Hector Climente
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/Rgin |
| Branch: RELEASE_3_8 |
| Last Commit: 91b6885 |
| Last Changed Date: 2018-10-30 11:42:08 -0400 (Tue, 30 Oct 2018) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:53:18 -0400 (Tue, 16 Apr 2019).
| Package 1298/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| Rgin 1.2.0 Hector Climente
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | [ WARNINGS ] | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: Rgin |
| Version: 1.2.0 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:Rgin.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings Rgin_1.2.0.tar.gz |
| StartedAt: 2019-04-16 02:35:49 -0400 (Tue, 16 Apr 2019) |
| EndedAt: 2019-04-16 02:35:59 -0400 (Tue, 16 Apr 2019) |
| EllapsedTime: 9.5 seconds |
| RetCode: 0 |
| Status: WARNINGS |
| CheckDir: Rgin.Rcheck |
| Warnings: 1 |
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### Running command:
###
### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:Rgin.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings Rgin_1.2.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/Rgin.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘Rgin/DESCRIPTION’ ... OK
* this is package ‘Rgin’ version ‘1.2.0’
* 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 ‘Rgin’ can be installed ... WARNING
Found the following significant warnings:
src/model_selection/grid_cv.cc:128:43: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/home/biocbuild/bbs-3.8-bioc/meat/Rgin.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
installed size is 94.1Mb
sub-directories of 1Mb or more:
include 3.1Mb
usrlib 90.9Mb
* 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 ... OK
* checking for missing documentation entries ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking include directives in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* 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: 1 WARNING, 2 NOTEs
See
‘/home/biocbuild/bbs-3.8-bioc/meat/Rgin.Rcheck/00check.log’
for details.
Rgin.Rcheck/00install.out
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###
### Running command:
###
### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL Rgin
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘Rgin’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c Rgin-init.c -o Rgin-init.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -lz -fpic -g -O2 -Wall -c src/feature_selection/feature_selector.cc -o src/feature_selection/feature_selector.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -lz -fpic -g -O2 -Wall -c src/feature_selection/scones.cc -o src/feature_selection/scones.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -lz -fpic -g -O2 -Wall -c src/feature_selection/shake.cc -o src/feature_selection/shake.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -lz -fpic -g -O2 -Wall -c src/gwas/CGWASData.cc -o src/gwas/CGWASData.o
src/gwas/CGWASData.cc: In static member function ‘static GWASData CGWASDataHelper::removeSamples4MissingData(const GWASData&, const uint&, bool)’:
src/gwas/CGWASData.cc:757:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(uint64 j=0; j<sindices.size(); j++) {
^
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -lz -fpic -g -O2 -Wall -c src/gwas/CScones.cc -o src/gwas/CScones.o
src/gwas/CScones.cc: In member function ‘VectorXd CScones::__computeChisqScore(const MatrixXd&, const VectorXd&)’:
src/gwas/CScones.cc:203:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (uint64 i = 0; i < X.cols(); i++) {
^
src/gwas/CScones.cc: In member function ‘VectorXd CScones::__computeCochranArmitageT(const MatrixXd&, const VectorXd&, const string&)’:
src/gwas/CScones.cc:225:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (uint64 i = 0; i < X.cols(); i++) {
^
src/gwas/CScones.cc: In member function ‘void CScones::test_associations()’:
src/gwas/CScones.cc:404:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (uint64 i=1; i <= __settings.gridsearch_depth; i++){
^
src/gwas/CScones.cc:436:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if (i < __settings.gridsearch_depth){
^
src/gwas/CScones.cc:464:26: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(uint64 i=0; i<__indicator_vector.rows();i++) {
