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This page was generated on 2025-03-17 12:08 -0400 (Mon, 17 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.3 (2025-02-28) -- "Trophy Case" 4756
palomino8Windows Server 2022 Datacenterx644.4.3 (2025-02-28 ucrt) -- "Trophy Case" 4487
merida1macOS 12.7.5 Montereyx86_644.4.3 (2025-02-28) -- "Trophy Case" 4514
kjohnson1macOS 13.6.6 Venturaarm644.4.3 (2025-02-28) -- "Trophy Case" 4441
taishanLinux (openEuler 24.03 LTS)aarch644.4.3 (2025-02-28) -- "Trophy Case" 4399
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

Package 410/2289HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cola 2.12.0  (landing page)
Zuguang Gu
Snapshot Date: 2025-03-13 13:00 -0400 (Thu, 13 Mar 2025)
git_url: https://git.bioconductor.org/packages/cola
git_branch: RELEASE_3_20
git_last_commit: a5fa7af
git_last_commit_date: 2024-10-29 10:34:13 -0400 (Tue, 29 Oct 2024)
nebbiolo2Linux (Ubuntu 24.04.1 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino8Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.5 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson1macOS 13.6.6 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for cola on merida1

To the developers/maintainers of the cola package:
- 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 Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: cola
Version: 2.12.0
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cola.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cola_2.12.0.tar.gz
StartedAt: 2025-03-14 01:02:36 -0400 (Fri, 14 Mar 2025)
EndedAt: 2025-03-14 01:09:58 -0400 (Fri, 14 Mar 2025)
EllapsedTime: 441.8 seconds
RetCode: 0
Status:   OK  
CheckDir: cola.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:cola.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings cola_2.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/cola.Rcheck’
* using R version 4.4.3 (2025-02-28)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cola/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cola’ version ‘2.12.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘cola’ can be installed ... OK
* used C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
* used SDK: ‘MacOSX11.3.sdk’
* checking installed package size ... NOTE
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data      3.2Mb
    extdata   1.0Mb
* 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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* 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 whether startup messages can be suppressed ... 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 is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                                                  user system elapsed
consensus_partition                             50.880  0.545  57.379
get_signatures-ConsensusPartition-method        11.032  0.215  12.698
compare_signatures-HierarchicalPartition-method  8.401  0.316  10.011
collect_classes-ConsensusPartitionList-method    7.751  0.063   8.542
top_rows_heatmap-matrix-method                   5.687  0.328   6.575
collect_classes-ConsensusPartition-method        4.519  0.153   5.315
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... 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
  ‘/Users/biocbuild/bbs-3.20-bioc/meat/cola.Rcheck/00check.log’
for details.


Installation output

cola.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL cola
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library’
* installing *source* package ‘cola’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 14.0.0 (clang-1400.0.29.202)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c atc.cpp -o atc.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c cal_consensus_mat.cpp -o cal_consensus_mat.o
clang++ -arch x86_64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/Rcpp/include' -I/opt/R/x86_64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c pdist.cpp -o pdist.o
clang++ -arch x86_64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/x86_64/lib -o cola.so RcppExports.o atc.o cal_consensus_mat.o pdist.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/00LOCK-cola/00new/cola/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cola)

Tests output

cola.Rcheck/tests/test-all.Rout


R version 4.4.3 (2025-02-28) -- "Trophy Case"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20

