##############################################################################
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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:fgsea.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings fgsea_1.22.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/fgsea.Rcheck'
* using R version 4.2.1 (2022-06-23 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'fgsea/DESCRIPTION' ... OK
* this is package 'fgsea' version '1.22.0'
* 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
* 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'
fgseaMultilevel: no visible binding for global variable 'modeFraction'
fgseaMultilevel: no visible binding for global variable 'denomProb'
fora: no visible binding for global variable 'pval'
Undefined global functions or variables:
  ES denomProb modeFraction 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 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 for x64 is not available
File 'F:/biocbuild/bbs-3.15-bioc/R/library/fgsea/libs/x64/fgsea.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)

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 ... OK
Examples with CPU (user + system) or elapsed time > 5s
                 user system elapsed
collapsePathways 6.44   0.16   16.81
mapIdsList       5.08   0.26   18.53
reactomePathways 2.28   0.30   38.28
fgsea            1.31   0.10   14.22
fgseaSimple      1.00   0.05   19.55
fgseaMultilevel  0.99   0.04   14.31
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
  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
  'F:/biocbuild/bbs-3.15-bioc/meat/fgsea.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL fgsea
###
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* installing to library 'F:/biocbuild/bbs-3.15-bioc/R/library'
* installing *source* package 'fgsea' ...
** using staged installation
** libs
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c RcppExports.cpp -o RcppExports.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c esCalculation.cpp -o esCalculation.o
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include'   -I"C:/rtools42/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 NumericVector&, const List&, const 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++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fgseaMultilevel.cpp -o fgseaMultilevel.o
In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/lexical_cast.hpp:30,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/tools/lexical_cast.hpp:12,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/tools/convert_from_string.hpp:14,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/constants/constants.hpp:14,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:20,
                 from fgseaMultilevelSupplement.h:9,
                 from fgseaMultilevel.cpp:2:
F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
  199 | 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]
   10 |     for (int i = 0; i < posRanks.size(); i++) {
      |                     ~~^~~~~~~~~~~~~~~~~
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c fgseaMultilevelSupplement.cpp -o fgseaMultilevelSupplement.o
In file included from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_categories.hpp:16,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/iterator/iterator_facade.hpp:13,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/range/iterator_range_core.hpp:27,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/lexical_cast.hpp:30,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/tools/lexical_cast.hpp:12,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/tools/convert_from_string.hpp:14,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/constants/constants.hpp:14,
                 from F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:20,
                 from fgseaMultilevelSupplement.h:9,
                 from fgseaMultilevelSupplement.cpp:1:
F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of 'assert_arg' [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
F:/biocbuild/bbs-3.15-bioc/R/library/BH/include/boost/mpl/assert.hpp:199:21: warning: unnecessary parentheses in declaration of 'assert_not_arg' [-Wparentheses]
  199 | failed ************ (boost::mpl::not_<Pred>::************
      |                     ^
fgseaMultilevelSupplement.cpp: In member function 'void EsRuler::duplicateSamples()':
fgseaMultilevelSupplement.cpp:44:37: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
   44 |     for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
      |                            ~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:54:41: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
   54 |     for (int sampleId = 0; 2 * sampleId < sampleSize; sampleId++) {
      |                            ~~~~~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:63:41: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
   63 |     for (int sampleId = 0; 2 * sampleId < sampleSize - 2; sampleId++) {
      |                            ~~~~~~~~~~~~~^~~~~~~~~~~~~~~~
fgseaMultilevelSupplement.cpp: In member function 'void EsRuler::extend(double, int, double)':
fgseaMultilevelSupplement.cpp:77:37: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
   77 |     for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
      |                            ~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:81:16: warning: unused variable 'currentES' [-Wunused-variable]
   81 |         double currentES = calcES(ranks, currentSamples[sampleId]);
      |                ^~~~~~~~~
fgseaMultilevelSupplement.cpp:94:31: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
   94 |             for (int j = 0; j < sampleSize; ++j) {
      |                             ~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:101:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  101 |         for (int i = 0; i < sampleSize; ++i) {
      |                         ~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:116:35: warning: comparison of integer expressions of different signedness: 'int' and 'unsigned int' [-Wsign-compare]
  116 |         for (int moves = 0; moves < sampleSize * pathwaySize;) {
      |                             ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:117:45: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  117 |             for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
      |                                    ~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:122:27: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
  122 |         for (int i = 0; i < sampleSize; ++i) {
      |                         ~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp: In member function 'int EsRuler::perturbate(const std::vector<double>&, int, EsRuler::SampleChunks&, double, std::mt19937&)':
fgseaMultilevelSupplement.cpp:264:14: warning: unused variable 'fl' [-Wunused-variable]
  264 |         bool fl = false;
      |              ^~
g++  -std=gnu++11 -I"F:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG  -I'F:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'F:/biocbuild/bbs-3.15-bioc/R/library/BH/include'   -I"C:/rtools42/x86_64-w64-mingw32.static.posix/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c util.cpp -o util.o
g++ -shared -s -static-libgcc -o fgsea.dll tmp.def RcppExports.o esCalculation.o fastGSEA.o fgseaMultilevel.o fgseaMultilevelSupplement.o util.o -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib/x64 -LC:/rtools42/x86_64-w64-mingw32.static.posix/lib -LF:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to F:/biocbuild/bbs-3.15-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)

R version 4.2.1 (2022-06-23 ucrt) -- "Funny-Looking Kid"
Copyright (C) 2022 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")
[ FAIL 0 | WARN 0 | SKIP 1 | PASS 115 ]

══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 115 ]
> 
> proc.time()
   user  system elapsed 
  46.03    3.14  294.04