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INSTALL report for SC3 on tokay1

This page was generated on 2020-04-15 12:25:58 -0400 (Wed, 15 Apr 2020).

Package 1519/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
SC3 1.14.0
Vladimir Kiselev
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/SC3
Branch: RELEASE_3_10
Last Commit: d2785b6
Last Changed Date: 2019-10-29 13:09:33 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: SC3
Version: 1.14.0
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/SC3_1.14.0.tar.gz && rm -rf SC3.buildbin-libdir && mkdir SC3.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SC3.buildbin-libdir SC3_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL SC3_1.14.0.zip && rm SC3_1.14.0.tar.gz SC3_1.14.0.zip
StartedAt: 2020-04-14 20:31:00 -0400 (Tue, 14 Apr 2020)
EndedAt: 2020-04-14 20:32:19 -0400 (Tue, 14 Apr 2020)
EllapsedTime: 78.9 seconds
RetCode: 0
Status:  OK  

Command output

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.10/bioc/src/contrib/SC3_1.14.0.tar.gz && rm -rf SC3.buildbin-libdir && mkdir SC3.buildbin-libdir && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=SC3.buildbin-libdir SC3_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.10-bioc\R\bin\R.exe CMD INSTALL SC3_1.14.0.zip && rm SC3_1.14.0.tar.gz SC3_1.14.0.zip
###
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100 1726k  100 1726k    0     0  10.2M      0 --:--:-- --:--:-- --:--:-- 10.4M

install for i386

* installing *source* package 'SC3' ...
** using staged installation
** libs
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c cppFunctions.cpp -o cppFunctions.o
cppFunctions.cpp: In function 'arma::mat consmx(arma::mat)':
cppFunctions.cpp:63:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < dat.n_cols; j++) {
                ^
cppFunctions.cpp:64:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < dat.n_rows; i++) {
                 ^
cppFunctions.cpp:65:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (k = i + 1; k < dat.n_rows; k++) {
                      ^
C:/Rtools/mingw_32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o SC3.dll tmp.def RcppExports.o cppFunctions.o -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.10-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:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.10-/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.10-bioc/R/library/RcppArmadillo/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=core2 -c cppFunctions.cpp -o cppFunctions.o
cppFunctions.cpp: In function 'arma::mat consmx(arma::mat)':
cppFunctions.cpp:63:16: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
  for (j = 0; j < dat.n_cols; j++) {
                ^
cppFunctions.cpp:64:17: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
   for (i = 0; i < dat.n_rows; i++) {
                 ^
cppFunctions.cpp:65:22: warning: comparison between signed and unsigned integer expressions [-Wsign-compare]
    for (k = i + 1; k < dat.n_rows; k++) {
                      ^
C:/Rtools/mingw_64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o SC3.dll tmp.def RcppExports.o cppFunctions.o -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lRlapack -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lRblas -lgfortran -lm -lquadmath -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.10-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.10-bioc/meat/SC3.buildbin-libdir/SC3/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'SC3' as SC3_1.14.0.zip
* DONE (SC3)
* installing to library 'C:/Users/biocbuild/bbs-3.10-bioc/R/library'
package 'SC3' successfully unpacked and MD5 sums checked