^
src/gwas/CScones.cc: In member function ‘MatrixXd CScones::__evaluateInformation()’:
src/gwas/CScones.cc:529:30: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(uint64 i=0; i<indicator_vector.rows();i++) {
^
src/gwas/CScones.cc: In member function ‘SparseMatrixXd CScones::__computeLaplacianMatrix()’:
src/gwas/CScones.cc:634:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (uint64 k = 0; k < W.outerSize(); ++k)
^
src/gwas/CScones.cc: In member function ‘void CScones::test_associations()’:
src/gwas/CScones.cc:400:21: warning: ‘best_eta_index’ may be used uninitialized in this function [-Wmaybe-uninitialized]
MatrixXd::Index best_eta_index, best_lambda_index;
^
src/gwas/CScones.cc:400:37: warning: ‘best_lambda_index’ may be used uninitialized in this function [-Wmaybe-uninitialized]
MatrixXd::Index best_eta_index, best_lambda_index;
^
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -lz -fpic -g -O2 -Wall -c src/io/CGWASDataIO.cc -o src/io/CGWASDataIO.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -lz -fpic -g -O2 -Wall -c src/io/CIOProgress.cc -o src/io/CIOProgress.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -lz -fpic -g -O2 -Wall -c src/io/CLogging.cc -o src/io/CLogging.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -lz -fpic -g -O2 -Wall -c src/io/CPlinkParser.cc -o src/io/CPlinkParser.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -lz -fpic -g -O2 -Wall -c src/io/CSconesIO.cc -o src/io/CSconesIO.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -lz -fpic -g -O2 -Wall -c src/io/grid_views.cc -o src/io/grid_views.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -lz -fpic -g -O2 -Wall -c src/model_selection/CCrossValidation.cc -o src/model_selection/CCrossValidation.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -lz -fpic -g -O2 -Wall -c src/model_selection/grid.cc -o src/model_selection/grid.o
src/model_selection/grid.cc: In member function ‘void Grid::__initGrid()’:
src/model_selection/grid.cc:35:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (uint64 e = 0; e < __etas.rows(); e++) {
^
src/model_selection/grid.cc:36:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (uint64 l = 0; l < __lambdas.rows(); l++) {
^
src/model_selection/grid.cc: In member function ‘void Grid::search()’:
src/model_selection/grid.cc:46:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (uint64 e = 0; e < __etas.rows(); e++) {
^
src/model_selection/grid.cc:47:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (uint64 l = 0; l < __lambdas.rows(); l++) {
^
src/model_selection/grid.cc: In member function ‘std::vector<Eigen::Matrix<double, -1, 1> > Grid::selected(const VectorXd&, const VectorXd&)’:
src/model_selection/grid.cc:68:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (uint64 e = 0; e < etas.rows(); e++) {
^
src/model_selection/grid.cc:69:24: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (uint64 l = 0; l < lambdas.rows(); l++) {
^
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -lz -fpic -g -O2 -Wall -c src/model_selection/grid_cv.cc -o src/model_selection/grid_cv.o
src/model_selection/grid_cv.cc: In destructor ‘virtual GridCV::˜GridCV()’:
src/model_selection/grid_cv.cc:42:9: warning: deleting object of polymorphic class type ‘CRegression’ which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor]
delete __classifier;
^
src/model_selection/grid_cv.cc: In member function ‘virtual void GridCV::scoreModels(uint)’:
src/model_selection/grid_cv.cc:128:43: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
if (aggregatedFolds(e,l).array().sum() > (__X->cols() * 0.05) | aggregatedFolds(e,l).array().sum() == 0) {
^
src/model_selection/grid_cv.cc: In member function ‘double GridCV::__computeInformation(VectorXd, uint)’:
src/model_selection/grid_cv.cc:170:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(uint64 i = 0; i < folds.rows(); i++) {
^
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -lz -fpic -g -O2 -Wall -c src/regression/CRegression.cc -o src/regression/CRegression.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -lz -fpic -g -O2 -Wall -c src/stats/CFisherF.cc -o src/stats/CFisherF.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -lz -fpic -g -O2 -Wall -c src/stats/CStats.cc -o src/stats/CStats.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -lz -fpic -g -O2 -Wall -c src/stats/univariate_association.cc -o src/stats/univariate_association.o
