Back to Multiple platform build/check report for BioC 3.22:   simplified   long
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

This page was generated on 2025-10-17 12:07 -0400 (Fri, 17 Oct 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 Patched (2025-08-23 r88802) -- "Great Square Root" 4887
lconwaymacOS 12.7.6 Montereyx86_644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4677
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-09-10 r88807) -- "Great Square Root" 4622
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4632
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 422/2353HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cola 2.15.0  (landing page)
Zuguang Gu
Snapshot Date: 2025-10-16 13:45 -0400 (Thu, 16 Oct 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 24.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
lconwaymacOS 12.7.6 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kjohnson3macOS 13.7.7 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 taishan

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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: cola
Version: 2.15.0
Command: /home/biocbuild/R/R/bin/R CMD check --install=check:cola.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings cola_2.15.0.tar.gz
StartedAt: 2025-10-17 07:29:52 -0000 (Fri, 17 Oct 2025)
EndedAt: 2025-10-17 07:33:42 -0000 (Fri, 17 Oct 2025)
EllapsedTime: 230.1 seconds
RetCode: 0
Status:   OK  
CheckDir: cola.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD check --install=check:cola.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings cola_2.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/cola.Rcheck’
* using R version 4.5.0 (2025-04-11)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0
    GNU Fortran (GCC) 14.2.0
* running under: openEuler 24.03 (LTS)
* 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: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
* checking installed package size ... INFO
  installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data      3.2Mb
    extdata   1.0Mb
    libs      2.1Mb
* 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 loading without being on the library search path ... 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                             29.548  0.371  30.043
get_signatures-ConsensusPartition-method         6.356  0.071   6.448
compare_signatures-HierarchicalPartition-method  5.602  0.219   5.846
* 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
  ‘/home/biocbuild/bbs-3.22-bioc/meat/cola.Rcheck/00check.log’
for details.


Installation output

cola.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R/bin/R CMD INSTALL cola
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-4.5.0/site-library’
* installing *source* package ‘cola’ ...
** this is package ‘cola’ version ‘2.15.0’
** using staged installation
** libs
using C++ compiler: ‘aarch64-unknown-linux-gnu-g++ (GCC) 14.2.0’
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c RcppExports.cpp -o RcppExports.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c atc.cpp -o atc.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c cal_consensus_mat.cpp -o cal_consensus_mat.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -I"/home/biocbuild/R/R-4.5.0/include" -DNDEBUG  -I'/home/biocbuild/R/R-4.5.0/site-library/Rcpp/include' -I/usr/local/include    -fPIC  -g -O2  -Wall -Werror=format-security  -c pdist.cpp -o pdist.o
/opt/ohpc/pub/compiler/gcc/14.2.0/bin/aarch64-unknown-linux-gnu-g++ -std=gnu++17 -shared -L/home/biocbuild/R/R-4.5.0/lib -L/usr/local/lib -o cola.so RcppExports.o atc.o cal_consensus_mat.o pdist.o -L/home/biocbuild/R/R-4.5.0/lib -lR
installing to /home/biocbuild/R/R-4.5.0/site-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 4.5.0 (2025-04-11) -- "How About a Twenty-Six"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu

