Back to Multiple platform build/check report for BioC 3.20:   simplified   long
ABCDE[F]GHIJKLMNOPQRSTUVWXYZ

This page was generated on 2024-11-20 12:07 -0500 (Wed, 20 Nov 2024).

HostnameOSArch (*)R versionInstalled pkgs
teran2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4481
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4479
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4359
lconwaymacOS 12.7.1 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4539
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.1 (2024-06-14) -- "Race for Your Life" 4493
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 1.32.0  (landing page)
Alexey Sergushichev
Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024)
git_url: https://git.bioconductor.org/packages/fgsea
git_branch: RELEASE_3_20
git_last_commit: a632ca6
git_last_commit_date: 2024-10-29 10:12:01 -0500 (Tue, 29 Oct 2024)
teran2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  


CHECK results for fgsea on kunpeng2

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: fgsea
Version: 1.32.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:fgsea.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings fgsea_1.32.0.tar.gz
StartedAt: 2024-11-20 07:51:45 -0000 (Wed, 20 Nov 2024)
EndedAt: 2024-11-20 07:55:46 -0000 (Wed, 20 Nov 2024)
EllapsedTime: 241.5 seconds
RetCode: 0
Status:   OK  
CheckDir: fgsea.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:fgsea.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings fgsea_1.32.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/fgsea.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 12.2.1 20220819 (openEuler 12.2.1-14)
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fgsea/DESCRIPTION’ ... OK
* this is package ‘fgsea’ version ‘1.32.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘fgsea’ can be installed ... OK
* used C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
* checking C++ specification ... NOTE
  Specified C++11: please drop specification unless essential
* checking installed package size ... NOTE
  installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    extdata   3.9Mb
    libs      4.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
License stub is invalid DCF.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
setUpBPPARAM: warning in MulticoreParam(workers = nproc, progress =
  TRUE): partial argument match of 'progress' to 'progressbar'
addGesecaScores: no visible global function definition for
  ‘DefaultAssay’
addGesecaScores: no visible global function definition for ‘GetAssay’
collapsePathways: no visible binding for global variable ‘pathway’
collapsePathways: no visible binding for global variable ‘ES’
collapsePathwaysGeseca: no visible binding for global variable
  ‘pvalCond’
collapsePathwaysGeseca: no visible binding for global variable
  ‘pathway’
collapsePathwaysGeseca: no visible binding for global variable
  ‘reciprocalPvalCond’
collapsePathwaysGeseca: no visible binding for global variable ‘pScore’
collapsePathwaysGeseca: no visible binding for global variable ‘pval’
fgseaMultilevel: no visible binding for global variable ‘modeFraction’
fgseaMultilevel: no visible binding for global variable ‘denomProb’
fora: no visible binding for global variable ‘es’
fora: no visible binding for global variable ‘k’
fora: no visible binding for global variable ‘m’
fora: no visible binding for global variable ‘pval’
geseca: no visible binding for global variable ‘gsScore’
geseca: no visible binding for global variable ‘log2err’
geseca: no visible binding for global variable ‘nGeScore’
geseca: no visible binding for global variable ‘pctVar’
geseca: no visible binding for global variable ‘size’
geseca: no visible binding for global variable ‘pathway’
geseca: no visible global function definition for ‘.’
geseca: no visible binding for global variable ‘pval’
geseca: no visible binding for global variable ‘padj’
gesecaSimple: no visible binding for global variable ‘pctVar’
gesecaSimple: no visible binding for global variable ‘size’
gesecaSimple: no visible binding for global variable ‘pval’
gesecaSimpleImpl: no visible binding for global variable ‘pval’
gesecaSimpleImpl: no visible binding for global variable ‘nGeScore’
gesecaSimpleImpl: no visible binding for global variable ‘padj’
gesecaSimpleImpl: no visible binding for global variable ‘size’
plotCoregulationProfile: no visible binding for global variable ‘id’
plotCoregulationProfile: no visible binding for global variable ‘gene’
plotCoregulationProfile: no visible binding for global variable
  ‘expressionValue’
plotCoregulationProfile: no visible binding for global variable ‘x’
plotCoregulationProfile: no visible binding for global variable ‘y’
plotCoregulationProfile: no visible binding for global variable
  ‘condition’
plotCoregulationProfileReduction: no visible global function definition
  for ‘DefaultAssay’
plotCoregulationProfileSpatial: no visible global function definition
  for ‘DefaultAssay’
plotGesecaTable: no visible global function definition for ‘modifyList’
plotGesecaTable: no visible binding for global variable ‘pathway’
plotGesecaTable: no visible binding for global variable ‘value’
plotGesecaTable : <anonymous>: no visible binding for global variable
  ‘pathway’
plotGesecaTable : <anonymous>: no visible binding for global variable
  ‘value’
plotGseaTable: no visible global function definition for ‘modifyList’
Undefined global functions or variables:
  . DefaultAssay ES GetAssay condition denomProb es expressionValue
  gene gsScore id k log2err m modeFraction modifyList nGeScore pScore
  padj pathway pctVar pval pvalCond reciprocalPvalCond size value x y
Consider adding
  importFrom("utils", "modifyList")
to your NAMESPACE file.
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                   user system elapsed
plotGseaTable    19.301  0.887  17.205
collapsePathways 12.667  0.570   9.529
mapIdsList        9.314  0.747   7.872
fgseaSimple       7.702  1.263   3.318
fgsea             7.120  0.382   4.099
fgseaMultilevel   6.797  0.323   3.673
geseca            5.536  0.817   3.854
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 5 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/fgsea.Rcheck/00check.log’
for details.