src/stats/univariate_association.cc: In member function ‘virtual VectorXd UnivariateAssociation::computeTrendTest(const string&)’:
src/stats/univariate_association.cc:86:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (uint64 i = 0; i < __X -> cols(); i++) {
^
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -lz -fpic -g -O2 -Wall -c src/stats/CChi2.cc -o src/stats/CChi2.o
src/stats/CChi2.cc: In static member function ‘static MatrixXd CChi2::get2DContingencyTable(const VectorXd&, const VectorXd&, bool)’:
src/stats/CChi2.cc:62:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (uint64 i = 0; i < x.size(); i++)
^
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -lz -fpic -g -O2 -Wall -c src/stats/CGamma.cc -o src/stats/CGamma.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -lz -fpic -g -O2 -Wall -c src/stats/CStudentT.cc -o src/stats/CStudentT.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -lz -fpic -g -O2 -Wall -c src/utils/CKernels.cc -o src/utils/CKernels.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -lz -fpic -g -O2 -Wall -c src/utils/CMisc.cc -o src/utils/CMisc.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -lz -fpic -g -O2 -Wall -c src/utils/CRootFinding.cc -o src/utils/CRootFinding.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -lz -fpic -g -O2 -Wall -c src/utils/random.cc -o src/utils/random.o
src/utils/random.cc: In function ‘VectorXd urand(int)’:
src/utils/random.cc:69:23: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (uint64 i = 0; i < size; i++) {
^
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -lz -fpic -g -O2 -Wall -c src/utils/StringHelper.cc -o src/utils/StringHelper.o
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -lz -fpic -g -O2 -Wall -c src/utils/utils.cc -o src/utils/utils.o
ar -crus libgin.a src/feature_selection/feature_selector.o src/feature_selection/scones.o src/feature_selection/shake.o src/gwas/CGWASData.o src/gwas/CScones.o src/io/CGWASDataIO.o src/io/CIOProgress.o src/io/CLogging.o src/io/CPlinkParser.o src/io/CSconesIO.o src/io/grid_views.o src/model_selection/CCrossValidation.o src/model_selection/grid.o src/model_selection/grid_cv.o src/regression/CRegression.o src/stats/CFisherF.o src/stats/CStats.o src/stats/univariate_association.o src/stats/CChi2.o src/stats/CGamma.o src/stats/CStudentT.o src/utils/CKernels.o src/utils/CMisc.o src/utils/CRootFinding.o src/utils/random.o src/utils/StringHelper.o src/utils/utils.o
ar: `u' modifier ignored since `D' is the default (see `U')
g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fopenmp -D_USE_KNETFILE -D_FILE_OFFSET_BITS=64 -U_FORTIFY_SOURCE -DBGZF_CACHE -DAS_GINLIB -DAS_RGINLIB -I./include -I./lib `/home/biocbuild/bbs-3.8-bioc/R/bin/Rscript -e "Rcpp:::CxxFlags()"` -lz -fpic -g -O2 -Wall -c lib/maxflow/maxflow.cpp -o lib/maxflow/maxflow.o
ar -crus libmaxflow.a lib/maxflow/maxflow.o
ar: `u' modifier ignored since `D' is the default (see `U')
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/acosh.c -o lib/Cephes/double/acosh.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/airy.c -o lib/Cephes/double/airy.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/asin.c -o lib/Cephes/double/asin.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/asinh.c -o lib/Cephes/double/asinh.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/atan.c -o lib/Cephes/double/atan.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/atanh.c -o lib/Cephes/double/atanh.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/bdtr.c -o lib/Cephes/double/bdtr.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/beta.c -o lib/Cephes/double/beta.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/btdtr.c -o lib/Cephes/double/btdtr.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/cbrt.c -o lib/Cephes/double/cbrt.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/chbevl.c -o lib/Cephes/double/chbevl.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/chdtr.c -o lib/Cephes/double/chdtr.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/clog.c -o lib/Cephes/double/clog.o