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 
  6.177   0.287   6.465 

Example timings

cola.Rcheck/cola-Ex.timings

nameusersystemelapsed
ATC0.1560.0000.155
ATC_approx000
ConsensusPartition-class0.0000.0000.001
ConsensusPartitionList-class000
DownSamplingConsensusPartition-class000
Extract.ConsensusPartitionList0.5750.0080.585
Extract.HierarchicalPartition0.2270.0040.232
ExtractExtract.ConsensusPartitionList0.1570.0040.161
ExtractExtract.HierarchicalPartition000
FCC0.1520.0280.179
HierarchicalPartition-class000
PAC0.4100.0200.432
aPAC0.1310.0000.132
adjust_matrix0.0080.0000.007
adjust_outlier0.0010.0000.001
all_leaves-HierarchicalPartition-method0.1080.0040.111
all_nodes-HierarchicalPartition-method0.1190.0000.119
all_partition_methods0.0010.0000.001
all_top_value_methods000
cola0.0770.0040.081
cola_opt0.0300.0000.029
cola_report-ConsensusPartition-method000
cola_report-ConsensusPartitionList-method000
cola_report-HierarchicalPartition-method0.0010.0000.000
cola_report-dispatch000
cola_rl0.0770.0000.077
collect_classes-ConsensusPartition-method2.4740.0762.555
collect_classes-ConsensusPartitionList-method4.3280.0954.435
collect_classes-HierarchicalPartition-method2.2510.0442.301
collect_classes-dispatch000
collect_plots-ConsensusPartition-method000
collect_plots-ConsensusPartitionList-method000
collect_plots-dispatch0.0000.0000.001
collect_stats-ConsensusPartition-method0.0000.0010.000
collect_stats-ConsensusPartitionList-method0.5380.0060.544
collect_stats-dispatch000
colnames-ConsensusPartition-method0.0000.0000.001
colnames-ConsensusPartitionList-method000
colnames-DownSamplingConsensusPartition-method000
colnames-HierarchicalPartition-method000
colnames-dispatch000
compare_partitions-ConsensusPartition-method0.0010.0000.000
compare_signatures-ConsensusPartition-method000
compare_signatures-HierarchicalPartition-method5.6020.2195.846
compare_signatures-dispatch0.0000.0000.001
concordance0.1450.0040.150
config_ATC0.0010.0000.001
consensus_heatmap-ConsensusPartition-method0.6850.0120.698
consensus_partition29.548 0.37130.043
consensus_partition_by_down_sampling000
correspond_between_rankings0.0780.0000.079
correspond_between_two_rankings0.0300.0040.034
david_enrichment000
dim.ConsensusPartition000
dim.ConsensusPartitionList000
dim.DownSamplingConsensusPartition000
dim.HierarchicalPartition000
dimension_reduction-ConsensusPartition-method0.8210.0040.827
dimension_reduction-DownSamplingConsensusPartition-method1.5070.0081.521
dimension_reduction-HierarchicalPartition-method0.7020.0080.712
dimension_reduction-dispatch0.0010.0000.000
dimension_reduction-matrix-method000
find_best_km000
functional_enrichment-ANY-method000
functional_enrichment-ConsensusPartition-method0.0000.0000.001
functional_enrichment-ConsensusPartitionList-method000
functional_enrichment-HierarchicalPartition-method000
functional_enrichment-dispatch000
get_anno-ConsensusPartition-method000
get_anno-ConsensusPartitionList-method000
get_anno-DownSamplingConsensusPartition-method0.0660.0040.070
get_anno-HierarchicalPartition-method000
get_anno-dispatch000
get_anno_col-ConsensusPartition-method000
get_anno_col-ConsensusPartitionList-method000
get_anno_col-HierarchicalPartition-method0.0010.0000.000
get_anno_col-dispatch000
get_children_nodes-HierarchicalPartition-method0.0000.0000.001
get_classes-ConsensusPartition-method0.1210.0080.129
get_classes-ConsensusPartitionList-method0.1380.0040.142
get_classes-DownSamplingConsensusPartition-method0.0710.0000.071
get_classes-HierarchicalPartition-method0.1250.0040.130
get_classes-dispatch0.0000.0000.001
get_consensus-ConsensusPartition-method0.1320.0040.136
get_matrix-ConsensusPartition-method0.2950.1000.396
get_matrix-ConsensusPartitionList-method0.2890.1040.393
