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This page was generated on 2024-12-23 12:05 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (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 713/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fgsea 1.32.2  (landing page)
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)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  YES
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  YES
merida1macOS 12.7.5 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson1macOS 13.6.6 Ventura / arm64  OK    ERROR  skippedskipped


INSTALL results for fgsea on palomino8

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.

raw results


Summary

Package: fgsea
Version: 1.32.2
Command: F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL fgsea
StartedAt: 2024-12-19 16:31:43 -0500 (Thu, 19 Dec 2024)
EndedAt: 2024-12-19 16:32:50 -0500 (Thu, 19 Dec 2024)
EllapsedTime: 66.7 seconds
RetCode: 0
Status:   OK  

Command output

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### Running command:
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###   F:\biocbuild\bbs-3.20-bioc\R\bin\R.exe CMD INSTALL fgsea
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* installing to library 'F:/biocbuild/bbs-3.20-bioc/R/library'
* installing *source* package 'fgsea' ...
** using staged installation
** libs
using C++ compiler: 'G__~1.EXE (GCC) 13.3.0'
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c ScoreCalculation.cpp -o ScoreCalculation.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c esCalculation.cpp -o esCalculation.o
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 long unsigned int'} [-Wsign-compare]
  446 |         for (int j = 0; j < S.size(); ++j) {
      |                         ~~^~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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 long unsigned int'} [-Wsign-compare]
   10 |     for (int i = 0; i < posRanks.size(); i++) {
      |                     ~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++17  -I"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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"F:/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.20-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.20-bioc/R/library/BH/include'   -I"C:/rtools44/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c util.cpp -o util.o
g++ -std=gnu++17 -shared -s -static-libgcc -o fgsea.dll tmp.def RcppExports.o ScoreCalculation.o ScoreRuler.o esCalculation.o fastGSEA.o fgseaMultilevel.o fgseaMultilevelSupplement.o geseca.o util.o -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools44/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.20-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.20-bioc/R/library/00LOCK-fgsea/00new/fgsea/libs/x64
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (fgsea)