lib/Cephes/double/clog.c:61:8: warning: conflicting types for built-in function ‘cabs’
double cabs (cmplx *);
^
lib/Cephes/double/clog.c:64:6: warning: conflicting types for built-in function ‘csqrt’
void csqrt ( cmplx *, cmplx * );
^
lib/Cephes/double/clog.c:68:6: warning: conflicting types for built-in function ‘clog’
void clog ( cmplx *, cmplx * );
^
lib/Cephes/double/clog.c:69:6: warning: conflicting types for built-in function ‘casin’
void casin ( cmplx *, cmplx * );
^
lib/Cephes/double/clog.c:70:6: warning: conflicting types for built-in function ‘cacos’
void cacos ( cmplx *, cmplx * );
^
lib/Cephes/double/clog.c:71:6: warning: conflicting types for built-in function ‘catan’
void catan ( cmplx *, cmplx * );
^
lib/Cephes/double/clog.c:142:6: warning: conflicting types for built-in function ‘cexp’
void cexp( z, w )
^
lib/Cephes/double/clog.c:187:6: warning: conflicting types for built-in function ‘csin’
void csin( z, w )
^
lib/Cephes/double/clog.c:255:6: warning: conflicting types for built-in function ‘ccos’
void ccos( z, w )
^
lib/Cephes/double/clog.c:304:6: warning: conflicting types for built-in function ‘ctan’
void ctan( z, w )
^
lib/Cephes/double/clog.c:765:1: warning: conflicting types for built-in function ‘csinh’
csinh (z, w)
^
lib/Cephes/double/clog.c:805:1: warning: conflicting types for built-in function ‘casinh’
casinh (z, w)
^
lib/Cephes/double/clog.c:847:1: warning: conflicting types for built-in function ‘ccosh’
ccosh (z, w)
^
lib/Cephes/double/clog.c:887:1: warning: conflicting types for built-in function ‘cacosh’
cacosh (z, w)
^
lib/Cephes/double/clog.c:929:1: warning: conflicting types for built-in function ‘ctanh’
ctanh (z, w)
^
lib/Cephes/double/clog.c:971:1: warning: conflicting types for built-in function ‘catanh’
catanh (z, w)
^
lib/Cephes/double/clog.c:1018:1: warning: conflicting types for built-in function ‘cpow’
cpow (a, z, w)
^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/cmplx.c -o lib/Cephes/double/cmplx.o
lib/Cephes/double/cmplx.c:76:15: warning: conflicting types for built-in function ‘cabs’
extern double cabs ( cmplx * );
^
lib/Cephes/double/cmplx.c:390:6: warning: conflicting types for built-in function ‘csqrt’
void csqrt( z, w )
^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/const.c -o lib/Cephes/double/const.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/cosh.c -o lib/Cephes/double/cosh.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/dawsn.c -o lib/Cephes/double/dawsn.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/drand.c -o lib/Cephes/double/drand.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/ei.c -o lib/Cephes/double/ei.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/ellie.c -o lib/Cephes/double/ellie.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/ellik.c -o lib/Cephes/double/ellik.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/ellpe.c -o lib/Cephes/double/ellpe.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/ellpj.c -o lib/Cephes/double/ellpj.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/ellpk.c -o lib/Cephes/double/ellpk.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/exp.c -o lib/Cephes/double/exp.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/exp10.c -o lib/Cephes/double/exp10.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/exp2.c -o lib/Cephes/double/exp2.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/expn.c -o lib/Cephes/double/expn.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/expx2.c -o lib/Cephes/double/expx2.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/fabs.c -o lib/Cephes/double/fabs.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/fac.c -o lib/Cephes/double/fac.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/fdtr.c -o lib/Cephes/double/fdtr.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/fresnl.c -o lib/Cephes/double/fresnl.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/gamma.c -o lib/Cephes/double/gamma.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/gdtr.c -o lib/Cephes/double/gdtr.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/hyp2f1.c -o lib/Cephes/double/hyp2f1.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/hyperg.c -o lib/Cephes/double/hyperg.o