get_matrix-DownSamplingConsensusPartition-method000
get_matrix-HierarchicalPartition-method000
get_matrix-dispatch000
get_membership-ConsensusPartition-method0.1320.0000.132
get_membership-ConsensusPartitionList-method0.1170.0080.125
get_membership-dispatch000
get_param-ConsensusPartition-method0.6930.0120.707
get_signatures-ConsensusPartition-method6.3560.0716.448
get_signatures-DownSamplingConsensusPartition-method0.0000.0000.001
get_signatures-HierarchicalPartition-method000
get_signatures-dispatch000
get_stats-ConsensusPartition-method0.1240.0000.125
get_stats-ConsensusPartitionList-method0.1200.0040.124
get_stats-dispatch000
golub_cola0.1580.0000.158
golub_cola_ds0.1170.0000.118
golub_cola_rh0.1650.0000.165
hierarchical_partition000
is_best_k-ConsensusPartition-method0.1240.0000.125
is_best_k-ConsensusPartitionList-method0.1250.0030.130
is_best_k-dispatch000
is_leaf_node-HierarchicalPartition-method0.1050.0040.110
is_stable_k-ConsensusPartition-method0.1300.0080.137
is_stable_k-ConsensusPartitionList-method0.1290.0040.133
is_stable_k-dispatch0.0010.0000.001
knee_finder20.0240.0040.028
knitr_add_tab_item000
knitr_insert_tabs000
map_to_entrez_id000
max_depth-HierarchicalPartition-method0.1070.0000.107
membership_heatmap-ConsensusPartition-method0.6030.0080.614
merge_node-HierarchicalPartition-method000
merge_node_param0.0010.0000.000
ncol-ConsensusPartition-method0.0000.0000.001
ncol-ConsensusPartitionList-method000
ncol-DownSamplingConsensusPartition-method000
ncol-HierarchicalPartition-method000
ncol-dispatch000
node_info-HierarchicalPartition-method0.0000.0000.001
node_level-HierarchicalPartition-method000
nrow-ConsensusPartition-method000
nrow-ConsensusPartitionList-method000
nrow-HierarchicalPartition-method0.0010.0000.000
nrow-dispatch0.0000.0000.001
plot_ecdf-ConsensusPartition-method0.1300.0080.139
predict_classes-ConsensusPartition-method0.0010.0000.000
predict_classes-dispatch000
predict_classes-matrix-method000
print.hc_table_suggest_best_k000
recalc_stats0.0000.0000.001
register_NMF000
register_SOM000
register_partition_methods0.5650.0040.570
register_top_value_methods0.0020.0000.001
relabel_class0.0110.0000.012
remove_partition_methods0.0000.0000.001
remove_top_value_methods000
rownames-ConsensusPartition-method000
rownames-ConsensusPartitionList-method000
rownames-HierarchicalPartition-method0.0010.0000.000
rownames-dispatch000
run_all_consensus_partition_methods000
select_partition_number-ConsensusPartition-method0.1400.0040.144
show-ConsensusPartition-method0.0000.0000.001
show-ConsensusPartitionList-method000
show-DownSamplingConsensusPartition-method0.0980.0040.102
show-HierarchicalPartition-method0.1660.0000.166
show-dispatch000
split_node-HierarchicalPartition-method000
suggest_best_k-ConsensusPartition-method0.1160.0080.125
suggest_best_k-ConsensusPartitionList-method0.1320.0040.136
suggest_best_k-HierarchicalPartition-method0.1170.0000.117
suggest_best_k-dispatch000
test_between_factors0.0120.0000.012
test_to_known_factors-ConsensusPartition-method0.1420.0080.151
test_to_known_factors-ConsensusPartitionList-method0.2890.0080.299
test_to_known_factors-DownSamplingConsensusPartition-method0.0950.0040.100
test_to_known_factors-HierarchicalPartition-method0.1360.0080.145
test_to_known_factors-dispatch000
top_elements_overlap0.2690.0000.269
top_rows_heatmap-ConsensusPartition-method000
top_rows_heatmap-ConsensusPartitionList-method000
top_rows_heatmap-HierarchicalPartition-method000
top_rows_heatmap-dispatch000
top_rows_heatmap-matrix-method4.0800.0604.151
top_rows_overlap-ConsensusPartitionList-method0.8940.0080.904
top_rows_overlap-HierarchicalPartition-method0.5900.0000.591
top_rows_overlap-dispatch000
top_rows_overlap-matrix-method0.1860.0000.186