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 
  9.112   0.635  10.901 

Example timings

cola.Rcheck/cola-Ex.timings

nameusersystemelapsed
ATC0.0500.0070.066
ATC_approx0.0010.0000.001
ConsensusPartition-class0.0000.0010.001
ConsensusPartitionList-class0.0000.0000.001
DownSamplingConsensusPartition-class000
Extract.ConsensusPartitionList0.9620.0391.140
Extract.HierarchicalPartition0.3440.0160.408
ExtractExtract.ConsensusPartitionList0.2710.0150.324
ExtractExtract.HierarchicalPartition0.0000.0000.001
FCC0.2670.0160.328
HierarchicalPartition-class0.0010.0000.000
PAC0.6200.0150.721
aPAC0.2250.0140.272
adjust_matrix0.0120.0040.020
adjust_outlier0.0010.0010.003
all_leaves-HierarchicalPartition-method0.1720.0100.203
all_nodes-HierarchicalPartition-method0.1800.0120.215
all_partition_methods0.0020.0010.003
all_top_value_methods0.0000.0010.001
cola0.1430.0020.170
cola_opt0.0470.0030.057
cola_report-ConsensusPartition-method000
cola_report-ConsensusPartitionList-method0.0000.0000.001
cola_report-HierarchicalPartition-method0.0010.0010.001
cola_report-dispatch0.0000.0010.001
cola_rl0.1320.0120.159
collect_classes-ConsensusPartition-method4.5190.1535.315
collect_classes-ConsensusPartitionList-method7.7510.0638.542
collect_classes-HierarchicalPartition-method3.0190.0663.510
collect_classes-dispatch000
collect_plots-ConsensusPartition-method0.0000.0010.001
collect_plots-ConsensusPartitionList-method0.0010.0010.001
collect_plots-dispatch0.0000.0000.001
collect_stats-ConsensusPartition-method0.0000.0000.001
collect_stats-ConsensusPartitionList-method0.9130.0261.100
collect_stats-dispatch0.0000.0010.001
colnames-ConsensusPartition-method0.0000.0010.001
colnames-ConsensusPartitionList-method000
colnames-DownSamplingConsensusPartition-method000
colnames-HierarchicalPartition-method0.0000.0000.001
colnames-dispatch000
compare_partitions-ConsensusPartition-method0.0000.0010.001
compare_signatures-ConsensusPartition-method0.0010.0000.001
compare_signatures-HierarchicalPartition-method 8.401 0.31610.011
compare_signatures-dispatch0.0000.0000.001
concordance0.2250.0140.278
config_ATC0.0010.0010.002
consensus_heatmap-ConsensusPartition-method1.1950.0211.385
consensus_partition50.880 0.54557.379
consensus_partition_by_down_sampling0.0000.0010.001
correspond_between_rankings0.1260.0040.145
correspond_between_two_rankings0.0540.0030.059
david_enrichment0.0000.0000.001
dim.ConsensusPartition0.0000.0000.002
dim.ConsensusPartitionList0.0000.0000.001
dim.DownSamplingConsensusPartition0.0000.0000.001
dim.HierarchicalPartition0.0010.0010.001
dimension_reduction-ConsensusPartition-method1.3830.0661.586
dimension_reduction-DownSamplingConsensusPartition-method3.1710.1073.655
dimension_reduction-HierarchicalPartition-method1.1780.0541.349
dimension_reduction-dispatch000
dimension_reduction-matrix-method0.0000.0000.001
find_best_km0.0000.0010.001
functional_enrichment-ANY-method0.0000.0010.001
functional_enrichment-ConsensusPartition-method000
functional_enrichment-ConsensusPartitionList-method000
functional_enrichment-HierarchicalPartition-method0.0010.0010.000
functional_enrichment-dispatch0.0000.0010.001
get_anno-ConsensusPartition-method0.0010.0000.000
get_anno-ConsensusPartitionList-method0.0000.0000.001
get_anno-DownSamplingConsensusPartition-method0.1070.0090.130
get_anno-HierarchicalPartition-method000
get_anno-dispatch0.0000.0000.001
get_anno_col-ConsensusPartition-method0.0000.0010.000
get_anno_col-ConsensusPartitionList-method0.0000.0010.001
get_anno_col-HierarchicalPartition-method0.0010.0010.001
get_anno_col-dispatch0.0000.0010.000
get_children_nodes-HierarchicalPartition-method0.0000.0010.000
get_classes-ConsensusPartition-method0.2250.0190.267
get_classes-ConsensusPartitionList-method0.2200.0130.270
get_classes-DownSamplingConsensusPartition-method0.1090.0150.139
get_classes-HierarchicalPartition-method0.2010.0120.239
get_classes-dispatch0.0000.0010.001
get_consensus-ConsensusPartition-method0.2450.0860.392
get_matrix-ConsensusPartition-method0.8561.6132.791
get_matrix-ConsensusPartitionList-method0.8781.6472.872
get_matrix-DownSamplingConsensusPartition-method0.0000.0010.000
