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

CHECK 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:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cola.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings cola_2.0.0.tar.gz
StartedAt: 2022-04-12 17:43:57 -0400 (Tue, 12 Apr 2022)
EndedAt: 2022-04-12 17:50:51 -0400 (Tue, 12 Apr 2022)
EllapsedTime: 414.4 seconds
RetCode: 0
Status:   OK  
CheckDir: cola.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:cola.install-out.txt --library=C:\Users\biocbuild\bbs-3.14-bioc\R\library --no-vignettes --timings cola_2.0.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.14-bioc/meat/cola.Rcheck'
* using R version 4.1.3 (2022-03-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'cola/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'cola' version '2.0.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'cola' can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data      3.5Mb
    extdata   1.0Mb
    libs      2.1Mb
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* loading checks for arch 'x64'
** checking whether the package can be loaded ... OK
** checking whether the package can be loaded with stated dependencies ... OK
** checking whether the package can be unloaded cleanly ... OK
** checking whether the namespace can be loaded with stated dependencies ... OK
** checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking compiled code ... NOTE
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cola/libs/i386/cola.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)
File 'C:/Users/biocbuild/bbs-3.14-bioc/R/library/cola/libs/x64/cola.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'printf', possibly from 'printf' (C)

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                         user system elapsed
get_signatures-ConsensusPartition-method 5.22   0.36    5.58
consensus_partition                      1.72   0.04   34.80
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                user system elapsed
get_signatures-ConsensusPartition-method        5.64   0.05    5.68
compare_signatures-HierarchicalPartition-method 4.63   0.15    5.08
consensus_partition                             1.80   0.00   35.92
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'test-all.R'
 OK
** running tests for arch 'x64' ...
  Running 'test-all.R'
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.14-bioc/meat/cola.Rcheck/00check.log'
for details.

Installation output

cola.Rcheck/00install.out

##############################################################################
##############################################################################
###
### 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
###
##############################################################################
##############################################################################


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

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0 10.7M    0  1136    0     0  13744      0  0:13:40 --:--:--  0:13:40 13686
 20 10.7M   20 2233k    0     0  2057k      0  0:00:05  0:00:01  0:00:04 2058k
 50 10.7M   50 5531k    0     0  2647k      0  0:00:04  0:00:02  0:00:02 2646k
 88 10.7M   88 9759k    0     0  3156k      0  0:00:03  0:00:03 --:--:-- 3156k
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

Tests output

cola.Rcheck/tests_i386/test-all.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> suppressWarnings(suppressPackageStartupMessages(library(cola)))
> 
> test_check("cola")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 18 ]
> 
> 
> proc.time()
   user  system elapsed 
   4.59    0.57   28.09

cola.Rcheck/tests_x64/test-all.Rout


R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(testthat)
> suppressWarnings(suppressPackageStartupMessages(library(cola)))
> 
> test_check("cola")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 18 ]
> 
> 
> proc.time()
   user  system elapsed 
   4.43    0.26   25.50