Installation output

fgsea.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL fgsea
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.4.1/site-library’
* installing *source* package ‘fgsea’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (conda-forge gcc 14.2.0-1) 14.2.0’
using C++11
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c ScoreCalculation.cpp -o ScoreCalculation.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c ScoreRuler.cpp -o ScoreRuler.o
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/math/special_functions/digamma.hpp:15,
                 from util.h:5,
                 from ScoreRuler.cpp:2:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
   23 | #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
      |      ^~~~~~~
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++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c esCalculation.cpp -o esCalculation.o
g++ -std=gnu++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c fastGSEA.cpp -o fastGSEA.o
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/math/special_functions/digamma.hpp:15,
                 from util.h:5,
                 from fastGSEA.cpp:13:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
   23 | #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
      |      ^~~~~~~
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++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/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++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c fgseaMultilevelSupplement.cpp -o fgseaMultilevelSupplement.o
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/math/special_functions/digamma.hpp:15,
                 from util.h:5,
                 from fgseaMultilevelSupplement.cpp:3:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
   23 | #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
      |      ^~~~~~~
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++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/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++11 -I"/home/biocbuild/R/R-4.4.1/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.4.1/site-library/Rcpp/include' -I'/home/biocbuild/R/R-4.4.1/site-library/BH/include' -I/usr/local/include    -fPIC  -g -O2  -Wall  -c util.cpp -o util.o
In file included from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/math/special_functions/detail/round_fwd.hpp:11,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
                 from /home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/math/special_functions/digamma.hpp:15,
                 from util.h:5,
                 from util.cpp:1:
/home/biocbuild/R/R-4.4.1/site-library/BH/include/boost/math/tools/config.hpp:23:6: warning: #warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)" [-Wcpp]
   23 | #    warning "The minimum language standard to use Boost.Math will be C++14 starting in July 2023 (Boost 1.82 release)"
      |      ^~~~~~~
g++ -std=gnu++11 -shared -L/home/biocbuild/R/R-4.4.1/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/R/R-4.4.1/lib -lR
installing to /home/biocbuild/R/R-4.4.1/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)

Tests output

fgsea.Rcheck/tests/testthat.Rout


R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> # setting R_TESTS to empty string because of
> # https://github.com/hadley/testthat/issues/144
> # revert this when that issue in R is fixed.
> Sys.setenv("R_TESTS" = "")
> 
> library(testthat)
> library(fgsea)
> 
> test_check("fgsea")

  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |===================================                                   |  50%
  |                                                                            
  |======================================================================| 100%


