Alexey Sergushichev
| Snapshot Date: 2025-12-08 13:40 -0500 (Mon, 08 Dec 2025) |
| git_url: https://git.bioconductor.org/packages/fgsea |
| git_branch: devel |
| git_last_commit: 4fd674d |
| git_last_commit_date: 2025-12-04 12:45:21 -0500 (Thu, 04 Dec 2025) |
| Back to Multiple platform build/check report for BioC 3.23: simplified long |
|
This page was generated on 2025-12-09 11:35 -0500 (Tue, 09 Dec 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | R Under development (unstable) (2025-10-20 r88955) -- "Unsuffered Consequences" | 4869 |
| kjohnson3 | macOS 13.7.7 Ventura | arm64 | R Under development (unstable) (2025-11-04 r88984) -- "Unsuffered Consequences" | 4576 |
| 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 728/2331 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| fgsea 1.37.2 (landing page) Alexey Sergushichev
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| kjohnson3 | macOS 13.7.7 Ventura / arm64 | OK | ERROR | skipped | skipped | |||||||||
|
To the developers/maintainers of the fgsea package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/fgsea.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: fgsea |
| Version: 1.37.2 |
| Command: /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL fgsea |
| StartedAt: 2025-12-08 15:10:59 -0500 (Mon, 08 Dec 2025) |
| EndedAt: 2025-12-08 15:11:42 -0500 (Mon, 08 Dec 2025) |
| EllapsedTime: 42.9 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.23-bioc/R/bin/R CMD INSTALL fgsea
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* installing to library ‘/home/biocbuild/bbs-3.23-bioc/R/site-library’
* installing *source* package ‘fgsea’ ...
** this is package ‘fgsea’ version ‘1.37.2’
** using staged installation
** libs
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'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/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'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ScoreCalculation.cpp -o ScoreCalculation.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'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c ScoreRuler.cpp -o ScoreRuler.o
ScoreRuler.cpp: In member function ‘void ScoreRuler::extend(double, int, double)’:
ScoreRuler.cpp:76:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
76 | for (moves = 0; moves < sampleSize * genesetSize;) {
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
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'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c esCalculation.cpp -o esCalculation.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'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/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:449:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
449 | for (int j = 0; j < S.size(); ++j) {
| ~~^~~~~~~~~~
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'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c fgseaMultilevel.cpp -o fgseaMultilevel.o
fgseaMultilevel.cpp: In function ‘Rcpp::DataFrame fgseaMultilevelCpp(const Rcpp::NumericVector&, SEXPREC* const&, int, int, int, double, bool, double, bool)’:
fgseaMultilevel.cpp:15:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<long int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
15 | for (int i = 0; i < posRanks.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
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'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c fgseaMultilevelSupplement.cpp -o fgseaMultilevelSupplement.o
fgseaMultilevelSupplement.cpp: In member function ‘bool EsRuler::resampleGenesets(random_engine_t&)’:
fgseaMultilevelSupplement.cpp:64:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
64 | for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
| ~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:76:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
76 | for (int sampleId = 0; sampleId < sampleSize; sampleId++){
| ~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:84:26: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
84 | while (startFrom < sampleSize && get<0>(stats[startFrom]) == get<0>(stats[0])) {
| ~~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:89:19: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
89 | if (startFrom == sampleSize) {
| ~~~~~~~~~~^~~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:101:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
101 | for (int i = startFrom; i < sampleSize; ++i) {
| ~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:116:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
116 | for (int i = startFrom; i < sampleSize; ++i) {
| ~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp: In member function ‘void EsRuler::extend(double, int, double)’:
fgseaMultilevelSupplement.cpp:144:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
144 | for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
| ~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:180:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
180 | for (int j = 0; j < sampleSize; ++j) {
| ~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:187:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
187 | for (int i = 0; i < sampleSize; ++i) {
| ~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:206:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
206 | for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
| ~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:212:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
212 | for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
| ~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:217:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
217 | for (int i = 0; i < sampleSize; ++i) {
| ~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp: In member function ‘std::tuple<double, bool, double> EsRuler::getPvalue(double, double, bool)’:
fgseaMultilevelSupplement.cpp:246:15: warning: unused variable ‘n’ [-Wunused-variable]
246 | int const n = (int) ranks.size();
| ^
fgseaMultilevelSupplement.cpp:247:15: warning: unused variable ‘k’ [-Wunused-variable]
247 | int const k = pathwaySize;
| ^
fgseaMultilevelSupplement.cpp: In member function ‘EsRuler::PerturbateResult EsRuler::perturbate_until(const std::vector<long int>&, int, SampleChunks&, gsea_t, random_engine_t&, const std::function<bool(int, int)>&)’:
fgseaMultilevelSupplement.cpp:435:14: warning: unused variable ‘fl’ [-Wunused-variable]
435 | bool fl = false;
| ^~
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'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c geseca.cpp -o geseca.o
geseca.cpp: In function ‘Rcpp::List gesecaCpp(const Rcpp::NumericMatrix&, const Rcpp::NumericVector&, unsigned int, unsigned int, int, double)’:
geseca.cpp:9:28: warning: comparison of integer expressions of different signedness: ‘unsigned int’ and ‘int’ [-Wsign-compare]
9 | for (unsigned i = 0; i < E.nrow(); i++){
| ~~^~~~~~~~~~
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'/home/biocbuild/bbs-3.23-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -c util.cpp -o util.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.23-bioc/R/lib -L/usr/local/lib -o fgsea.so RcppExports.o ScoreCalculation.o ScoreRuler.o esCalculation.o fastGSEA.o fgseaMultilevel.o fgseaMultilevelSupplement.o geseca.o util.o -L/home/biocbuild/bbs-3.23-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.23-bioc/R/site-library/00LOCK-fgsea/00new/fgsea/libs
** R
** data
*** moving datasets to lazyload DB
** 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 (fgsea)