Example timings

cola.Rcheck/examples_i386/cola-Ex.timings

nameusersystemelapsed
ATC0.030.000.03
ATC_approx000
ConsensusPartition-class000
ConsensusPartitionList-class000
DownSamplingConsensusPartition-class000
Extract.ConsensusPartitionList0.480.060.55
Extract.HierarchicalPartition0.20.00.2
ExtractExtract.ConsensusPartitionList0.220.030.25
ExtractExtract.HierarchicalPartition000
FCC0.240.020.25
HierarchicalPartition-class000
PAC0.230.000.24
aPAC0.280.010.29
adjust_matrix000
adjust_outlier000
all_leaves-HierarchicalPartition-method0.140.030.18
all_nodes-HierarchicalPartition-method0.160.020.17
all_partition_methods0.010.000.01
all_top_value_methods000
cola0.070.000.07
cola_opt0.030.000.03
cola_report-ConsensusPartition-method000
cola_report-ConsensusPartitionList-method000
cola_report-HierarchicalPartition-method000
cola_report-dispatch000
cola_rl0.120.030.15
collect_classes-ConsensusPartition-method2.180.192.36
collect_classes-ConsensusPartitionList-method3.320.053.38
collect_classes-HierarchicalPartition-method1.530.041.58
collect_classes-dispatch000
collect_plots-ConsensusPartition-method000
collect_plots-ConsensusPartitionList-method000
collect_plots-dispatch000
collect_stats-ConsensusPartition-method000
collect_stats-ConsensusPartitionList-method0.470.000.47
collect_stats-dispatch000
colnames-ConsensusPartition-method000
colnames-ConsensusPartitionList-method000
colnames-DownSamplingConsensusPartition-method000
colnames-HierarchicalPartition-method000
colnames-dispatch000
compare_partitions-ConsensusPartition-method000
compare_signatures-ConsensusPartition-method000
compare_signatures-HierarchicalPartition-method4.160.194.56
compare_signatures-dispatch000
concordance0.360.020.37
config_ATC000
consensus_heatmap-ConsensusPartition-method0.860.000.86
consensus_partition 1.72 0.0434.80
consensus_partition_by_down_sampling000
correspond_between_rankings0.060.000.06
correspond_between_two_rankings0.030.000.03
david_enrichment000
dim.ConsensusPartition000
dim.ConsensusPartitionList000
dim.DownSamplingConsensusPartition000
dim.HierarchicalPartition000
dimension_reduction-ConsensusPartition-method1.000.021.02
dimension_reduction-DownSamplingConsensusPartition-method1.920.041.97
dimension_reduction-HierarchicalPartition-method1.100.051.14
dimension_reduction-dispatch000
dimension_reduction-matrix-method000
find_best_km000
functional_enrichment-ANY-method000
functional_enrichment-ConsensusPartition-method000
functional_enrichment-ConsensusPartitionList-method000
functional_enrichment-HierarchicalPartition-method000
functional_enrichment-dispatch000
get_anno-ConsensusPartition-method000
get_anno-ConsensusPartitionList-method000
get_anno-DownSamplingConsensusPartition-method0.120.000.12
get_anno-HierarchicalPartition-method000
get_anno-dispatch000
get_anno_col-ConsensusPartition-method000
get_anno_col-ConsensusPartitionList-method000
get_anno_col-HierarchicalPartition-method000
get_anno_col-dispatch000
get_children_nodes-HierarchicalPartition-method000
get_classes-ConsensusPartition-method0.200.020.22
get_classes-ConsensusPartitionList-method0.220.000.22
get_classes-DownSamplingConsensusPartition-method0.100.030.13
get_classes-HierarchicalPartition-method0.180.000.18
get_classes-dispatch000
get_consensus-ConsensusPartition-method0.220.030.25
get_matrix-ConsensusPartition-method0.530.160.69
get_matrix-ConsensusPartitionList-method0.550.120.67
get_matrix-HierarchicalPartition-method000
get_matrix-dispatch000
get_membership-ConsensusPartition-method0.240.020.25
get_membership-ConsensusPartitionList-method0.210.010.24
get_membership-dispatch000
get_param-ConsensusPartition-method0.220.020.23
get_signatures-ConsensusPartition-method5.220.365.58
get_signatures-DownSamplingConsensusPartition-method000
get_signatures-HierarchicalPartition-method000
get_signatures-dispatch000
get_stats-ConsensusPartition-method0.250.000.25
get_stats-ConsensusPartitionList-method0.220.000.22
get_stats-dispatch000
golub_cola0.760.000.77
golub_cola_ds0.140.000.14
golub_cola_rh0.220.000.22
hierarchical_partition000
is_best_k-ConsensusPartition-method0.220.000.22
is_best_k-ConsensusPartitionList-method0.220.000.22
is_best_k-dispatch000
is_leaf_node-HierarchicalPartition-method0.190.000.18
is_stable_k-ConsensusPartition-method0.200.010.22
is_stable_k-ConsensusPartitionList-method0.230.000.24
is_stable_k-dispatch000
knee_finder20.040.020.04
knitr_add_tab_item000
knitr_insert_tabs000
map_to_entrez_id000
max_depth-HierarchicalPartition-method0.150.030.19
membership_heatmap-ConsensusPartition-method0.530.020.55
merge_node-HierarchicalPartition-method000
merge_node_param000
ncol-ConsensusPartition-method000
ncol-ConsensusPartitionList-method000
ncol-DownSamplingConsensusPartition-method000
ncol-HierarchicalPartition-method000
ncol-dispatch000
node_info-HierarchicalPartition-method000
node_level-HierarchicalPartition-method000
nrow-ConsensusPartition-method000
nrow-ConsensusPartitionList-method000
nrow-HierarchicalPartition-method000
nrow-dispatch000
plot_ecdf-ConsensusPartition-method0.220.010.24
predict_classes-ConsensusPartition-method000
predict_classes-dispatch000
predict_classes-matrix-method000
print.hc_table_suggest_best_k000
recalc_stats000
register_NMF000
register_SOM000
register_partition_methods0.470.000.47
register_top_value_methods000
relabel_class0.010.000.01
remove_partition_methods000
remove_top_value_methods000
rownames-ConsensusPartition-method000
rownames-ConsensusPartitionList-method000
rownames-HierarchicalPartition-method000
rownames-dispatch000
run_all_consensus_partition_methods000
select_partition_number-ConsensusPartition-method0.200.000.21
show-ConsensusPartition-method000
show-ConsensusPartitionList-method000
show-DownSamplingConsensusPartition-method0.130.000.13
show-HierarchicalPartition-method0.20.00.2
show-dispatch000
split_node-HierarchicalPartition-method000
suggest_best_k-ConsensusPartition-method0.190.010.20
suggest_best_k-ConsensusPartitionList-method0.190.020.21
suggest_best_k-HierarchicalPartition-method0.150.010.17
suggest_best_k-dispatch000
test_between_factors0.020.000.01
test_to_known_factors-ConsensusPartition-method0.270.000.27
test_to_known_factors-ConsensusPartitionList-method0.450.020.47
test_to_known_factors-DownSamplingConsensusPartition-method0.150.000.15
test_to_known_factors-HierarchicalPartition-method0.190.000.19
test_to_known_factors-dispatch000
top_elements_overlap0.190.000.18
top_rows_heatmap-ConsensusPartition-method000
top_rows_heatmap-ConsensusPartitionList-method000
top_rows_heatmap-HierarchicalPartition-method000
top_rows_heatmap-dispatch000
top_rows_heatmap-matrix-method3.440.333.77
top_rows_overlap-ConsensusPartitionList-method1.030.041.07
top_rows_overlap-HierarchicalPartition-method0.670.020.71
top_rows_overlap-dispatch000
top_rows_overlap-matrix-method0.140.020.15

