############################################################################## ############################################################################## ### ### Running command: ### ### C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/GenoGAM_2.12.0.tar.gz && rm -rf GenoGAM.buildbin-libdir && mkdir GenoGAM.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=GenoGAM.buildbin-libdir GenoGAM_2.12.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL GenoGAM_2.12.0.zip && rm GenoGAM_2.12.0.tar.gz GenoGAM_2.12.0.zip ### ############################################################################## ############################################################################## % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 17 3287k 17 574k 0 0 856k 0 0:00:03 --:--:-- 0:00:03 856k 68 3287k 68 2251k 0 0 1346k 0 0:00:02 0:00:01 0:00:01 1346k 100 3287k 100 3287k 0 0 1578k 0 0:00:02 0:00:02 --:--:-- 1578k install for i386 * installing *source* package 'GenoGAM' ... ** using staged installation ** libs "C:/rtools40/mingw32/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I../inst/include -DARMA_64BIT_WORD=1 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -fopenmp -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-3~1.14-/R/include" -DNDEBUG -I../inst/include -DARMA_64BIT_WORD=1 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c matrixMult.cpp -o matrixMult.o C:/rtools40/mingw32/bin/g++ -shared -s -static-libgcc -o GenoGAM.dll tmp.def RcppExports.o matrixMult.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/GenoGAM.buildbin-libdir/00LOCK-GenoGAM/00new/GenoGAM/libs/i386 ** R ** inst ** byte-compile and prepare package for lazy loading Warning: replacing previous import 'HDF5Array::h5ls' by 'rhdf5::h5ls' when loading 'GenoGAM' Warning: replacing previous import 'S4Vectors::na.omit' by 'stats::na.omit' when loading 'GenoGAM' ** help *** installing help indices converting help for package 'GenoGAM' finding HTML links ... done Coordinates-class html GenoGAM-class html GenoGAM html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/GenoGAM.buildbin-libdir/00LOCK-GenoGAM/00new/GenoGAM/help/GenoGAM.html GenoGAMDataSet-class html GenoGAMDataSet-metrics html GenoGAMDataSet-subsetting html GenoGAMDataSetList-class html GenoGAMDataSetList-metrics html GenoGAMDataSetList-subsetting html GenoGAMFamily-class html GenoGAMList-class html GenoGAMList-subsetting html GenoGAMSettings-class html asCoordinates html callPeaks html computeRegionSignificance html computeSignificance html computeSizeFactors html fitGenoGAM html REDIRECT:topic Previous alias or file overwritten by alias: C:/Users/biocbuild/bbs-3.14-bioc/meat/GenoGAM.buildbin-libdir/00LOCK-GenoGAM/00new/GenoGAM/help/genogam.html makeTestGenoGAM html makeTestGenoGAMDataSet html makeTestGenoGAMDataSetList html makeTestGenoGAMList html plotGenoGAM html readData html writeToBEDFile html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location Warning: replacing previous import 'HDF5Array::h5ls' by 'rhdf5::h5ls' when loading 'GenoGAM' Warning: replacing previous import 'S4Vectors::na.omit' by 'stats::na.omit' when loading 'GenoGAM' ** testing if installed package can be loaded from final location Warning: replacing previous import 'HDF5Array::h5ls' by 'rhdf5::h5ls' when loading 'GenoGAM' Warning: replacing previous import 'S4Vectors::na.omit' by 'stats::na.omit' when loading 'GenoGAM' ** testing if installed package keeps a record of temporary installation path install for x64 * installing *source* package 'GenoGAM' ... ** libs "C:/rtools40/mingw64/bin/"g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -I../inst/include -DARMA_64BIT_WORD=1 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -fopenmp -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-3~1.14-/R/include" -DNDEBUG -I../inst/include -DARMA_64BIT_WORD=1 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include' -I"C:/extsoft/include" -fopenmp -O2 -Wall -mfpmath=sse -msse2 -mstackrealign -c matrixMult.cpp -o matrixMult.o C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o GenoGAM.dll tmp.def RcppExports.o matrixMult.o -fopenmp -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/GenoGAM.buildbin-libdir/GenoGAM/libs/x64 ** testing if installed package can be loaded Warning: replacing previous import 'HDF5Array::h5ls' by 'rhdf5::h5ls' when loading 'GenoGAM' Warning: replacing previous import 'S4Vectors::na.omit' by 'stats::na.omit' when loading 'GenoGAM' * MD5 sums packaged installation of 'GenoGAM' as GenoGAM_2.12.0.zip * DONE (GenoGAM) * installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library' package 'GenoGAM' successfully unpacked and MD5 sums checked