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This page was generated on 2025-08-09 12:08 -0400 (Sat, 09 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.2 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4818
palomino8Windows Server 2022 Datacenterx644.5.1 (2025-06-13 ucrt) -- "Great Square Root" 4553
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4595
kjohnson3macOS 13.7.1 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4537
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 414/2317HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cola 2.15.0  (landing page)
Zuguang Gu
Snapshot Date: 2025-08-08 13:45 -0400 (Fri, 08 Aug 2025)
git_url: https://git.bioconductor.org/packages/cola
git_branch: devel
git_last_commit: 783b598
git_last_commit_date: 2025-04-15 11:40:31 -0400 (Tue, 15 Apr 2025)
nebbiolo2Linux (Ubuntu 24.04.2 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
lconwaymacOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.1 Ventura / arm64  OK    OK    OK    OK  UNNEEDED, same version is already published


CHECK results for cola on lconway

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: 2.15.0
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_2.15.0.tar.gz
StartedAt: 2025-08-08 20:08:10 -0400 (Fri, 08 Aug 2025)
EndedAt: 2025-08-08 20:11:46 -0400 (Fri, 08 Aug 2025)
EllapsedTime: 216.4 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_2.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.22-bioc/meat/cola.Rcheck’
* using R version 4.5.1 (2025-06-13)
* using platform: x86_64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 14.2.0
* 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 ‘2.15.0’
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 27 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ... INFO
  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 ... NOTE
License stub is invalid DCF.
* 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 ... NOTE
Non-topic package-anchored link(s) in Rd file 'collect_classes-ConsensusPartitionList-method.Rd':
  ‘[ComplexHeatmap:draw-HeatmapList-method]{draw,HeatmapList-method}’

See section 'Cross-references' in the 'Writing R Extensions' manual.

Found the following Rd file(s) with Rd \link{} targets missing package
anchors:
  predict_classes-ConsensusPartition-method.Rd: colorRamp2
  predict_classes-matrix-method.Rd: colorRamp2
Please provide package anchors for all Rd \link{} targets not in the
package itself and the base packages.
* 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                      20.919  0.270  21.284
get_signatures-ConsensusPartition-method  5.220  0.171   5.424
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.22-bioc/meat/cola.Rcheck/00check.log’
for details.


Installation output

cola.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘cola’ ...
** this is package ‘cola’ version ‘2.15.0’
** 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/4.5-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/4.5-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/4.5-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/4.5-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
installing to /Library/Frameworks/R.framework/Versions/4.5-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 4.5.1 (2025-06-13) -- "Great Square Root"
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 
  4.867   0.402   5.304 

