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INSTALL report for scde on tokay2

This page was generated on 2018-10-17 08:41:21 -0400 (Wed, 17 Oct 2018).

Package 1322/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scde 2.8.0
Jean Fan
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/scde
Branch: RELEASE_3_7
Last Commit: 014e900
Last Changed Date: 2018-04-30 10:35:39 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 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
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: scde
Version: 2.8.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/scde_2.8.0.tar.gz && rm -rf scde.buildbin-libdir && mkdir scde.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scde.buildbin-libdir scde_2.8.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL scde_2.8.0.zip && rm scde_2.8.0.tar.gz scde_2.8.0.zip
StartedAt: 2018-10-16 20:20:16 -0400 (Tue, 16 Oct 2018)
EndedAt: 2018-10-16 20:22:45 -0400 (Tue, 16 Oct 2018)
EllapsedTime: 149.5 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.7/bioc/src/contrib/scde_2.8.0.tar.gz && rm -rf scde.buildbin-libdir && mkdir scde.buildbin-libdir && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scde.buildbin-libdir scde_2.8.0.tar.gz && C:\Users\biocbuild\bbs-3.7-bioc\R\bin\R.exe CMD INSTALL scde_2.8.0.zip && rm scde_2.8.0.tar.gz scde_2.8.0.zip
###
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100 1082k  100 1082k    0     0  15.9M      0 --:--:-- --:--:-- --:--:-- 17.9M

install for i386

* installing *source* package 'scde' ...
** libs
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c bwpca.cpp -o bwpca.o
bwpca.cpp: In function 'void set_random_matrix(arma::mat&, arma::mat&)':
bwpca.cpp:23:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j=0;j<target.n_rows;j++) {
                  ^
bwpca.cpp:27:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0;i<target.n_cols;i++) {
                  ^
bwpca.cpp:30:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(int j=0;j<target.n_rows;j++) {
                      ^
bwpca.cpp: In function 'void set_random_matrices(arma::mat&, arma::mat&, arma::mat&, arma::mat&)':
bwpca.cpp:40:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j=0;j<target1.n_rows;j++) {
                  ^
bwpca.cpp:44:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0;i<target1.n_cols;i++) {
                  ^
bwpca.cpp:47:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(int j=0;j<target1.n_rows;j++) {
                      ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c jpmatLogBoot.cpp -o jpmatLogBoot.o
jpmatLogBoot.cpp: In function 'SEXPREC* logBootPosterior(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
jpmatLogBoot.cpp:200:24: warning: unused variable 'maxv' [-Wunused-variable]
                 double maxv=nbp.max(maxij);
                        ^
jpmatLogBoot.cpp: In function 'SEXPREC* logBootBatchPosterior(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
jpmatLogBoot.cpp:443:10: warning: unused variable 'maxv' [-Wunused-variable]
   double maxv=nbp.max(maxij);
          ^
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c matSlideMult.cpp -o matSlideMult.o
C:/Rtools/mingw_32/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pagoda.cpp -o pagoda.o
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o scde.dll tmp.def bwpca.o jpmatLogBoot.o matSlideMult.o pagoda.o -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/scde.buildbin-libdir/scde/libs/i386
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'scde'
    finding HTML links ... done
    ViewPagodaApp-class                     html  
    bwpca                                   html  
    clean.counts                            html  
    clean.gos                               html  
    es.mef.small                            html  
    knn                                     html  
    knn.error.models                        html  
    make.pagoda.app                         html  
    o.ifm                                   html  
    pagoda.cluster.cells                    html  
    pagoda.effective.cells                  html  
    pagoda.gene.clusters                    html  
    pagoda.pathway.wPCA                     html  
    pagoda.reduce.loading.redundancy        html  
    pagoda.reduce.redundancy                html  
    pagoda.show.pathways                    html  
    pagoda.subtract.aspect                  html  
    pagoda.top.aspects                      html  
    pagoda.varnorm                          html  
    pagoda.view.aspects                     html  
    papply                                  html  
    pollen                                  html  
    scde                                    html  
    scde.browse.diffexp                     html  
    scde.edff                               html  
    scde.error.models                       html  
    scde.expression.difference              html  
    scde.expression.magnitude               html  
    scde.expression.prior                   html  
    scde.failure.probability                html  
    scde.fit.models.to.reference            html  
    scde.posteriors                         html  
    scde.test.gene.expression.difference    html  
    show.app                                html  
    view.aspects                            html  
    winsorize.matrix                        html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
In R CMD INSTALL

install for x64

* installing *source* package 'scde' ...
** libs
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c bwpca.cpp -o bwpca.o
bwpca.cpp: In function 'void set_random_matrix(arma::mat&, arma::mat&)':
bwpca.cpp:23:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j=0;j<target.n_rows;j++) {
                  ^
bwpca.cpp:27:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0;i<target.n_cols;i++) {
                  ^
bwpca.cpp:30:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(int j=0;j<target.n_rows;j++) {
                      ^
bwpca.cpp: In function 'void set_random_matrices(arma::mat&, arma::mat&, arma::mat&, arma::mat&)':
bwpca.cpp:40:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int j=0;j<target1.n_rows;j++) {
                  ^
bwpca.cpp:44:18: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
     for(int i=0;i<target1.n_cols;i++) {
                  ^
bwpca.cpp:47:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
         for(int j=0;j<target1.n_rows;j++) {
                      ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c jpmatLogBoot.cpp -o jpmatLogBoot.o
jpmatLogBoot.cpp: In function 'SEXPREC* logBootPosterior(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
jpmatLogBoot.cpp:200:24: warning: unused variable 'maxv' [-Wunused-variable]
                 double maxv=nbp.max(maxij);
                        ^
jpmatLogBoot.cpp: In function 'SEXPREC* logBootBatchPosterior(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
jpmatLogBoot.cpp:443:10: warning: unused variable 'maxv' [-Wunused-variable]
   double maxv=nbp.max(maxij);
          ^
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c matSlideMult.cpp -o matSlideMult.o
C:/Rtools/mingw_64/bin/g++  -I"C:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.7-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c pagoda.cpp -o pagoda.o
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o scde.dll tmp.def bwpca.o jpmatLogBoot.o matSlideMult.o pagoda.o -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lRlapack -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.7-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.7-bioc/meat/scde.buildbin-libdir/scde/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scde' as scde_2.8.0.zip
* DONE (scde)
In R CMD INSTALL
In R CMD INSTALL
* installing to library 'C:/Users/biocbuild/bbs-3.7-bioc/R/library'
package 'scde' successfully unpacked and MD5 sums checked
In R CMD INSTALL