MIMOSA 1.24.0
Greg Finak
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/MIMOSA |
| Branch: RELEASE_3_10 |
| Last Commit: 8dd361e |
| Last Changed Date: 2019-10-29 13:08:52 -0400 (Tue, 29 Oct 2019) |
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |  |
| tokay1 | Windows Server 2012 R2 Standard / x64 | [ OK ] | OK | WARNINGS | 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/3.10/bioc/src/contrib/MIMOSA_1.24.0.tar.gz && rm -rf MIMOSA.buildbin-libdir && mkdir MIMOSA.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MIMOSA.buildbin-libdir MIMOSA_1.24.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL MIMOSA_1.24.0.zip && rm MIMOSA_1.24.0.tar.gz MIMOSA_1.24.0.zip
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install for i386
* installing *source* package 'MIMOSA' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -O2 -Wall -mtune=core2 -c BetaMix.cpp -o BetaMix.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -O2 -Wall -mtune=core2 -c MCMC.cpp -o MCMC.o
MCMC.cpp: In function 'SEXPREC* fitMCMC(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
MCMC.cpp:73:9: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
if(file==NULL|fileP==NULL){
^
MCMC.cpp:88:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(alphas.size()!=stim.ncol()){
^
MCMC.cpp:188:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<alphas.size();i++){
^
MCMC.cpp:191:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<alphau.size();i++){
^
MCMC.cpp:523:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<p.size();j++){
^
MCMC.cpp:542:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int obs=0;obs<alphas.size();obs++){
^
MCMC.cpp:545:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int obs=0;obs<alphau.size();obs++){
^
MCMC.cpp: In function 'double lkbeta(const std::vector<double>&)':
MCMC.cpp:627:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<alpha.size();i++){
^
MCMC.cpp: In function 'void simZ(double&, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<bool>&, int, int)':
MCMC.cpp:677:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i < lnull.size(); i++){
^
MCMC.cpp: In function 'double normconstIBeta(double, double, double, double)':
MCMC.cpp:811:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<upper.size();i++){
^
MCMC.cpp: In function 'double nc(double, double, double, double, double)':
MCMC.cpp:884:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<(s.size()-1);i++){
^
MCMC.cpp:889:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<s.size();i++){
^
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c MIMOSA_init.c -o MIMOSA_init.o
C:/Rtools/mingw_32/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O3 -Wall -std=gnu99 -mtune=core2 -c betaintegral.c -o betaintegral.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -O2 -Wall -mtune=core2 -c betaintegralRcpp.cpp -o betaintegralRcpp.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o MIMOSA.dll tmp.def BetaMix.o MCMC.o MIMOSA_init.o betaintegral.o betaintegralRcpp.o -lm -lstdc++ -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -IC:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/MIMOSA.buildbin-libdir/00LOCK-MIMOSA/00new/MIMOSA/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 'MIMOSA'
finding HTML links ... done
BetaMixResult-class html
ConstructMIMOSAExpressionSet html
ICS html
MDMix html
MIMOSA-accessors html
MIMOSA-package html
MIMOSA html
MIMOSAExpressionSet html
MIMOSAResult-class html
MIMOSAResult html
asinh_trans html
boxplotMIMOSAResultList html
combine.MIMOSA html
countsTable html
fdr html
fitMCMC html
pData html
print html
show html
volcanoPlot 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 'MIMOSA' ...
** libs
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -O2 -Wall -mtune=core2 -c BetaMix.cpp -o BetaMix.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -O2 -Wall -mtune=core2 -c MCMC.cpp -o MCMC.o
MCMC.cpp: In function 'SEXPREC* fitMCMC(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
MCMC.cpp:73:9: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
if(file==NULL|fileP==NULL){
^
MCMC.cpp:88:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
if(alphas.size()!=stim.ncol()){
^
MCMC.cpp:188:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<alphas.size();i++){
^
MCMC.cpp:191:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<alphau.size();i++){
^
MCMC.cpp:523:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int j=0;j<p.size();j++){
^
MCMC.cpp:542:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int obs=0;obs<alphas.size();obs++){
^
MCMC.cpp:545:21: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int obs=0;obs<alphau.size();obs++){
^
MCMC.cpp: In function 'double lkbeta(const std::vector<double>&)':
MCMC.cpp:627:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<alpha.size();i++){
^
MCMC.cpp: In function 'void simZ(double&, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<double>&, std::vector<bool>&, int, int)':
MCMC.cpp:677:12: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(i=0;i < lnull.size(); i++){
^
MCMC.cpp: In function 'double normconstIBeta(double, double, double, double)':
MCMC.cpp:811:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<upper.size();i++){
^
MCMC.cpp: In function 'double nc(double, double, double, double, double)':
MCMC.cpp:884:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<(s.size()-1);i++){
^
MCMC.cpp:889:15: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
for(int i=0;i<s.size();i++){
^
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c MIMOSA_init.c -o MIMOSA_init.o
C:/Rtools/mingw_64/bin/gcc -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -O2 -Wall -std=gnu99 -mtune=core2 -c betaintegral.c -o betaintegral.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -I"C:/extsoft/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include" -O2 -Wall -mtune=core2 -c betaintegralRcpp.cpp -o betaintegralRcpp.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o MIMOSA.dll tmp.def BetaMix.o MCMC.o MIMOSA_init.o betaintegral.o betaintegralRcpp.o -lm -lstdc++ -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -IC:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/MIMOSA.buildbin-libdir/MIMOSA/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MIMOSA' as MIMOSA_1.24.0.zip
* DONE (MIMOSA)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'MIMOSA' successfully unpacked and MD5 sums checked