Example timings

cola.Rcheck/cola-Ex.timings

nameusersystemelapsed
ATC0.0300.0050.035
ATC_approx000
ConsensusPartition-class0.0000.0000.001
ConsensusPartitionList-class000
DownSamplingConsensusPartition-class0.0010.0000.000
Extract.ConsensusPartitionList0.5890.0270.637
Extract.HierarchicalPartition0.1370.0050.143
ExtractExtract.ConsensusPartitionList0.4610.0080.471
ExtractExtract.HierarchicalPartition000
FCC0.1450.0060.152
HierarchicalPartition-class000
PAC0.1360.0070.143
aPAC0.1390.0080.148
adjust_matrix0.0060.0020.009
adjust_outlier0.0010.0000.001
all_leaves-HierarchicalPartition-method0.1040.0030.108
all_nodes-HierarchicalPartition-method0.0940.0040.100
all_partition_methods0.0010.0000.001
all_top_value_methods0.0010.0000.001
cola0.0600.0020.062
cola_opt0.0210.0020.023
cola_report-ConsensusPartition-method000
cola_report-ConsensusPartitionList-method000
cola_report-HierarchicalPartition-method0.0010.0010.001
cola_report-dispatch000
cola_rl0.0740.0050.080
collect_classes-ConsensusPartition-method2.1210.0632.197
collect_classes-ConsensusPartitionList-method3.2530.0253.289
collect_classes-HierarchicalPartition-method1.6170.0461.675
collect_classes-dispatch000
collect_plots-ConsensusPartition-method000
collect_plots-ConsensusPartitionList-method000
collect_plots-dispatch000
collect_stats-ConsensusPartition-method000
collect_stats-ConsensusPartitionList-method0.4690.0080.479
collect_stats-dispatch000
colnames-ConsensusPartition-method0.0000.0010.001
colnames-ConsensusPartitionList-method000
colnames-DownSamplingConsensusPartition-method000
colnames-HierarchicalPartition-method000
colnames-dispatch000
compare_partitions-ConsensusPartition-method0.0000.0000.001
compare_signatures-ConsensusPartition-method0.0000.0010.001
compare_signatures-HierarchicalPartition-method4.6180.1884.859
compare_signatures-dispatch0.0010.0000.000
concordance0.1450.0100.155
config_ATC0.0010.0000.001
consensus_heatmap-ConsensusPartition-method0.5350.0090.547
consensus_partition20.919 0.27021.284
consensus_partition_by_down_sampling0.0000.0010.000
correspond_between_rankings0.0680.0030.072
correspond_between_two_rankings0.0350.0020.037
david_enrichment000
dim.ConsensusPartition000
dim.ConsensusPartitionList000
dim.DownSamplingConsensusPartition0.0010.0000.000
dim.HierarchicalPartition000
dimension_reduction-ConsensusPartition-method0.7540.0520.813
dimension_reduction-DownSamplingConsensusPartition-method1.3190.0641.395
dimension_reduction-HierarchicalPartition-method1.1930.0331.232
dimension_reduction-dispatch000
dimension_reduction-matrix-method0.0000.0000.001
find_best_km0.0010.0000.000
functional_enrichment-ANY-method000
functional_enrichment-ConsensusPartition-method0.0000.0010.000
functional_enrichment-ConsensusPartitionList-method000
functional_enrichment-HierarchicalPartition-method0.0000.0000.001
functional_enrichment-dispatch000
get_anno-ConsensusPartition-method000
get_anno-ConsensusPartitionList-method000
get_anno-DownSamplingConsensusPartition-method0.0650.0040.068
get_anno-HierarchicalPartition-method000
get_anno-dispatch0.0000.0000.001
get_anno_col-ConsensusPartition-method000
get_anno_col-ConsensusPartitionList-method000
get_anno_col-HierarchicalPartition-method0.0000.0010.000
get_anno_col-dispatch000
get_children_nodes-HierarchicalPartition-method000
get_classes-ConsensusPartition-method0.1360.0080.146
get_classes-ConsensusPartitionList-method0.1290.0060.135
get_classes-DownSamplingConsensusPartition-method0.0880.0160.104
get_classes-HierarchicalPartition-method0.1180.0030.121
get_classes-dispatch000
get_consensus-ConsensusPartition-method0.1430.0310.174
get_matrix-ConsensusPartition-method0.3620.5180.891
get_matrix-ConsensusPartitionList-method0.3550.5650.928
get_matrix-DownSamplingConsensusPartition-method000
