##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/scde_2.22.0.tar.gz && rm -rf scde.buildbin-libdir && mkdir scde.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=scde.buildbin-libdir scde_2.22.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL scde_2.22.0.zip && rm scde_2.22.0.tar.gz scde_2.22.0.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  1 1083k    1 13287    0     0   156k      0  0:00:06 --:--:--  0:00:06  156k
100 1083k  100 1083k    0     0  1803k      0 --:--:-- --:--:-- --:--:-- 1802k

install for i386

* installing *source* package 'scde' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/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"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/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"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/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"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/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 -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/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"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/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"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/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"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/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"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include' -I'C:/Users/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 -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/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_2.22.0.zip
* DONE (scde)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'scde' successfully unpacked and MD5 sums checked