BASiCS 1.4.7
Catalina A. Vallejos , Nils Eling
| Snapshot Date: 2019-04-12 17:01:30 -0400 (Fri, 12 Apr 2019) |
| URL: https://git.bioconductor.org/packages/BASiCS |
| Branch: RELEASE_3_8 |
| Last Commit: 56a7c64 |
| Last Changed Date: 2019-03-22 06:17:40 -0400 (Fri, 22 Mar 2019) |
| malbec1 | Linux (Ubuntu 16.04.6 LTS) / x86_64 | OK | OK | OK | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | OK | OK | |
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.8/bioc/src/contrib/BASiCS_1.4.7.tar.gz && rm -rf BASiCS.buildbin-libdir && mkdir BASiCS.buildbin-libdir && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BASiCS.buildbin-libdir BASiCS_1.4.7.tar.gz && C:\Users\biocbuild\bbs-3.8-bioc\R\bin\R.exe CMD INSTALL BASiCS_1.4.7.zip && rm BASiCS_1.4.7.tar.gz BASiCS_1.4.7.zip
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install for i386
* installing *source* package 'BASiCS' ...
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c BASiCS_DenoisedRates.cpp -o BASiCS_DenoisedRates.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c BASiCS_MCMCcpp.cpp -o BASiCS_MCMCcpp.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c BASiCS_MCMCcppNoSpikes.cpp -o BASiCS_MCMCcppNoSpikes.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c BASiCS_MCMCcppReg.cpp -o BASiCS_MCMCcppReg.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c BASiCS_MCMCcppRegNoSpikes.cpp -o BASiCS_MCMCcppRegNoSpikes.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c general_utils.cpp -o general_utils.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c utils_MCMCcpp.cpp -o utils_MCMCcpp.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c utils_MCMCcppNoSpikes.cpp -o utils_MCMCcppNoSpikes.o
utils_MCMCcppNoSpikes.cpp: In function 'arma::mat muUpdateNoSpikes(const vec&, const vec&, const mat&, const vec&, const vec&, const vec&, const double&, const int&, const int&, arma::vec&, arma::vec&, arma::vec&, const double&, const int&, const uvec&, const uvec&, const int&)':
utils_MCMCcppNoSpikes.cpp:54:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < ConstrainGene.size(); i++) {
^
utils_MCMCcppNoSpikes.cpp:75:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < NotConstrainGene.size(); i++) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c utils_MCMCcppReg.cpp -o utils_MCMCcppReg.o
utils_MCMCcppReg.cpp: In function 'arma::mat designMatrix(const int&, const vec&, const double&)':
utils_MCMCcppReg.cpp:16:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=1; i < myu.size(); i++) {
^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c utils_MCMCcppRegNoSpikes.cpp -o utils_MCMCcppRegNoSpikes.o
utils_MCMCcppRegNoSpikes.cpp: In function 'arma::mat muUpdateRegNoSpikes(const vec&, const vec&, const mat&, const vec&, const vec&, const vec&, const vec&, const double&, const int&, const int&, arma::vec&, arma::vec&, arma::vec&, const double&, const int&, const uvec&, const uvec&, const int&, const int&, const vec&, const vec&, const mat&, const double&, double)':
utils_MCMCcppRegNoSpikes.cpp:67:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < ConstrainGene.size(); i++) {
^
utils_MCMCcppRegNoSpikes.cpp:88:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < NotConstrainGene.size(); i++) {
^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o BASiCS.dll tmp.def BASiCS_DenoisedRates.o BASiCS_MCMCcpp.o BASiCS_MCMCcppNoSpikes.o BASiCS_MCMCcppReg.o BASiCS_MCMCcppRegNoSpikes.o RcppExports.o general_utils.o utils_MCMCcpp.o utils_MCMCcppNoSpikes.o utils_MCMCcppReg.o utils_MCMCcppRegNoSpikes.o -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/BASiCS.buildbin-libdir/BASiCS/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package 'BASiCS'
finding HTML links ... done
BASiCS-deprecated html
BASiCS_Chain-methods html
BASiCS_Chain html
BASiCS_D_TestDE html
BASiCS_DenoisedCounts html
finding level-2 HTML links ... done
BASiCS_DenoisedRates html
