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INSTALL report for MIMOSA on tokay2

This page was generated on 2019-04-09 12:16:15 -0400 (Tue, 09 Apr 2019).

Package 983/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
MIMOSA 1.21.1
Greg Finak
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/MIMOSA
Branch: master
Last Commit: 6c2aa33
Last Changed Date: 2019-01-04 13:39:22 -0400 (Fri, 04 Jan 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: MIMOSA
Version: 1.21.1
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/MIMOSA_1.21.1.tar.gz && rm -rf MIMOSA.buildbin-libdir && mkdir MIMOSA.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MIMOSA.buildbin-libdir MIMOSA_1.21.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL MIMOSA_1.21.1.zip && rm MIMOSA_1.21.1.tar.gz MIMOSA_1.21.1.zip
StartedAt: 2019-04-08 19:02:15 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 19:06:42 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 266.9 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/MIMOSA_1.21.1.tar.gz && rm -rf MIMOSA.buildbin-libdir && mkdir MIMOSA.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=MIMOSA.buildbin-libdir MIMOSA_1.21.1.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL MIMOSA_1.21.1.zip && rm MIMOSA_1.21.1.tar.gz MIMOSA_1.21.1.zip
###
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100 73935  100 73935    0     0  1037k      0 --:--:-- --:--:-- --:--:-- 1164k

install for i386

* installing *source* package 'MIMOSA' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include"   -O2 -Wall  -mtune=generic -c BetaMix.cpp -o BetaMix.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include"   -O2 -Wall  -mtune=generic -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, std::allocator<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::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<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˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c MIMOSA_init.c -o MIMOSA_init.o
C:/Rtools/mingw_32/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O3 -Wall  -std=gnu99 -mtune=generic -c betaintegral.c -o betaintegral.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include"   -O2 -Wall  -mtune=generic -c betaintegralRcpp.cpp -o betaintegralRcpp.o
C:/Rtools/mingw_32/bin/g++ -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˜1.9-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -IC:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-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++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include"   -O2 -Wall  -mtune=generic -c BetaMix.cpp -o BetaMix.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include"   -O2 -Wall  -mtune=generic -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, std::allocator<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::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<double> >&, std::vector<double, std::allocator<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˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c MIMOSA_init.c -o MIMOSA_init.o
C:/Rtools/mingw_64/bin/gcc  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -std=gnu99 -mtune=generic -c betaintegral.c -o betaintegral.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include"   -O2 -Wall  -mtune=generic -c betaintegralRcpp.cpp -o betaintegralRcpp.o
C:/Rtools/mingw_64/bin/g++ -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˜1.9-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -IC:/Users/biocbuild/bbs-3.9-bioc/R/library/RcppArmadillo/include -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/MIMOSA.buildbin-libdir/MIMOSA/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MIMOSA' as MIMOSA_1.21.1.zip
* DONE (MIMOSA)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'MIMOSA' successfully unpacked and MD5 sums checked