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This page was generated on 2025-03-20 13:54 -0400 (Thu, 20 Mar 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | R Under development (unstable) (2025-01-20 r87609) -- "Unsuffered Consequences" | 869 |
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Package 81/217 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | |||||||
fgsea 1.33.4 (landing page) Alexey Sergushichev
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | ERROR | skipped | |||||||
To the developers/maintainers of the fgsea package: - 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: 1.33.4 |
Command: /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data fgsea |
StartedAt: 2025-03-20 12:36:14 -0400 (Thu, 20 Mar 2025) |
EndedAt: 2025-03-20 12:36:36 -0400 (Thu, 20 Mar 2025) |
EllapsedTime: 22.0 seconds |
RetCode: 1 |
Status: ERROR |
PackageFile: None |
PackageFileSize: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/rapidbuild/bbs-3.21-bioc-rapid/R/bin/R CMD build --keep-empty-dirs --no-resave-data fgsea ### ############################################################################## ############################################################################## * checking for file ‘fgsea/DESCRIPTION’ ... OK * preparing ‘fgsea’: * checking DESCRIPTION meta-information ... OK * cleaning src * installing the package to build vignettes ----------------------------------- * installing *source* package ‘fgsea’ ... ** this is package ‘fgsea’ version ‘1.33.4’ ** using staged installation ** libs using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’ g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c RcppExports.cpp -o RcppExports.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c ScoreCalculation.cpp -o ScoreCalculation.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c esCalculation.cpp -o esCalculation.o g++ -std=gnu++17 -I"/home/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -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/rapidbuild/bbs-3.21-bioc-rapid/R/include" -DNDEBUG -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/Rcpp/include' -I'/media/volume/teran2_disk/rapidbuild/bbs-3.21-bioc-rapid/R/site-library/BH/include' -I/usr/local/include -fpic -g -O2 -Wall -Werror=format-security -DR_NO_REMAP -c util.cpp -o util.o g++ -std=gnu++17 -shared -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 installing to /tmp/Rtmp6hq3gT/Rinstd536953cd4362/00LOCK-fgsea/00new/fgsea/libs ** R Warning in dir.create(outCodeDir) : cannot create dir '/tmp/Rtmp6hq3gT/Rinstd536953cd4362/00LOCK-fgsea/00new/fgsea/R', reason 'No space left on device' Error in .install_package_code_files(".", instdir) : cannot open directory '/tmp/Rtmp6hq3gT/Rinstd536953cd4362/00LOCK-fgsea/00new/fgsea/R' ERROR: unable to collate and parse R files for package ‘fgsea’ * removing ‘/tmp/Rtmp6hq3gT/Rinstd536953cd4362/fgsea’ ----------------------------------- ERROR: package installation failed