lib/Cephes/double/hyperg.c: In function ‘hyperg’:
lib/Cephes/double/hyperg.c:110:3: warning: ‘pcanc’ may be used uninitialized in this function [-Wmaybe-uninitialized]
if( acanc < pcanc )
^
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/i0.c -o lib/Cephes/double/i0.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/i1.c -o lib/Cephes/double/i1.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/igami.c -o lib/Cephes/double/igami.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/incbet.c -o lib/Cephes/double/incbet.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/incbi.c -o lib/Cephes/double/incbi.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/igam.c -o lib/Cephes/double/igam.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/isnan.c -o lib/Cephes/double/isnan.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/iv.c -o lib/Cephes/double/iv.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/j0.c -o lib/Cephes/double/j0.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/j1.c -o lib/Cephes/double/j1.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/jn.c -o lib/Cephes/double/jn.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/jv.c -o lib/Cephes/double/jv.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/k0.c -o lib/Cephes/double/k0.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/k1.c -o lib/Cephes/double/k1.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/kn.c -o lib/Cephes/double/kn.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/kolmogorov.c -o lib/Cephes/double/kolmogorov.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/log.c -o lib/Cephes/double/log.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/log2.c -o lib/Cephes/double/log2.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/log10.c -o lib/Cephes/double/log10.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/lrand.c -o lib/Cephes/double/lrand.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/nbdtr.c -o lib/Cephes/double/nbdtr.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/ndtr.c -o lib/Cephes/double/ndtr.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/ndtri.c -o lib/Cephes/double/ndtri.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/pdtr.c -o lib/Cephes/double/pdtr.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/planck.c -o lib/Cephes/double/planck.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/polevl.c -o lib/Cephes/double/polevl.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/polmisc.c -o lib/Cephes/double/polmisc.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/polylog.c -o lib/Cephes/double/polylog.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/polyn.c -o lib/Cephes/double/polyn.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/pow.c -o lib/Cephes/double/pow.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/powi.c -o lib/Cephes/double/powi.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/psi.c -o lib/Cephes/double/psi.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/rgamma.c -o lib/Cephes/double/rgamma.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/round.c -o lib/Cephes/double/round.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/shichi.c -o lib/Cephes/double/shichi.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/sici.c -o lib/Cephes/double/sici.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/sin.c -o lib/Cephes/double/sin.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/sindg.c -o lib/Cephes/double/sindg.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/sinh.c -o lib/Cephes/double/sinh.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/spence.c -o lib/Cephes/double/spence.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/stdtr.c -o lib/Cephes/double/stdtr.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/struve.c -o lib/Cephes/double/struve.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/tan.c -o lib/Cephes/double/tan.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/tandg.c -o lib/Cephes/double/tandg.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/tanh.c -o lib/Cephes/double/tanh.