get_matrix-HierarchicalPartition-method0.0010.0010.001
get_matrix-dispatch0.0000.0010.001
get_membership-ConsensusPartition-method0.2370.0690.356
get_membership-ConsensusPartitionList-method0.2170.0130.266
get_membership-dispatch0.0010.0000.001
get_param-ConsensusPartition-method0.2390.0280.314
get_signatures-ConsensusPartition-method11.032 0.21512.698
get_signatures-DownSamplingConsensusPartition-method0.0010.0000.000
get_signatures-HierarchicalPartition-method000
get_signatures-dispatch0.0010.0010.001
get_stats-ConsensusPartition-method0.2210.0120.246
get_stats-ConsensusPartitionList-method0.2220.0150.242
get_stats-dispatch0.0000.0000.001
golub_cola0.3020.0130.329
golub_cola_ds0.1640.0110.182
golub_cola_rh0.2670.0120.339
hierarchical_partition0.0000.0000.001
is_best_k-ConsensusPartition-method0.2200.0100.279
is_best_k-ConsensusPartitionList-method0.2430.0120.276
is_best_k-dispatch0.0000.0010.001
is_leaf_node-HierarchicalPartition-method0.1730.0090.200
is_stable_k-ConsensusPartition-method0.2710.0150.315
is_stable_k-ConsensusPartitionList-method0.2410.0100.270
is_stable_k-dispatch0.0000.0000.001
knee_finder20.0380.0080.052
knitr_add_tab_item0.0000.0000.001
knitr_insert_tabs0.0000.0010.001
map_to_entrez_id0.0000.0000.001
max_depth-HierarchicalPartition-method0.1730.0090.195
membership_heatmap-ConsensusPartition-method1.0220.0181.197
merge_node-HierarchicalPartition-method0.0000.0000.001
merge_node_param0.0000.0000.001
ncol-ConsensusPartition-method0.0000.0010.001
ncol-ConsensusPartitionList-method0.0000.0010.000
ncol-DownSamplingConsensusPartition-method0.0010.0000.001
ncol-HierarchicalPartition-method0.0000.0010.001
ncol-dispatch0.0000.0000.003
node_info-HierarchicalPartition-method0.0000.0010.001
node_level-HierarchicalPartition-method0.0000.0000.001
nrow-ConsensusPartition-method0.0000.0010.000
nrow-ConsensusPartitionList-method000
nrow-HierarchicalPartition-method0.0010.0010.001
nrow-dispatch0.0000.0010.001
plot_ecdf-ConsensusPartition-method0.2590.0130.284
predict_classes-ConsensusPartition-method0.0000.0000.001
predict_classes-dispatch0.0000.0000.001
predict_classes-matrix-method0.0000.0010.001
print.hc_table_suggest_best_k0.0000.0000.001
recalc_stats0.0000.0010.000
register_NMF0.0000.0000.001
register_SOM0.0010.0010.001
register_partition_methods0.7310.0470.867
register_top_value_methods0.0020.0010.004
relabel_class0.0190.0070.030
remove_partition_methods0.0010.0000.001
remove_top_value_methods0.0000.0010.001
rownames-ConsensusPartition-method0.0000.0010.001
rownames-ConsensusPartitionList-method0.0000.0010.001
rownames-HierarchicalPartition-method0.0000.0010.001
rownames-dispatch000
run_all_consensus_partition_methods0.0000.0000.001
select_partition_number-ConsensusPartition-method0.2480.0120.320
show-ConsensusPartition-method0.0010.0010.001
show-ConsensusPartitionList-method0.0000.0010.001
show-DownSamplingConsensusPartition-method0.1610.0100.179
show-HierarchicalPartition-method0.2650.0120.291
show-dispatch0.0010.0010.001
split_node-HierarchicalPartition-method000
suggest_best_k-ConsensusPartition-method0.2180.0100.239
suggest_best_k-ConsensusPartitionList-method0.2420.0120.263
suggest_best_k-HierarchicalPartition-method0.1880.0110.208
suggest_best_k-dispatch0.0000.0010.001
test_between_factors0.0200.0010.021
test_to_known_factors-ConsensusPartition-method0.2720.0160.342
test_to_known_factors-ConsensusPartitionList-method0.5590.0190.664
test_to_known_factors-DownSamplingConsensusPartition-method0.1630.0100.201
test_to_known_factors-HierarchicalPartition-method0.2000.0100.239
test_to_known_factors-dispatch0.0000.0010.001
top_elements_overlap0.4530.0260.523
top_rows_heatmap-ConsensusPartition-method000
top_rows_heatmap-ConsensusPartitionList-method0.0000.0000.001
top_rows_heatmap-HierarchicalPartition-method0.0000.0010.001
top_rows_heatmap-dispatch0.0000.0010.001
top_rows_heatmap-matrix-method5.6870.3286.575
top_rows_overlap-ConsensusPartitionList-method1.4960.0741.692
top_rows_overlap-HierarchicalPartition-method0.9570.0451.119
top_rows_overlap-dispatch0.0010.0010.001
top_rows_overlap-matrix-method0.3250.0050.364