BASiCS_DetectHVG_LVG html
BASiCS_Filter html
BASiCS_LoadChain html
BASiCS_MCMC html
BASiCS_Sim html
BASiCS_Summary-methods html
BASiCS_Summary html
BASiCS_TestDE html
BASiCS_VarThresholdSearchHVG_LVG html
BASiCS_VarianceDecomp html
BASiCS_showFit-BASiCS_Chain-method html
ChainRNA html
ChainRNAReg html
ChainSC html
ChainSCReg html
Summary-BASiCS_Chain-method html
colnames-BASiCS_Chain-method html
displayChainBASiCS-BASiCS_Chain-method
html
displaySummaryBASiCS-BASiCS_Summary-method
html
makeExampleBASiCS_Data html
newBASiCS_Chain html
newBASiCS_Data html
plot-BASiCS_Chain-method html
plot-BASiCS_Summary-method html
rownames-BASiCS_Chain-method html
subset-BASiCS_Chain-method html
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL
install for x64
* installing *source* package 'BASiCS' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c BASiCS_DenoisedRates.cpp -o BASiCS_DenoisedRates.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c BASiCS_MCMCcpp.cpp -o BASiCS_MCMCcpp.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c BASiCS_MCMCcppNoSpikes.cpp -o BASiCS_MCMCcppNoSpikes.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c BASiCS_MCMCcppReg.cpp -o BASiCS_MCMCcppReg.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c BASiCS_MCMCcppRegNoSpikes.cpp -o BASiCS_MCMCcppRegNoSpikes.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c general_utils.cpp -o general_utils.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c utils_MCMCcpp.cpp -o utils_MCMCcpp.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c utils_MCMCcppNoSpikes.cpp -o utils_MCMCcppNoSpikes.o
utils_MCMCcppNoSpikes.cpp: In function 'arma::mat muUpdateNoSpikes(const vec&, const vec&, const mat&, const vec&, const vec&, const vec&, const double&, const int&, const int&, arma::vec&, arma::vec&, arma::vec&, const double&, const int&, const uvec&, const uvec&, const int&)':
utils_MCMCcppNoSpikes.cpp:54:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < ConstrainGene.size(); i++) {
^
utils_MCMCcppNoSpikes.cpp:75:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < NotConstrainGene.size(); i++) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c utils_MCMCcppReg.cpp -o utils_MCMCcppReg.o
utils_MCMCcppReg.cpp: In function 'arma::mat designMatrix(const int&, const vec&, const double&)':
utils_MCMCcppReg.cpp:16:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=1; i < myu.size(); i++) {
^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.8-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -mtune=generic -c utils_MCMCcppRegNoSpikes.cpp -o utils_MCMCcppRegNoSpikes.o
utils_MCMCcppRegNoSpikes.cpp: In function 'arma::mat muUpdateRegNoSpikes(const vec&, const vec&, const mat&, const vec&, const vec&, const vec&, const vec&, const double&, const int&, const int&, arma::vec&, arma::vec&, arma::vec&, const double&, const int&, const uvec&, const uvec&, const int&, const int&, const vec&, const vec&, const mat&, const double&, double)':
utils_MCMCcppRegNoSpikes.cpp:67:19: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < ConstrainGene.size(); i++) {
^
utils_MCMCcppRegNoSpikes.cpp:88:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for (int i=0; i < NotConstrainGene.size(); i++) {
^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o BASiCS.dll tmp.def BASiCS_DenoisedRates.o BASiCS_MCMCcpp.o BASiCS_MCMCcppNoSpikes.o BASiCS_MCMCcppReg.o BASiCS_MCMCcppRegNoSpikes.o RcppExports.o general_utils.o utils_MCMCcpp.o utils_MCMCcppNoSpikes.o utils_MCMCcppReg.o utils_MCMCcppRegNoSpikes.o -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.8-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.8-bioc/meat/BASiCS.buildbin-libdir/BASiCS/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BASiCS' as BASiCS_1.4.7.zip
* DONE (BASiCS)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.8-bioc/R/library'
package 'BASiCS' successfully unpacked and MD5 sums checked
In R CMD INSTALL