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### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:fgsea.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings fgsea_1.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/fgsea.Rcheck’
* using R version 4.0.5 (2021-03-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fgsea/DESCRIPTION’ ... OK
* this is package ‘fgsea’ version ‘1.16.0’
* 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
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   1.9Mb
    libs      2.8Mb
* 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 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
collapsePathways 10.332  0.312   6.371
fgseaSimple       9.880  0.676   3.519
mapIdsList        8.800  0.628   5.745
fgseaMultilevel   7.260  0.256   2.819
fgsea             6.776  0.236   2.885
* 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: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.12-bioc/meat/fgsea.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL fgsea
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* installing to library ‘/home/biocbuild/bbs-3.12-bioc/R/library’
* installing *source* package ‘fgsea’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c esCalculation.cpp -o esCalculation.o
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -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 between signed and unsigned integer expressions [-Wsign-compare]
         for (int j = 0; j < S.size(); ++j) {
                         ~~^~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/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 NumericVector&, const NumericVector&, int, int, int, double, bool)’:
fgseaMultilevel.cpp:10:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int i = 0; i < posRanks.size(); i++) {
                     ~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c fgseaMultilevelSupplement.cpp -o fgseaMultilevelSupplement.o
fgseaMultilevelSupplement.cpp: In member function ‘void EsRuler::duplicateSamples()’:
fgseaMultilevelSupplement.cpp:44:37: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
                            ~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:54:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for (int sampleId = 0; 2 * sampleId < sampleSize; sampleId++) {
                            ~~~~~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:63:41: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     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 between signed and unsigned integer expressions [-Wsign-compare]
     for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
                            ~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:81:16: warning: unused variable ‘currentES’ [-Wunused-variable]
         double currentES = calcES(ranks, currentSamples[sampleId]);
                ^~~~~~~~~
fgseaMultilevelSupplement.cpp:94:31: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int j = 0; j < sampleSize; ++j) {
                             ~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:101:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int i = 0; i < sampleSize; ++i) {
                         ~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:116:35: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for (int moves = 0; moves < sampleSize * pathwaySize;) {
                             ~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:117:45: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
             for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
                                    ~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:122:27: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         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]
         bool fl = false;
              ^~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.12-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c util.cpp -o util.o
g++ -std=gnu++11 -shared -L/home/biocbuild/bbs-3.12-bioc/R/lib -L/usr/local/lib -o fgsea.so RcppExports.o esCalculation.o fastGSEA.o fgseaMultilevel.o fgseaMultilevelSupplement.o util.o -L/home/biocbuild/bbs-3.12-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.12-bioc/R/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)

R version 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

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Type 'license()' or 'licence()' for distribution details.

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> # 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")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• On Bioconductor (1)

[ FAIL 0 | WARN 0 | SKIP 1 | PASS 98 ]
> 
> proc.time()
   user  system elapsed 
 71.820   4.628  55.171