Elana J. Fertig
| Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019) |
| URL: https://git.bioconductor.org/packages/CoGAPS |
| Branch: RELEASE_3_8 |
| Last Commit: 0bb2e91 |
| Last Changed Date: 2019-02-23 12:13:39 -0400 (Sat, 23 Feb 2019) |
| Back to Multiple platform build/check report for BioC 3.8 |
|
This page was generated on 2019-04-16 11:48:57 -0400 (Tue, 16 Apr 2019).
| Package 304/1649 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| CoGAPS 3.2.40 Elana J. Fertig
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | [ OK ] | OK | OK | | ||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
| Package: CoGAPS |
| Version: 3.2.40 |
| Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL CoGAPS |
| StartedAt: 2019-04-15 18:15:48 -0400 (Mon, 15 Apr 2019) |
| EndedAt: 2019-04-15 18:18:02 -0400 (Mon, 15 Apr 2019) |
| EllapsedTime: 133.9 seconds |
| RetCode: 0 |
| Status: OK |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL CoGAPS ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’ * installing *source* package ‘CoGAPS’ ... checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... no checking for suffix of object files... o checking whether we are using the GNU C++ compiler... yes checking whether g++ accepts -g... yes checking how to run the C++ preprocessor... g++ -E checking whether we are using the GNU C++ compiler... (cached) yes checking whether g++ accepts -g... (cached) yes checking for C++ compiler vendor... gnu checking for a sed that does not truncate output... /bin/sed checking for C++ compiler version... 5.4.0 checking for OpenMP flag of C++ compiler... -fopenmp building on gnu compiler version 5.4.0 Using AVX instructions if available configure: creating ./config.status config.status: creating src/Makevars ** libs g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c Cogaps.cpp -o Cogaps.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c GapsParameters.cpp -o GapsParameters.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c GapsResult.cpp -o GapsResult.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c GapsRunner.cpp -o GapsRunner.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c GapsStatistics.cpp -o GapsStatistics.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c RcppExports.cpp -o RcppExports.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c test-runner.cpp -o test-runner.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c atomic/AtomicDomain.cpp -o atomic/AtomicDomain.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c atomic/ProposalQueue.cpp -o atomic/ProposalQueue.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c data_structures/HashSets.cpp -o data_structures/HashSets.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c data_structures/HybridMatrix.cpp -o data_structures/HybridMatrix.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c data_structures/HybridVector.cpp -o data_structures/HybridVector.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c data_structures/Matrix.cpp -o data_structures/Matrix.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c data_structures/SparseIterator.cpp -o data_structures/SparseIterator.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c data_structures/SparseMatrix.cpp -o data_structures/SparseMatrix.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c data_structures/SparseVector.cpp -o data_structures/SparseVector.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c data_structures/Vector.cpp -o data_structures/Vector.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c file_parser/CsvParser.cpp -o file_parser/CsvParser.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c file_parser/FileParser.cpp -o file_parser/FileParser.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c file_parser/GctParser.cpp -o file_parser/GctParser.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c file_parser/TsvParser.cpp -o file_parser/TsvParser.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c file_parser/MtxParser.cpp -o file_parser/MtxParser.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c gibbs_sampler/AlphaParameters.cpp -o gibbs_sampler/AlphaParameters.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c gibbs_sampler/DenseStoragePolicy.cpp -o gibbs_sampler/DenseStoragePolicy.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c gibbs_sampler/SparseStoragePolicy.cpp -o gibbs_sampler/SparseStoragePolicy.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c math/Math.cpp -o math/Math.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c math/MatrixMath.cpp -o math/MatrixMath.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c math/Random.cpp -o math/Random.o g++ -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG -DBOOST_MATH_PROMOTE_DOUBLE_POLICY=0 -D__GAPS_R_BUILD__ -Iinclude -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I/usr/local/include -fopenmp -march=native -fpic -g -O2 -Wall -c math/VectorMath.cpp -o math/VectorMath.o g++ -shared -L/home/biocbuild/bbs-3.8-bioc/R/lib -L/usr/local/lib -o CoGAPS.so Cogaps.o GapsParameters.o GapsResult.o GapsRunner.o GapsStatistics.o RcppExports.o test-runner.o atomic/AtomicDomain.o atomic/ProposalQueue.o data_structures/HashSets.o data_structures/HybridMatrix.o data_structures/HybridVector.o data_structures/Matrix.o data_structures/SparseIterator.o data_structures/SparseMatrix.o data_structures/SparseVector.o data_structures/Vector.o file_parser/CsvParser.o file_parser/FileParser.o file_parser/GctParser.o file_parser/TsvParser.o file_parser/MtxParser.o gibbs_sampler/AlphaParameters.o gibbs_sampler/DenseStoragePolicy.o gibbs_sampler/SparseStoragePolicy.o math/Math.o math/MatrixMath.o math/Random.o math/VectorMath.o -fopenmp /home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/lib/libhdf5_cpp.a /home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/lib/libhdf5.a /home/biocbuild/bbs-3.8-bioc/R/library/Rhdf5lib/lib/libsz.a -lz -L/home/biocbuild/bbs-3.8-bioc/R/lib -lR installing to /home/biocbuild/bbs-3.8-bioc/R/library/CoGAPS/libs ** R ** data ** 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 * DONE (CoGAPS)