Alexey Sergushichev
| Snapshot Date: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024) |
| git_url: https://git.bioconductor.org/packages/fgsea |
| git_branch: RELEASE_3_20 |
| git_last_commit: 4620281 |
| git_last_commit_date: 2024-12-19 09:55:27 -0500 (Thu, 19 Dec 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-12-23 12:03 -0500 (Mon, 23 Dec 2024).
| 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 |
| 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 713/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| fgsea 1.32.2 (landing page) Alexey Sergushichev
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | ERROR | skipped | skipped | |||||||||
| kjohnson1 | macOS 13.6.6 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: 1.32.2 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL fgsea |
| StartedAt: 2024-12-19 15:38:07 -0500 (Thu, 19 Dec 2024) |
| EndedAt: 2024-12-19 15:38:42 -0500 (Thu, 19 Dec 2024) |
| EllapsedTime: 35.0 seconds |
| RetCode: 0 |
| Status: OK |
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### Running command:
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### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL fgsea
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* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘fgsea’ ...
** 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-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c ScoreCalculation.cpp -o ScoreCalculation.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -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-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c esCalculation.cpp -o esCalculation.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c fastGSEA.cpp -o fastGSEA.o
fastGSEA.cpp: In function ‘Rcpp::NumericVector calcGseaStatBatchCpp(const Rcpp::NumericVector&, const Rcpp::List&, const Rcpp::IntegerVector&)’:
fastGSEA.cpp:446:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<int>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
446 | for (int j = 0; j < S.size(); ++j) {
| ~~^~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c fgseaMultilevel.cpp -o fgseaMultilevel.o
fgseaMultilevel.cpp: In function ‘Rcpp::DataFrame fgseaMultilevelCpp(const Rcpp::NumericVector&, const Rcpp::NumericVector&, int, int, int, double, bool)’:
fgseaMultilevel.cpp:10:23: warning: comparison of integer expressions of different signedness: ‘int’ and ‘std::vector<double>::size_type’ {aka ‘long unsigned int’} [-Wsign-compare]
10 | for (int i = 0; i < posRanks.size(); i++) {
| ~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c fgseaMultilevelSupplement.cpp -o fgseaMultilevelSupplement.o
fgseaMultilevelSupplement.cpp: In member function ‘void EsRuler::duplicateSamples()’:
fgseaMultilevelSupplement.cpp:40:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
40 | for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
| ~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:50:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
50 | for (int sampleId = 0; 2 * sampleId < sampleSize; sampleId++) {
| ~~~~~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:59:41: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
59 | for (int sampleId = 0; 2 * sampleId < sampleSize - 2; sampleId++) {
| ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
fgseaMultilevelSupplement.cpp: In member function ‘void EsRuler::extend(double, int, double)’:
fgseaMultilevelSupplement.cpp:73:37: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
73 | for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
| ~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:77:16: warning: unused variable ‘currentES’ [-Wunused-variable]
77 | double currentES = calcES(ranks, currentSamples[sampleId]);
| ^~~~~~~~~
fgseaMultilevelSupplement.cpp:90:31: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
90 | for (int j = 0; j < sampleSize; ++j) {
| ~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:97:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
97 | for (int i = 0; i < sampleSize; ++i) {
| ~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:112:35: warning: comparison of integer expressions of different signedness: ‘int’ and ‘unsigned int’ [-Wsign-compare]
112 | for (int moves = 0; moves < sampleSize * pathwaySize;) {
| ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:113:45: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
113 | for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
| ~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:118:27: warning: comparison of integer expressions of different signedness: ‘int’ and ‘const unsigned int’ [-Wsign-compare]
118 | for (int i = 0; i < sampleSize; ++i) {
| ~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp: In member function ‘int EsRuler::perturbate(const std::vector<double>&, int, SampleChunks&, double, std::mt19937&)’:
fgseaMultilevelSupplement.cpp:270:14: warning: unused variable ‘fl’ [-Wunused-variable]
270 | bool fl = false;
| ^~
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -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-3.20-bioc/R/include" -DNDEBUG -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -c util.cpp -o util.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-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-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-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)