Back to Multiple platform build/check report for BioC 3.14
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This page was generated on 2022-04-13 12:06:22 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

INSTALL results for cola on tokay2


To the developers/maintainers of the cola package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cola.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 373/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cola 2.0.0  (landing page)
Zuguang Gu
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/cola
git_branch: RELEASE_3_14
git_last_commit: 236148e
git_last_commit_date: 2021-10-26 12:49:03 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: cola
Version: 2.0.0
Command: C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/cola_2.0.0.tar.gz && rm -rf cola.buildbin-libdir && mkdir cola.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cola.buildbin-libdir cola_2.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL cola_2.0.0.zip && rm cola_2.0.0.tar.gz cola_2.0.0.zip
StartedAt: 2022-04-12 05:24:06 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 05:31:28 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 442.1 seconds
RetCode: 0
Status:   OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.207.166/BBS/3.14/bioc/src/contrib/cola_2.0.0.tar.gz && rm -rf cola.buildbin-libdir && mkdir cola.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=cola.buildbin-libdir cola_2.0.0.tar.gz && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL cola_2.0.0.zip && rm cola_2.0.0.tar.gz cola_2.0.0.zip
###
##############################################################################
##############################################################################


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  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
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100 10.7M  100 10.7M    0     0  3284k      0  0:00:03  0:00:03 --:--:-- 3284k

install for i386

* installing *source* package 'cola' ...
** 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:/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-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c atc.cpp -o atc.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:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cal_consensus_mat.cpp -o cal_consensus_mat.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:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pdist.cpp -o pdist.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o cola.dll tmp.def RcppExports.o atc.o cal_consensus_mat.o pdist.o -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/cola.buildbin-libdir/00LOCK-cola/00new/cola/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'cola'
    finding HTML links ... done
    ATC                                     html  
    ATC_approx                              html  
    ConsensusPartition-class                html  
    ConsensusPartitionList-class            html  
    DownSamplingConsensusPartition-class    html  
    Extract.ConsensusPartitionList          html  
    Extract.HierarchicalPartition           html  
    ExtractExtract.ConsensusPartitionList   html  
    ExtractExtract.HierarchicalPartition    html  
    FCC                                     html  
    HierarchicalPartition-class             html  
    PAC                                     html  
    aPAC                                    html  
    adjust_matrix                           html  
    adjust_outlier                          html  
    all_leaves-HierarchicalPartition-method
                                            html  
    all_nodes-HierarchicalPartition-method
                                            html  
    all_partition_methods                   html  
    all_top_value_methods                   html  
    cola                                    html  
    cola_opt                                html  
    cola_report-ConsensusPartition-method   html  
    cola_report-ConsensusPartitionList-method
                                            html  
    cola_report-HierarchicalPartition-method
                                            html  
    cola_report-dispatch                    html  
    cola_rl                                 html  
    collect_classes-ConsensusPartition-method
                                            html  
    collect_classes-ConsensusPartitionList-method
                                            html  
    collect_classes-HierarchicalPartition-method
                                            html  
    collect_classes-dispatch                html  
    collect_plots-ConsensusPartition-method
                                            html  
    collect_plots-ConsensusPartitionList-method
                                            html  
    collect_plots-dispatch                  html  
    collect_stats-ConsensusPartition-method
                                            html  
    collect_stats-ConsensusPartitionList-method
                                            html  
    collect_stats-dispatch                  html  
    colnames-ConsensusPartition-method      html  
    colnames-ConsensusPartitionList-method
                                            html  
    colnames-DownSamplingConsensusPartition-method
                                            html  
    colnames-HierarchicalPartition-method   html  
    colnames-dispatch                       html  
    compare_partitions-ConsensusPartition-method
                                            html  
    compare_signatures-ConsensusPartition-method
                                            html  
    compare_signatures-HierarchicalPartition-method
                                            html  
    compare_signatures-dispatch             html  
    concordance                             html  
    config_ATC                              html  
    consensus_heatmap-ConsensusPartition-method
                                            html  
    consensus_partition                     html  
    consensus_partition_by_down_sampling    html  
    correspond_between_rankings             html  
    correspond_between_two_rankings         html  
    david_enrichment                        html  
    dim.ConsensusPartition                  html  
    dim.ConsensusPartitionList              html  
    dim.DownSamplingConsensusPartition      html  
    dim.HierarchicalPartition               html  
    dimension_reduction-ConsensusPartition-method
                                            html  
    dimension_reduction-DownSamplingConsensusPartition-method
                                            html  
    dimension_reduction-HierarchicalPartition-method
                                            html  
    dimension_reduction-dispatch            html  
    dimension_reduction-matrix-method       html  
    find_best_km                            html  
    functional_enrichment-ANY-method        html  
    functional_enrichment-ConsensusPartition-method
                                            html  
    functional_enrichment-ConsensusPartitionList-method
                                            html  
    functional_enrichment-HierarchicalPartition-method
                                            html  
    functional_enrichment-dispatch          html  
    get_anno-ConsensusPartition-method      html  
    get_anno-ConsensusPartitionList-method
                                            html  
    get_anno-DownSamplingConsensusPartition-method
                                            html  
    get_anno-HierarchicalPartition-method   html  
    get_anno-dispatch                       html  
    get_anno_col-ConsensusPartition-method
                                            html  
    get_anno_col-ConsensusPartitionList-method
                                            html  
    get_anno_col-HierarchicalPartition-method
                                            html  
    get_anno_col-dispatch                   html  
    get_children_nodes-HierarchicalPartition-method
                                            html  
    get_classes-ConsensusPartition-method   html  
    get_classes-ConsensusPartitionList-method
                                            html  
    get_classes-DownSamplingConsensusPartition-method
                                            html  
    get_classes-HierarchicalPartition-method
                                            html  
    get_classes-dispatch                    html  
    get_consensus-ConsensusPartition-method
                                            html  
    get_matrix-ConsensusPartition-method    html  
    get_matrix-ConsensusPartitionList-method
                                            html  
    get_matrix-HierarchicalPartition-method
                                            html  
    get_matrix-dispatch                     html  
    get_membership-ConsensusPartition-method
                                            html  
    get_membership-ConsensusPartitionList-method
                                            html  
    get_membership-dispatch                 html  
    get_param-ConsensusPartition-method     html  
    get_signatures-ConsensusPartition-method
                                            html  
    get_signatures-DownSamplingConsensusPartition-method
                                            html  
    get_signatures-HierarchicalPartition-method
                                            html  
    get_signatures-dispatch                 html  
    get_stats-ConsensusPartition-method     html  
    get_stats-ConsensusPartitionList-method
                                            html  
    get_stats-dispatch                      html  
    golub_cola                              html  
    golub_cola_ds                           html  
    golub_cola_rh                           html  
    hierarchical_partition                  html  
    is_best_k-ConsensusPartition-method     html  
    is_best_k-ConsensusPartitionList-method
                                            html  
    is_best_k-dispatch                      html  
    is_leaf_node-HierarchicalPartition-method
                                            html  
    is_stable_k-ConsensusPartition-method   html  
    is_stable_k-ConsensusPartitionList-method
                                            html  
    is_stable_k-dispatch                    html  
    knee_finder2                            html  
    knitr_add_tab_item                      html  
    knitr_insert_tabs                       html  
    map_to_entrez_id                        html  
    max_depth-HierarchicalPartition-method
                                            html  
    membership_heatmap-ConsensusPartition-method
                                            html  
    merge_node-HierarchicalPartition-method
                                            html  
    merge_node_param                        html  
    ncol-ConsensusPartition-method          html  
    ncol-ConsensusPartitionList-method      html  
    ncol-DownSamplingConsensusPartition-method
                                            html  
    ncol-HierarchicalPartition-method       html  
    ncol-dispatch                           html  
    node_info-HierarchicalPartition-method
                                            html  
    node_level-HierarchicalPartition-method
                                            html  
    nrow-ConsensusPartition-method          html  
    nrow-ConsensusPartitionList-method      html  
    nrow-HierarchicalPartition-method       html  
    nrow-dispatch                           html  
    plot_ecdf-ConsensusPartition-method     html  
    predict_classes-ConsensusPartition-method
                                            html  
    finding level-2 HTML links ... done

