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CHECK report for fgsea on tokay2

This page was generated on 2020-10-17 11:56:34 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE fgsea PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 596/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fgsea 1.14.0
Alexey Sergushichev
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/fgsea
Branch: RELEASE_3_11
Last Commit: 6389c58
Last Changed Date: 2020-04-27 14:58:58 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: fgsea
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:fgsea.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings fgsea_1.14.0.tar.gz
StartedAt: 2020-10-17 04:02:58 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:12:47 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 589.0 seconds
RetCode: 0
Status:  OK  
CheckDir: fgsea.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:fgsea.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings fgsea_1.14.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/fgsea.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'fgsea/DESCRIPTION' ... OK
* this is package 'fgsea' version '1.14.0'
* 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 whether package 'fgsea' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 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
collapsePathways: no visible binding for global variable 'pathway'
collapsePathways: no visible binding for global variable 'ES'
fora: no visible binding for global variable 'pval'
Undefined global functions or variables:
  ES pathway pval
* 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 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 for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/fgsea/libs/i386/fgsea.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.11-bioc/R/library/fgsea/libs/x64/fgsea.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
mapIdsList       5.53   0.27   19.20
collapsePathways 3.93   0.27   17.95
fgseaMultilevel  1.64   0.06   15.08
fgsea            1.42   0.23   15.75
fgseaSimple      1.08   0.10   25.63
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
mapIdsList       4.50   0.14   17.18
collapsePathways 3.51   0.13   16.41
fgsea            1.25   0.14   20.78
fgseaMultilevel  1.25   0.11   13.61
fgseaSimple      1.11   0.06   26.84
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/fgsea.Rcheck/00check.log'
for details.

Installation output

fgsea.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/fgsea_1.14.0.tar.gz && rm -rf fgsea.buildbin-libdir && mkdir fgsea.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=fgsea.buildbin-libdir fgsea_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL fgsea_1.14.0.zip && rm fgsea_1.14.0.tar.gz fgsea_1.14.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  999k  100  999k    0     0  4849k      0 --:--:-- --:--:-- --:--:-- 5021k

install for i386

* installing *source* package 'fgsea' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c esCalculation.cpp -o esCalculation.o
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c fastGSEA.cpp -o fastGSEA.o
fastGSEA.cpp: In function 'Rcpp::NumericVector calcGseaStatBatchCpp(const NumericVector&, const List&, const IntegerVector&)':
fastGSEA.cpp:461:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'unsigned int'} [-Wsign-compare]
         for (int j = 0; j < S.size(); ++j) {
                         ~~^~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c fgseaMultilevel.cpp -o fgseaMultilevel.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/iter_apply.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/find_if_pred.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/find_if.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/find.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/contains_impl.hpp:20,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/contains.hpp:20,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/policies/policy.hpp:10,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:15,
                 from fgseaMultilevelSupplement.h:7,
                 from fgseaMultilevel.cpp:2:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
fgseaMultilevel.cpp: In function 'Rcpp::DataFrame fgseaMultilevelCpp(const NumericVector&, const 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 'unsigned int'} [-Wsign-compare]
     for (int i = 0; i < posRanks.size(); i++) {
                     ~~^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c fgseaMultilevelSupplement.cpp -o fgseaMultilevelSupplement.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/iter_apply.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/find_if_pred.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/find_if.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/find.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/contains_impl.hpp:20,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/contains.hpp:20,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/policies/policy.hpp:10,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:15,
                 from fgseaMultilevelSupplement.h:7,
                 from fgseaMultilevelSupplement.cpp:1:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
fgseaMultilevelSupplement.cpp: In function 'void fillRandomSample(std::set<int>&, std::mt19937&, long unsigned int, unsigned int)':
fgseaMultilevelSupplement.cpp:31:50: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
     while (static_cast<int>(randomSample.size()) < pathwaySize) {
            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
fgseaMultilevelSupplement.cpp: In member function 'void EsRuler::duplicateSamples()':
fgseaMultilevelSupplement.cpp:56:37: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
     for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
                            ~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:66:41: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
     for (int sampleId = 0; 2 * sampleId < sampleSize; sampleId++) {
                            ~~~~~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:75:41: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
     for (int sampleId = 0; 2 * sampleId < sampleSize - 2; sampleId++) {
                            ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
fgseaMultilevelSupplement.cpp: In member function 'void EsRuler::extend(double, int, double)':
fgseaMultilevelSupplement.cpp:89:37: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
     for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
                            ~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:107:35: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
         for (int moves = 0; moves < sampleSize * pathwaySize;) {
                             ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:108:47: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
             for (int sample_id = 0; sample_id < sampleSize; sample_id++) {
                                     ~~~~~~~~~~^~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fgsea_init.c -o fgsea_init.o
C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o fgsea.dll tmp.def RcppExports.o esCalculation.o fastGSEA.o fgseaMultilevel.o fgseaMultilevelSupplement.o fgsea_init.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/fgsea.buildbin-libdir/00LOCK-fgsea/00new/fgsea/libs/i386
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'fgsea'
    finding HTML links ... done
    calcGseaStat                            html  
    calcGseaStatBatchCpp                    html  
    collapsePathways                        html  
    collapsePathwaysORA                     html  
    examplePathways                         html  
    exampleRanks                            html  
    fgsea                                   html  
    fgseaLabel                              html  
    fgseaMultilevel                         html  
    fgseaSimple                             html  
    fgseaSimpleImpl                         html  
    fora                                    html  
    gmtPathways                             html  
    mapIdsList                              html  
    multilevelError                         html  
    multilevelImpl                          html  
    plotEnrichment                          html  
    plotGseaTable                           html  
    reactomePathways                        html  
    writeGmtPathways                        html  
** 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