get_matrix-HierarchicalPartition-method000
get_matrix-dispatch000
get_membership-ConsensusPartition-method0.1380.0240.164
get_membership-ConsensusPartitionList-method0.1290.0040.134
get_membership-dispatch000
get_param-ConsensusPartition-method0.1470.0170.165
get_signatures-ConsensusPartition-method5.2200.1715.424
get_signatures-DownSamplingConsensusPartition-method0.0000.0010.000
get_signatures-HierarchicalPartition-method000
get_signatures-dispatch0.0000.0010.000
get_stats-ConsensusPartition-method0.1520.0050.157
get_stats-ConsensusPartitionList-method0.1500.0080.159
get_stats-dispatch000
golub_cola0.1640.0040.170
golub_cola_ds0.1030.0030.107
golub_cola_rh0.1680.0050.177
hierarchical_partition0.0010.0010.000
is_best_k-ConsensusPartition-method0.1500.0050.157
is_best_k-ConsensusPartitionList-method0.1390.0040.144
is_best_k-dispatch0.0000.0000.001
is_leaf_node-HierarchicalPartition-method0.1020.0020.106
is_stable_k-ConsensusPartition-method0.1980.0130.213
is_stable_k-ConsensusPartitionList-method0.1360.0040.141
is_stable_k-dispatch0.0000.0000.001
knee_finder20.0220.0040.029
knitr_add_tab_item0.0000.0010.000
knitr_insert_tabs000
map_to_entrez_id000
max_depth-HierarchicalPartition-method0.1020.0040.107
membership_heatmap-ConsensusPartition-method0.5210.0070.528
merge_node-HierarchicalPartition-method0.0000.0010.000
merge_node_param000
ncol-ConsensusPartition-method000
ncol-ConsensusPartitionList-method000
ncol-DownSamplingConsensusPartition-method000
ncol-HierarchicalPartition-method000
ncol-dispatch0.0010.0000.000
node_info-HierarchicalPartition-method0.0000.0010.001
node_level-HierarchicalPartition-method0.0010.0000.000
nrow-ConsensusPartition-method000
nrow-ConsensusPartitionList-method000
nrow-HierarchicalPartition-method0.0000.0000.001
nrow-dispatch0.0000.0000.001
plot_ecdf-ConsensusPartition-method0.1490.0080.158
predict_classes-ConsensusPartition-method0.0000.0010.000
predict_classes-dispatch0.0000.0000.001
predict_classes-matrix-method000
print.hc_table_suggest_best_k0.0000.0010.001
recalc_stats000
register_NMF000
register_SOM0.0010.0010.000
register_partition_methods0.6100.0180.632
register_top_value_methods0.0020.0000.002
relabel_class0.0120.0030.014
remove_partition_methods0.0000.0010.001
remove_top_value_methods000
rownames-ConsensusPartition-method0.0000.0000.001
rownames-ConsensusPartitionList-method0.0000.0000.001
rownames-HierarchicalPartition-method0.0000.0000.001
rownames-dispatch000
run_all_consensus_partition_methods000
select_partition_number-ConsensusPartition-method0.1390.0030.144
show-ConsensusPartition-method000
show-ConsensusPartitionList-method000
show-DownSamplingConsensusPartition-method0.0850.0030.089
show-HierarchicalPartition-method0.1530.0040.157
show-dispatch0.0000.0010.000
split_node-HierarchicalPartition-method000
suggest_best_k-ConsensusPartition-method0.1220.0030.126
suggest_best_k-ConsensusPartitionList-method0.1330.0040.138
suggest_best_k-HierarchicalPartition-method0.1040.0030.108
suggest_best_k-dispatch000
test_between_factors0.0090.0010.009
test_to_known_factors-ConsensusPartition-method0.1560.0040.163
test_to_known_factors-ConsensusPartitionList-method0.2740.0090.285
test_to_known_factors-DownSamplingConsensusPartition-method0.0810.0020.085
test_to_known_factors-HierarchicalPartition-method0.1220.0030.125
test_to_known_factors-dispatch000
top_elements_overlap0.2390.0270.268
top_rows_heatmap-ConsensusPartition-method0.0010.0010.000
top_rows_heatmap-ConsensusPartitionList-method000
top_rows_heatmap-HierarchicalPartition-method000
top_rows_heatmap-dispatch000
top_rows_heatmap-matrix-method3.9840.2894.307
top_rows_overlap-ConsensusPartitionList-method0.7970.0430.847
top_rows_overlap-HierarchicalPartition-method0.5670.0170.592
top_rows_overlap-dispatch000
top_rows_overlap-matrix-method0.1530.0030.156