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INSTALL report for SC3 on tokay2

This page was generated on 2020-10-17 11:57:44 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE SC3 PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1579/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SC3 1.16.0
Vladimir Kiselev
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/SC3
Branch: RELEASE_3_11
Last Commit: efe119e
Last Changed Date: 2020-04-27 14:53:50 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  OK  OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SC3
Version: 1.16.0
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/SC3_1.16.0.tar.gz && rm -rf SC3.buildbin-libdir && mkdir SC3.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SC3.buildbin-libdir SC3_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL SC3_1.16.0.zip && rm SC3_1.16.0.tar.gz SC3_1.16.0.zip
StartedAt: 2020-10-16 18:00:02 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 18:01:36 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 93.6 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/SC3_1.16.0.tar.gz && rm -rf SC3.buildbin-libdir && mkdir SC3.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SC3.buildbin-libdir SC3_1.16.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL SC3_1.16.0.zip && rm SC3_1.16.0.tar.gz SC3_1.16.0.zip
###
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100 1739k  100 1739k    0     0  22.7M      0 --:--:-- --:--:-- --:--:-- 24.9M

install for i386

* installing *source* package 'SC3' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c cppFunctions.cpp -o cppFunctions.o
cppFunctions.cpp: In function 'arma::mat consmx(arma::mat)':
cppFunctions.cpp:63:16: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
  for (j = 0; j < dat.n_cols; j++) {
              ~~^~~~~~~~~~~~
cppFunctions.cpp:64:17: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for (i = 0; i < dat.n_rows; i++) {
               ~~^~~~~~~~~~~~
cppFunctions.cpp:65:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
    for (k = i + 1; k < dat.n_rows; k++) {
                    ~~^~~~~~~~~~~~
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o SC3.dll tmp.def RcppExports.o cppFunctions.o -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/SC3.buildbin-libdir/00LOCK-SC3/00new/SC3/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 'SC3'
    finding HTML links ... done
    ED1                                     html  
    ED2                                     html  
    ann                                     html  
    calculate_distance                      html  
    calculate_stability                     html  
    consensus_matrix                        html  
    consmx                                  html  
    estkTW                                  html  
    get_auroc                               html  
    get_biolgy                              html  
    get_de_genes                            html  
    get_marker_genes                        html  
    get_outl_cells                          html  
    get_processed_dataset                   html  
    markers_for_heatmap                     html  
    norm_laplacian                          html  
    organise_de_genes                       html  
    organise_marker_genes                   html  
    prepare_for_svm                         html  
    reindex_clusters                        html  
    sc3                                     html  
    sc3_calc_biology                        html  
    sc3_calc_consens                        html  
    sc3_calc_dists                          html  
    sc3_calc_transfs                        html  
    sc3_estimate_k                          html  
    sc3_export_results_xls                  html  
    sc3_interactive                         html  
    sc3_kmeans                              html  
    sc3_plot_cluster_stability              html  
    sc3_plot_consensus                      html  
    sc3_plot_de_genes                       html  
    sc3_plot_expression                     html  
    sc3_plot_markers                        html  
    sc3_plot_silhouette                     html  
    sc3_prepare                             html  
    sc3_run_svm                             html  
    support_vector_machines                 html  
    tmult                                   html  
    transformation                          html  
    yan                                     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 'SC3' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.11-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/Rcpp/include' -I'C:/Users/biocbuild/bbs-3.11-bioc/R/library/RcppArmadillo/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c cppFunctions.cpp -o cppFunctions.o
cppFunctions.cpp: In function 'arma::mat consmx(arma::mat)':
cppFunctions.cpp:63:16: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
  for (j = 0; j < dat.n_cols; j++) {
              ~~^~~~~~~~~~~~
cppFunctions.cpp:64:17: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
   for (i = 0; i < dat.n_rows; i++) {
               ~~^~~~~~~~~~~~
cppFunctions.cpp:65:22: warning: comparison of integer expressions of different signedness: 'int' and 'const uword' {aka 'const unsigned int'} [-Wsign-compare]
    for (k = i + 1; k < dat.n_rows; k++) {
                    ~~^~~~~~~~~~~~
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o SC3.dll tmp.def RcppExports.o cppFunctions.o -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.11-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.11-bioc/meat/SC3.buildbin-libdir/SC3/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SC3' as SC3_1.16.0.zip
* DONE (SC3)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'SC3' successfully unpacked and MD5 sums checked