  |                                                                            
  |                                                                      |   0%
  |                                                                            
  |=                                                                     |   1%
  |                                                                            
  |==                                                                    |   3%
  |                                                                            
  |===                                                                   |   4%
  |                                                                            
  |====                                                                  |   5%
  |                                                                            
  |=====                                                                 |   7%
  |                                                                            
  |======                                                                |   8%
  |                                                                            
  |=======                                                               |  10%
  |                                                                            
  |========                                                              |  11%
  |                                                                            
  |=========                                                             |  12%
  |                                                                            
  |==========                                                            |  14%
  |                                                                            
  |===========                                                           |  15%
  |                                                                            
  |============                                                          |  16%
  |                                                                            
  |============                                                          |  18%
  |                                                                            
  |=============                                                         |  19%
  |                                                                            
  |==============                                                        |  21%
  |                                                                            
  |===============                                                       |  22%
  |                                                                            
  |================                                                      |  23%
  |                                                                            
  |=================                                                     |  25%
  |                                                                            
  |==================                                                    |  26%
  |                                                                            
  |===================                                                   |  27%
  |                                                                            
  |====================                                                  |  29%
  |                                                                            
  |=====================                                                 |  30%
  |                                                                            
  |======================                                                |  32%
  |                                                                            
  |=======================                                               |  33%
  |                                                                            
  |========================                                              |  34%
  |                                                                            
  |=========================                                             |  36%
  |                                                                            
  |==========================                                            |  37%
  |                                                                            
  |===========================                                           |  38%
  |                                                                            
  |============================                                          |  40%
  |                                                                            
  |=============================                                         |  41%
  |                                                                            
  |==============================                                        |  42%
  |                                                                            
  |===============================                                       |  44%
  |                                                                            
  |================================                                      |  45%
  |                                                                            
  |=================================                                     |  47%
  |                                                                            
  |==================================                                    |  48%
  |                                                                            
  |===================================                                   |  49%
  |                                                                            
  |===================================                                   |  51%
  |                                                                            
  |====================================                                  |  52%
  |                                                                            
  |=====================================                                 |  53%
  |                                                                            
  |======================================                                |  55%
  |                                                                            
  |=======================================                               |  56%
  |                                                                            
  |========================================                              |  58%
  |                                                                            
  |=========================================                             |  59%
  |                                                                            
  |==========================================                            |  60%
  |                                                                            
  |===========================================                           |  62%
  |                                                                            
  |============================================                          |  63%
  |                                                                            
  |=============================================                         |  64%
  |                                                                            
  |==============================================                        |  66%
  |                                                                            
  |===============================================                       |  67%
  |                                                                            
  |================================================                      |  68%
  |                                                                            
  |=================================================                     |  70%
  |                                                                            
  |==================================================                    |  71%
  |                                                                            
  |===================================================                   |  73%
  |                                                                            
  |====================================================                  |  74%
  |                                                                            
  |=====================================================                 |  75%
  |                                                                            
  |======================================================                |  77%
  |                                                                            
  |=======================================================               |  78%
  |                                                                            
  |========================================================              |  79%
  |                                                                            
  |=========================================================             |  81%
  |                                                                            
  |==========================================================            |  82%
  |                                                                            
  |==========================================================            |  84%
  |                                                                            
  |===========================================================           |  85%
  |                                                                            
  |============================================================          |  86%
  |                                                                            
  |=============================================================         |  88%
  |                                                                            
  |==============================================================        |  89%
  |                                                                            
  |===============================================================       |  90%
  |                                                                            
  |================================================================      |  92%
  |                                                                            
  |=================================================================     |  93%
  |                                                                            
  |==================================================================    |  95%
  |                                                                            
  |===================================================================   |  96%
  |                                                                            
  |====================================================================  |  97%
  |                                                                            
  |===================================================================== |  99%
  |                                                                            
  |======================================================================| 100%

[ FAIL 0 | WARN 2 | SKIP 1 | PASS 142 ]

══ Skipped tests (1) ═══════════════════════════════════════════════════════════
• On Bioconductor (1): 'test_gsea_analysis.R:80:5'

[ FAIL 0 | WARN 2 | SKIP 1 | PASS 142 ]
> 
> proc.time()
   user  system elapsed 
114.185  16.874 102.069 

Example timings

fgsea.Rcheck/fgsea-Ex.timings

nameusersystemelapsed
calcGseaStat0.0400.0000.041
collapsePathways12.667 0.570 9.529
collapsePathwaysORA0.1800.0270.206
fgsea7.1200.3824.099
fgseaLabel000
fgseaMultilevel6.7970.3233.673
fgseaSimple7.7021.2633.318
fora0.9910.1860.144
geseca5.5360.8173.854
gesecaSimple0.1370.0361.680
gmtPathways1.3010.3390.104
mapIdsList9.3140.7477.872
multilevelError000
plotEnrichment0.0010.0000.002
plotEnrichmentData0.5580.0680.629
plotGseaTable19.301 0.88717.205
reactomePathways2.2870.0932.490
writeGmtPathways0.0460.0000.046