install for x64

* installing *source* package 'fgsea' ...
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c esCalculation.cpp -o esCalculation.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c fastGSEA.cpp -o fastGSEA.o
fastGSEA.cpp: In function 'Rcpp::NumericVector calcGseaStatBatchCpp(const NumericVector&, const List&, const IntegerVector&)':
fastGSEA.cpp:461:27: warning: comparison of integer expressions of different signedness: 'int' and 'std::vector<int>::size_type' {aka 'long long unsigned int'} [-Wsign-compare]
         for (int j = 0; j < S.size(); ++j) {
                         ~~^~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c fgseaMultilevel.cpp -o fgseaMultilevel.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/iter_apply.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/find_if_pred.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/find_if.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/find.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/contains_impl.hpp:20,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/contains.hpp:20,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/policies/policy.hpp:10,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:15,
                 from fgseaMultilevelSupplement.h:7,
                 from fgseaMultilevel.cpp:2:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
fgseaMultilevel.cpp: In function 'Rcpp::DataFrame fgseaMultilevelCpp(const NumericVector&, const 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]
     for (int i = 0; i < posRanks.size(); i++) {
                     ~~^~~~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c fgseaMultilevelSupplement.cpp -o fgseaMultilevelSupplement.o
In file included from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/iter_apply.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/find_if_pred.hpp:14,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/find_if.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/find.hpp:17,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/aux_/contains_impl.hpp:20,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/contains.hpp:20,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/policies/policy.hpp:10,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
                 from C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:15,
                 from fgseaMultilevelSupplement.h:7,
                 from fgseaMultilevelSupplement.cpp:1:
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
 failed ************ (Pred::************
                     ^
C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
 failed ************ (boost::mpl::not_<Pred>::************
                     ^
fgseaMultilevelSupplement.cpp: In function 'void fillRandomSample(std::set<int>&, std::mt19937&, long unsigned int, unsigned int)':
fgseaMultilevelSupplement.cpp:31:50: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
     while (static_cast<int>(randomSample.size()) < pathwaySize) {
            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~
fgseaMultilevelSupplement.cpp: In member function 'void EsRuler::duplicateSamples()':
fgseaMultilevelSupplement.cpp:56:37: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
     for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
                            ~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:66:41: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
     for (int sampleId = 0; 2 * sampleId < sampleSize; sampleId++) {
                            ~~~~~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:75:41: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
     for (int sampleId = 0; 2 * sampleId < sampleSize - 2; sampleId++) {
                            ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
fgseaMultilevelSupplement.cpp: In member function 'void EsRuler::extend(double, int, double)':
fgseaMultilevelSupplement.cpp:89:37: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
     for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
                            ~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:107:35: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
         for (int moves = 0; moves < sampleSize * pathwaySize;) {
                             ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:108:47: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
             for (int sample_id = 0; sample_id < sampleSize; sample_id++) {
                                     ~~~~~~~~~~^~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"gcc  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/BH/include'   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c fgsea_init.c -o fgsea_init.o
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o fgsea.dll tmp.def RcppExports.o esCalculation.o fastGSEA.o fgseaMultilevel.o fgseaMultilevelSupplement.o fgsea_init.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/fgsea.buildbin-libdir/fgsea/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'fgsea' as fgsea_1.14.0.zip
* DONE (fgsea)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'fgsea' successfully unpacked and MD5 sums checked

Tests output

fgsea.Rcheck/tests_i386/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

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")
== testthat results  ===========================================================
[ OK: 96 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  41.32    1.67  141.20

fgsea.Rcheck/tests_x64/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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")
== testthat results  ===========================================================
[ OK: 96 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
  41.90    1.37  132.18

Example timings

fgsea.Rcheck/examples_i386/fgsea-Ex.timings

nameusersystemelapsed
calcGseaStat0.040.000.04
collapsePathways 3.93 0.2717.95
collapsePathwaysORA0.130.000.12
fgsea 1.42 0.2315.75
fgseaLabel000
fgseaMultilevel 1.64 0.0615.08
fgseaSimple 1.08 0.1025.63
fora0.080.010.09
gmtPathways0.250.001.47
mapIdsList 5.53 0.2719.20
multilevelError000
plotEnrichment0.000.010.02
plotGseaTable0.470.020.48
reactomePathways2.610.032.64
writeGmtPathways0.030.020.10

fgsea.Rcheck/examples_x64/fgsea-Ex.timings

nameusersystemelapsed
calcGseaStat0.020.010.03
collapsePathways 3.51 0.1316.41
collapsePathwaysORA0.140.000.14
fgsea 1.25 0.1420.78
fgseaLabel000
fgseaMultilevel 1.25 0.1113.61
fgseaSimple 1.11 0.0626.84
fora0.160.000.16
gmtPathways0.120.000.12
mapIdsList 4.50 0.1417.18
multilevelError000
plotEnrichment0.000.020.01
plotGseaTable0.380.000.38
reactomePathways1.890.112.00
writeGmtPathways0.030.001.47