cola.Rcheck/examples_x64/cola-Ex.timings

nameusersystemelapsed
ATC0.030.000.03
ATC_approx000
ConsensusPartition-class000
ConsensusPartitionList-class000
DownSamplingConsensusPartition-class000
Extract.ConsensusPartitionList0.510.000.52
Extract.HierarchicalPartition0.160.010.17
ExtractExtract.ConsensusPartitionList0.280.000.28
ExtractExtract.HierarchicalPartition000
FCC0.190.000.19
HierarchicalPartition-class000
PAC0.440.020.45
aPAC0.220.010.24
adjust_matrix0.010.000.01
adjust_outlier000
all_leaves-HierarchicalPartition-method0.220.000.22
all_nodes-HierarchicalPartition-method0.170.000.17
all_partition_methods0.020.000.02
all_top_value_methods000
cola0.080.020.09
cola_opt0.030.000.03
cola_report-ConsensusPartition-method000
cola_report-ConsensusPartitionList-method000
cola_report-HierarchicalPartition-method000
cola_report-dispatch000
cola_rl0.120.010.14
collect_classes-ConsensusPartition-method2.030.082.11
collect_classes-ConsensusPartitionList-method3.050.023.07
collect_classes-HierarchicalPartition-method1.560.001.56
collect_classes-dispatch000
collect_plots-ConsensusPartition-method000
collect_plots-ConsensusPartitionList-method000
collect_plots-dispatch000
collect_stats-ConsensusPartition-method000
collect_stats-ConsensusPartitionList-method0.420.000.42
collect_stats-dispatch000
colnames-ConsensusPartition-method000
colnames-ConsensusPartitionList-method000
colnames-DownSamplingConsensusPartition-method000
colnames-HierarchicalPartition-method000
colnames-dispatch000
compare_partitions-ConsensusPartition-method000
compare_signatures-ConsensusPartition-method000
compare_signatures-HierarchicalPartition-method4.630.155.08
compare_signatures-dispatch000
concordance0.270.020.28
config_ATC000
consensus_heatmap-ConsensusPartition-method0.620.000.63
consensus_partition 1.80 0.0035.92
consensus_partition_by_down_sampling000
correspond_between_rankings0.030.030.06
correspond_between_two_rankings0.010.020.03
david_enrichment000
dim.ConsensusPartition000
dim.ConsensusPartitionList000
dim.DownSamplingConsensusPartition000
dim.HierarchicalPartition000
dimension_reduction-ConsensusPartition-method0.800.010.81
dimension_reduction-DownSamplingConsensusPartition-method1.280.061.35
dimension_reduction-HierarchicalPartition-method1.190.001.18
dimension_reduction-dispatch000
dimension_reduction-matrix-method000
find_best_km000
functional_enrichment-ANY-method000
functional_enrichment-ConsensusPartition-method000
functional_enrichment-ConsensusPartitionList-method000
functional_enrichment-HierarchicalPartition-method000
functional_enrichment-dispatch000
get_anno-ConsensusPartition-method000
get_anno-ConsensusPartitionList-method000
get_anno-DownSamplingConsensusPartition-method0.070.000.08
get_anno-HierarchicalPartition-method000
get_anno-dispatch000
get_anno_col-ConsensusPartition-method000
get_anno_col-ConsensusPartitionList-method000
get_anno_col-HierarchicalPartition-method000
get_anno_col-dispatch000
get_children_nodes-HierarchicalPartition-method000
get_classes-ConsensusPartition-method0.160.020.18
get_classes-ConsensusPartitionList-method0.170.000.17
get_classes-DownSamplingConsensusPartition-method0.100.000.09
get_classes-HierarchicalPartition-method0.140.000.14
get_classes-dispatch000
get_consensus-ConsensusPartition-method0.170.010.19
get_matrix-ConsensusPartition-method0.450.160.61
get_matrix-ConsensusPartitionList-method0.390.230.62
