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This page was generated on 2021-12-03 13:04:48 -0500 (Fri, 03 Dec 2021).

INSTALL results for fgsea on nebbiolo2

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raw results

Package 640/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
fgsea 1.20.0  (landing page)
Alexey Sergushichev
Snapshot Date: 2021-12-02 01:55:06 -0500 (Thu, 02 Dec 2021)
git_url: https://git.bioconductor.org/packages/fgsea
git_branch: RELEASE_3_14
git_last_commit: b704f81
git_last_commit_date: 2021-10-26 12:28:46 -0500 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    ERROR    OK  

Summary

Package: fgsea
Version: 1.20.0
Command: /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL fgsea
StartedAt: 2021-12-02 03:14:27 -0500 (Thu, 02 Dec 2021)
EndedAt: 2021-12-02 03:14:54 -0500 (Thu, 02 Dec 2021)
EllapsedTime: 26.8 seconds
RetCode: 0
Status:   OK  

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL fgsea
###
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/library’
* installing *source* package ‘fgsea’ ...
** using staged installation
** libs
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-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-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-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 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/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c fgseaMultilevel.cpp -o fgseaMultilevel.o
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/iter_apply.hpp:17,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/find_if_pred.hpp:14,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/find_if.hpp:17,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/find.hpp:17,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/contains_impl.hpp:20,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/contains.hpp:20,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/math/policies/policy.hpp:10,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:15,
                 from fgseaMultilevelSupplement.h:9,
                 from fgseaMultilevel.cpp:2:
/home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.14-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 unsigned int’} [-Wsign-compare]
   10 |     for (int i = 0; i < posRanks.size(); i++) {
      |                     ~~^~~~~~~~~~~~~~~~~
g++ -std=gnu++11 -I"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-bioc/R/library/BH/include' -I/usr/local/include   -fpic  -g -O2  -Wall -c fgseaMultilevelSupplement.cpp -o fgseaMultilevelSupplement.o
In file included from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/iter_apply.hpp:17,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/find_if_pred.hpp:14,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/find_if.hpp:17,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/find.hpp:17,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/aux_/contains_impl.hpp:20,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/contains.hpp:20,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/math/policies/policy.hpp:10,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
                 from /home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:15,
                 from fgseaMultilevelSupplement.h:9,
                 from fgseaMultilevelSupplement.cpp:1:
/home/biocbuild/bbs-3.14-bioc/R/library/BH/include/boost/mpl/assert.hpp:194:21: warning: unnecessary parentheses in declaration of ‘assert_arg’ [-Wparentheses]
  194 | failed ************ (Pred::************
      |                     ^
/home/biocbuild/bbs-3.14-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"/home/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'/home/biocbuild/bbs-3.14-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-3.14-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-3.14-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.14-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)