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/unity.c -o lib/Cephes/double/unity.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/yn.c -o lib/Cephes/double/yn.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/zeta.c -o lib/Cephes/double/zeta.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/zetac.c -o lib/Cephes/double/zetac.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/sqrt.c -o lib/Cephes/double/sqrt.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/floor.c -o lib/Cephes/double/floor.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/setprec.c -o lib/Cephes/double/setprec.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -I"/home/biocbuild/bbs-3.8-bioc/R/library/RcppEigen/include" -I/usr/local/include -fpic -g -O2 -Wall -c lib/Cephes/double/mtherr.c -o lib/Cephes/double/mtherr.o
lib/Cephes/double/mtherr.c:66:14: warning: ‘ermsg’ defined but not used [-Wunused-variable]
static char *ermsg[7] = {
^
ar -crus libcephes.a lib/Cephes/double/acosh.o lib/Cephes/double/airy.o lib/Cephes/double/asin.o lib/Cephes/double/asinh.o lib/Cephes/double/atan.o lib/Cephes/double/atanh.o lib/Cephes/double/bdtr.o lib/Cephes/double/beta.o lib/Cephes/double/btdtr.o lib/Cephes/double/cbrt.o lib/Cephes/double/chbevl.o lib/Cephes/double/chdtr.o lib/Cephes/double/clog.o lib/Cephes/double/cmplx.o lib/Cephes/double/const.o lib/Cephes/double/cosh.o lib/Cephes/double/dawsn.o lib/Cephes/double/drand.o lib/Cephes/double/ei.o lib/Cephes/double/ellie.o lib/Cephes/double/ellik.o lib/Cephes/double/ellpe.o lib/Cephes/double/ellpj.o lib/Cephes/double/ellpk.o lib/Cephes/double/exp.o lib/Cephes/double/exp10.o lib/Cephes/double/exp2.o lib/Cephes/double/expn.o lib/Cephes/double/expx2.o lib/Cephes/double/fabs.o lib/Cephes/double/fac.o lib/Cephes/double/fdtr.o lib/Cephes/double/fresnl.o lib/Cephes/double/gamma.o lib/Cephes/double/gdtr.o lib/Cephes/double/hyp2f1.o lib/Cephes/double/hyperg.o lib/Cephes/double/i0.o lib/Cephes/double/i1.o lib/Cephes/double/igami.o lib/Cephes/double/incbet.o lib/Cephes/double/incbi.o lib/Cephes/double/igam.o lib/Cephes/double/isnan.o lib/Cephes/double/iv.o lib/Cephes/double/j0.o lib/Cephes/double/j1.o lib/Cephes/double/jn.o lib/Cephes/double/jv.o lib/Cephes/double/k0.o lib/Cephes/double/k1.o lib/Cephes/double/kn.o lib/Cephes/double/kolmogorov.o lib/Cephes/double/log.o lib/Cephes/double/log2.o lib/Cephes/double/log10.o lib/Cephes/double/lrand.o lib/Cephes/double/nbdtr.o lib/Cephes/double/ndtr.o lib/Cephes/double/ndtri.o lib/Cephes/double/pdtr.o lib/Cephes/double/planck.o lib/Cephes/double/polevl.o lib/Cephes/double/polmisc.o lib/Cephes/double/polylog.o lib/Cephes/double/polyn.o lib/Cephes/double/pow.o lib/Cephes/double/powi.o lib/Cephes/double/psi.o lib/Cephes/double/rgamma.o lib/Cephes/double/round.o lib/Cephes/double/shichi.o lib/Cephes/double/sici.o lib/Cephes/double/sin.o lib/Cephes/double/sindg.o lib/Cephes/double/sinh.o lib/Cephes/double/spence.o lib/Cephes/double/stdtr.o lib/Cephes/double/struve.o lib/Cephes/double/tan.o lib/Cephes/double/tandg.o lib/Cephes/double/tanh.o lib/Cephes/double/unity.o lib/Cephes/double/yn.o lib/Cephes/double/zeta.o lib/Cephes/double/zetac.o lib/Cephes/double/sqrt.o lib/Cephes/double/floor.o lib/Cephes/double/setprec.o lib/Cephes/double/mtherr.o
ar: `u' modifier ignored since `D' is the default (see `U')
cp -r include "/home/biocbuild/bbs-3.8-bioc/R/library/Rgin"
cp -r lib/Cephes "/home/biocbuild/bbs-3.8-bioc/R/library/Rgin/include"
cp -r lib/maxflow "/home/biocbuild/bbs-3.8-bioc/R/library/Rgin/include"
mkdir -p "/home/biocbuild/bbs-3.8-bioc/R/library/Rgin/usrlib"
cp libgin.a libmaxflow.a libcephes.a "/home/biocbuild/bbs-3.8-bioc/R/library/Rgin/usrlib"
gcc -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o Rgin.so Rgin-init.o -pthread -fopenmp /home/biocbuild/bbs-3.8-bioc/R/library/Rgin/usrlib/libgin.a /home/biocbuild/bbs-3.8-bioc/R/library/Rgin/usrlib/libmaxflow.a /home/biocbuild/bbs-3.8-bioc/R/library/Rgin/usrlib/libcephes.a -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/Rgin/libs
** R
** byte-compile and prepare package for lazy loading
** help
No man pages found in package ‘Rgin’
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rgin)