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### Running command:
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### C:\cygwin\bin\curl.exe -O http://172.29.0.3/BBS/3.12/bioc/src/contrib/fgsea_1.16.0.tar.gz && rm -rf fgsea.buildbin-libdir && mkdir fgsea.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=fgsea.buildbin-libdir fgsea_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL fgsea_1.16.0.zip && rm fgsea_1.16.0.tar.gz fgsea_1.16.0.zip
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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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-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:446:27: 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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/aux_/iter_apply.hpp:17,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/aux_/find_if_pred.hpp:14,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/find_if.hpp:17,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/find.hpp:17,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/aux_/contains_impl.hpp:20,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/contains.hpp:20,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/math/policies/policy.hpp:10,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:15,
from fgseaMultilevelSupplement.h:9,
from fgseaMultilevel.cpp:2:
C:/Users/biocbuild/bbs-3.12-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-3.12-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>::************
^
In file included from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/math/constants/constants.hpp:11,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:20,
from fgseaMultilevelSupplement.h:9,
from fgseaMultilevel.cpp:2:
C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/math/tools/cxx03_warn.hpp:99:88: note: #pragma message: CAUTION: One or more C++11 features were found to be unavailable
BOOST_PRAGMA_MESSAGE("CAUTION: One or more C++11 features were found to be unavailable")
^
In file included from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/math/constants/constants.hpp:11,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:20,
from fgseaMultilevelSupplement.h:9,
from fgseaMultilevel.cpp:2:
C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/math/tools/cxx03_warn.hpp:100:139: note: #pragma message: CAUTION: Compiling Boost.Math in pre-C++11 conformance modes is now deprecated and will be removed from March 2021.
BOOST_PRAGMA_MESSAGE("CAUTION: Compiling Boost.Math in pre-C++11 conformance modes is now deprecated and will be removed from March 2021.")
^
C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/math/tools/cxx03_warn.hpp:101:106: note: #pragma message: CAUTION: Define BOOST_MATH_DISABLE_DEPRECATED_03_WARNING to suppress this message.
BOOST_PRAGMA_MESSAGE("CAUTION: Define BOOST_MATH_DISABLE_DEPRECATED_03_WARNING to suppress this message.")
^
C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/math/tools/cxx03_warn.hpp:102:108: note: #pragma message: CAUTION: This message was generated due to the define: BOOST_NO_CXX11_THREAD_LOCAL
BOOST_PRAGMA_MESSAGE("CAUTION: This message was generated due to the define: " BOOST_MATH_CXX03_WARN_REASON)
^
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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/aux_/iter_apply.hpp:17,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/aux_/find_if_pred.hpp:14,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/find_if.hpp:17,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/find.hpp:17,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/aux_/contains_impl.hpp:20,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/contains.hpp:20,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/math/policies/policy.hpp:10,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:15,
from fgseaMultilevelSupplement.h:9,
from fgseaMultilevelSupplement.cpp:1:
C:/Users/biocbuild/bbs-3.12-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-3.12-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>::************
^
In file included from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/math/constants/constants.hpp:11,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:20,
from fgseaMultilevelSupplement.h:9,
from fgseaMultilevelSupplement.cpp:1:
C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/math/tools/cxx03_warn.hpp:99:88: note: #pragma message: CAUTION: One or more C++11 features were found to be unavailable
BOOST_PRAGMA_MESSAGE("CAUTION: One or more C++11 features were found to be unavailable")
^
In file included from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/math/constants/constants.hpp:11,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:20,
from fgseaMultilevelSupplement.h:9,
from fgseaMultilevelSupplement.cpp:1:
C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/math/tools/cxx03_warn.hpp:100:139: note: #pragma message: CAUTION: Compiling Boost.Math in pre-C++11 conformance modes is now deprecated and will be removed from March 2021.
BOOST_PRAGMA_MESSAGE("CAUTION: Compiling Boost.Math in pre-C++11 conformance modes is now deprecated and will be removed from March 2021.")
^
C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/math/tools/cxx03_warn.hpp:101:106: note: #pragma message: CAUTION: Define BOOST_MATH_DISABLE_DEPRECATED_03_WARNING to suppress this message.
BOOST_PRAGMA_MESSAGE("CAUTION: Define BOOST_MATH_DISABLE_DEPRECATED_03_WARNING to suppress this message.")
^
C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/math/tools/cxx03_warn.hpp:102:108: note: #pragma message: CAUTION: This message was generated due to the define: BOOST_NO_CXX11_THREAD_LOCAL
BOOST_PRAGMA_MESSAGE("CAUTION: This message was generated due to the define: " BOOST_MATH_CXX03_WARN_REASON)
^
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]
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]
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]
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]
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 of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
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]
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]
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]
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]
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;
^~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c util.cpp -o util.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 util.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-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:446:27: 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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/aux_/iter_apply.hpp:17,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/aux_/find_if_pred.hpp:14,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/find_if.hpp:17,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/find.hpp:17,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/aux_/contains_impl.hpp:20,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/contains.hpp:20,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/math/policies/policy.hpp:10,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:15,
from fgseaMultilevelSupplement.h:9,
from fgseaMultilevel.cpp:2:
C:/Users/biocbuild/bbs-3.12-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-3.12-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-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-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-3.12-bioc/R/library/BH/include/boost/mpl/aux_/na_assert.hpp:23,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/arg.hpp:25,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/placeholders.hpp:24,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/apply.hpp:24,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/aux_/iter_apply.hpp:17,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/aux_/find_if_pred.hpp:14,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/find_if.hpp:17,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/find.hpp:17,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/aux_/contains_impl.hpp:20,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/mpl/contains.hpp:20,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/math/policies/policy.hpp:10,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/math/special_functions/math_fwd.hpp:29,
from C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include/boost/math/special_functions/digamma.hpp:15,
from fgseaMultilevelSupplement.h:9,
from fgseaMultilevelSupplement.cpp:1:
C:/Users/biocbuild/bbs-3.12-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-3.12-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 member function 'void EsRuler::duplicateSamples()':
fgseaMultilevelSupplement.cpp:44:37: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:54:41: 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:63:41: 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:77:37: warning: comparison of integer expressions of different signedness: 'int' and 'const unsigned int' [-Wsign-compare]
for (int sampleId = 0; sampleId < sampleSize; sampleId++) {
~~~~~~~~~^~~~~~~~~~~~
fgseaMultilevelSupplement.cpp:81:16: warning: unused variable 'currentES' [-Wunused-variable]
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]
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]
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]
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]
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]
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;
^~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.12-bioc/R/library/BH/include' -I"C:/extsoft/include" -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c util.cpp -o util.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 util.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/fgsea.buildbin-libdir/fgsea/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'fgsea' as fgsea_1.16.0.zip
* DONE (fgsea)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'fgsea' successfully unpacked and MD5 sums checked