get_matrix-HierarchicalPartition-method000
get_matrix-dispatch000
get_membership-ConsensusPartition-method0.170.020.19
get_membership-ConsensusPartitionList-method0.160.010.17
get_membership-dispatch000
get_param-ConsensusPartition-method0.170.000.18
get_signatures-ConsensusPartition-method5.640.055.68
get_signatures-DownSamplingConsensusPartition-method000
get_signatures-HierarchicalPartition-method000
get_signatures-dispatch000
get_stats-ConsensusPartition-method0.170.000.17
get_stats-ConsensusPartitionList-method0.160.000.16
get_stats-dispatch000
golub_cola0.180.000.18
golub_cola_ds0.110.000.11
golub_cola_rh0.170.000.17
hierarchical_partition000
is_best_k-ConsensusPartition-method0.180.010.19
is_best_k-ConsensusPartitionList-method0.180.000.19
is_best_k-dispatch000
is_leaf_node-HierarchicalPartition-method0.130.020.14
is_stable_k-ConsensusPartition-method0.160.000.15
is_stable_k-ConsensusPartitionList-method0.170.000.17
is_stable_k-dispatch000
knee_finder20.030.000.03
knitr_add_tab_item000
knitr_insert_tabs000
map_to_entrez_id000
max_depth-HierarchicalPartition-method0.120.000.12
membership_heatmap-ConsensusPartition-method0.550.010.56
merge_node-HierarchicalPartition-method000
merge_node_param000
ncol-ConsensusPartition-method000
ncol-ConsensusPartitionList-method000
ncol-DownSamplingConsensusPartition-method000
ncol-HierarchicalPartition-method000
ncol-dispatch000
node_info-HierarchicalPartition-method000
node_level-HierarchicalPartition-method000
nrow-ConsensusPartition-method000
nrow-ConsensusPartitionList-method000
nrow-HierarchicalPartition-method000
nrow-dispatch000
plot_ecdf-ConsensusPartition-method0.170.000.18
predict_classes-ConsensusPartition-method000
predict_classes-dispatch000
predict_classes-matrix-method000
print.hc_table_suggest_best_k000
recalc_stats000
register_NMF000
register_SOM000
register_partition_methods0.60.00.6
register_top_value_methods000
relabel_class0.010.000.01
remove_partition_methods000
remove_top_value_methods000
rownames-ConsensusPartition-method000
rownames-ConsensusPartitionList-method000
rownames-HierarchicalPartition-method000
rownames-dispatch000
run_all_consensus_partition_methods000
select_partition_number-ConsensusPartition-method0.170.010.19
show-ConsensusPartition-method000
show-ConsensusPartitionList-method000
show-DownSamplingConsensusPartition-method0.130.000.12
show-HierarchicalPartition-method0.170.000.18
show-dispatch000
split_node-HierarchicalPartition-method000
suggest_best_k-ConsensusPartition-method0.140.020.17
suggest_best_k-ConsensusPartitionList-method0.170.010.19
suggest_best_k-HierarchicalPartition-method0.140.000.14
suggest_best_k-dispatch000
test_between_factors0.020.000.01
test_to_known_factors-ConsensusPartition-method0.160.040.19
test_to_known_factors-ConsensusPartitionList-method0.310.000.31
test_to_known_factors-DownSamplingConsensusPartition-method0.140.000.14
test_to_known_factors-HierarchicalPartition-method0.190.010.21
test_to_known_factors-dispatch000
top_elements_overlap0.290.000.29
top_rows_heatmap-ConsensusPartition-method000
top_rows_heatmap-ConsensusPartitionList-method000
top_rows_heatmap-HierarchicalPartition-method000
top_rows_heatmap-dispatch000
top_rows_heatmap-matrix-method3.570.313.88
top_rows_overlap-ConsensusPartitionList-method0.920.000.92
top_rows_overlap-HierarchicalPartition-method0.640.000.64
top_rows_overlap-dispatch000
top_rows_overlap-matrix-method0.120.020.14