‘signatureSearch’ ...
** this is package ‘signatureSearch’ version ‘1.25.1’
** using staged installation
** libs
specified C++11
using C compiler: ‘gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c fastGSEA.cpp -o fastGSEA.o
fastGSEA.cpp: In function ‘Rcpp::NumericVector calcGseaStatBatchCpp(const Rcpp::NumericVector&, const Rcpp::List&, const Rcpp::IntegerVector&)’:
fastGSEA.cpp:444:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
444 | for (int j = 0; j < S.size(); ++j) {
| ~~^~~~~~~~~~
gcc -std=gnu2x -I"/home/biocbuild/bbs-3.23-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.23-bioc/R/site-library/Rcpp/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c fgsea_init.c -o fgsea_init.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o signatureSearch.so RcppExports.o fastGSEA.o fgsea_init.o -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-signatureSearch/00new/signatureSearch/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import ‘SummarizedExperiment::shift’ by ‘data.table::shift’ when loading ‘signatureSearch’
Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘signatureSearch’
Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘signatureSearch’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import ‘SummarizedExperiment::shift’ by ‘data.table::shift’ when loading ‘signatureSearch’
Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘signatureSearch’
Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘signatureSearch’
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
Warning: replacing previous import ‘SummarizedExperiment::shift’ by ‘data.table::shift’ when loading ‘signatureSearch’
Warning: replacing previous import ‘AnnotationDbi::head’ by ‘utils::head’ when loading ‘signatureSearch’
Warning: replacing previous import ‘AnnotationDbi::tail’ by ‘utils::tail’ when loading ‘signatureSearch’
** testing if installed package keeps a record of temporary installation path
* DONE (signatureSearch)