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This page was generated on 2021-10-14 12:05:50 -0400 (Thu, 14 Oct 2021).

BUILD BIN results for scde on riesling1

To the developers/maintainers of the scde package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/scde.git to
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raw results

Package 1696/2056HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
scde 2.21.0  (landing page)
Jean Fan
Snapshot Date: 2021-10-13 14:50:09 -0400 (Wed, 13 Oct 2021)
git_url: https://git.bioconductor.org/packages/scde
git_branch: master
git_last_commit: ef036d2
git_last_commit_date: 2021-05-19 12:16:38 -0400 (Wed, 19 May 2021)
nebbiolo2Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    NA  

Summary

Package: scde
Version: 2.21.0
Command: rm -rf scde.buildbin-libdir && mkdir scde.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scde.buildbin-libdir scde_2.21.0.tar.gz
StartedAt: 2021-10-14 07:24:19 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 07:28:52 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 272.6 seconds
RetCode: 0
Status:   OK  
PackageFile: scde_2.21.0.zip
PackageFileSize: 2.961 MiB

Command output

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###
### Running command:
###
###   rm -rf scde.buildbin-libdir && mkdir scde.buildbin-libdir && D:\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scde.buildbin-libdir scde_2.21.0.tar.gz
###
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install for i386

* installing *source* package 'scde' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c bwpca.cpp -o bwpca.o
bwpca.cpp: In function 'void set_random_matrix(arma::mat&, arma::mat&)':
bwpca.cpp:23:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int j=0;j<target.n_rows;j++) {
                 ~^~~~~~~~~~~~~~
bwpca.cpp:27:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int i=0;i<target.n_cols;i++) {
                 ~^~~~~~~~~~~~~~
bwpca.cpp:30:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int j=0;j<target1.n_rows;j++) {
                 ~^~~~~~~~~~~~~~~
bwpca.cpp:44:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int i=0;i<target1.n_cols;i++) {
                 ~^~~~~~~~~~~~~~~
bwpca.cpp:47:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
         for(int j=0;j<target1.n_rows;j++) {
                     ~^~~~~~~~~~~~~~~
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c matSlideMult.cpp -o matSlideMult.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pagoda.cpp -o pagoda.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o scde.dll tmp.def bwpca.o jpmatLogBoot.o matSlideMult.o pagoda.o -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lRlapack -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/i386 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/scde.buildbin-libdir/00LOCK-scde/00new/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 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 'scde' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c bwpca.cpp -o bwpca.o
bwpca.cpp: In function 'void set_random_matrix(arma::mat&, arma::mat&)':
bwpca.cpp:23:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int j=0;j<target.n_rows;j++) {
                 ~^~~~~~~~~~~~~~
bwpca.cpp:27:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int i=0;i<target.n_cols;i++) {
                 ~^~~~~~~~~~~~~~
bwpca.cpp:30:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-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 of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int j=0;j<target1.n_rows;j++) {
                 ~^~~~~~~~~~~~~~~
bwpca.cpp:44:18: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
     for(int i=0;i<target1.n_cols;i++) {
                 ~^~~~~~~~~~~~~~~
bwpca.cpp:47:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
         for(int j=0;j<target1.n_rows;j++) {
                     ~^~~~~~~~~~~~~~~
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -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:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c matSlideMult.cpp -o matSlideMult.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"D:/biocbuild/bbs-3.14-bioc/R/include" -DNDEBUG  -I'D:/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.14-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pagoda.cpp -o pagoda.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o scde.dll tmp.def bwpca.o jpmatLogBoot.o matSlideMult.o pagoda.o -LD:/biocbuild/bbs-3.14-bioc/R/bin/x64 -lRlapack -LD:/biocbuild/bbs-3.14-bioc/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LD:/biocbuild/bbs-3.14-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.14-bioc/meat/scde.buildbin-libdir/scde/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'scde' as scde_2.21.0.zip
* DONE (scde)