    predict_classes-dispatch                html  
    predict_classes-matrix-method           html  
    print.hc_table_suggest_best_k           html  
    recalc_stats                            html  
    register_NMF                            html  
    register_SOM                            html  
    register_partition_methods              html  
    register_top_value_methods              html  
    relabel_class                           html  
    remove_partition_methods                html  
    remove_top_value_methods                html  
    rownames-ConsensusPartition-method      html  
    rownames-ConsensusPartitionList-method
                                            html  
    rownames-HierarchicalPartition-method   html  
    rownames-dispatch                       html  
    run_all_consensus_partition_methods     html  
    select_partition_number-ConsensusPartition-method
                                            html  
    show-ConsensusPartition-method          html  
    show-ConsensusPartitionList-method      html  
    show-DownSamplingConsensusPartition-method
                                            html  
    show-HierarchicalPartition-method       html  
    show-dispatch                           html  
    split_node-HierarchicalPartition-method
                                            html  
    suggest_best_k-ConsensusPartition-method
                                            html  
    suggest_best_k-ConsensusPartitionList-method
                                            html  
    suggest_best_k-HierarchicalPartition-method
                                            html  
    suggest_best_k-dispatch                 html  
    test_between_factors                    html  
    test_to_known_factors-ConsensusPartition-method
                                            html  
    test_to_known_factors-ConsensusPartitionList-method
                                            html  
    test_to_known_factors-DownSamplingConsensusPartition-method
                                            html  
    test_to_known_factors-HierarchicalPartition-method
                                            html  
    test_to_known_factors-dispatch          html  
    top_elements_overlap                    html  
    top_rows_heatmap-ConsensusPartition-method
                                            html  
    top_rows_heatmap-ConsensusPartitionList-method
                                            html  
    top_rows_heatmap-HierarchicalPartition-method
                                            html  
    top_rows_heatmap-dispatch               html  
    top_rows_heatmap-matrix-method          html  
    top_rows_overlap-ConsensusPartitionList-method
                                            html  
    top_rows_overlap-HierarchicalPartition-method
                                            html  
    top_rows_overlap-dispatch               html  
    top_rows_overlap-matrix-method          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 'cola' ...
** 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:/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-3~1.14-/R/include" -DNDEBUG  -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rcpp/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c atc.cpp -o atc.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:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c cal_consensus_mat.cpp -o cal_consensus_mat.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:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c pdist.cpp -o pdist.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o cola.dll tmp.def RcppExports.o atc.o cal_consensus_mat.o pdist.o -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/cola.buildbin-libdir/cola/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'cola' as cola_2.0.0.zip
* DONE (cola)
* installing to library 'C:/Users/biocbuild/bbs-3.14-bioc/R/library'
package 'cola' successfully unpacked and MD5 sums checked