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This page was generated on 2025-03-17 11:39 -0400 (Mon, 17 Mar 2025).

HostnameOSArch (*)R versionInstalled pkgs
palomino7Windows Server 2022 Datacenterx64R Under development (unstable) (2025-03-01 r87860 ucrt) -- "Unsuffered Consequences" 4545
lconwaymacOS 12.7.1 Montereyx86_64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4576
kjohnson3macOS 13.7.1 Venturaarm64R Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences" 4528
kunpeng2Linux (openEuler 24.03 LTS)aarch64R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" 4459
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 412/2313HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cola 2.13.1  (landing page)
Zuguang Gu
Snapshot Date: 2025-03-16 13:40 -0400 (Sun, 16 Mar 2025)
git_url: https://git.bioconductor.org/packages/cola
git_branch: devel
git_last_commit: 1f071f7
git_last_commit_date: 2025-02-06 04:31:44 -0400 (Thu, 06 Feb 2025)
palomino7Windows 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
kunpeng2Linux (openEuler 24.03 LTS) / aarch64  OK    OK    OK  


CHECK results for cola on kjohnson3

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: 2.13.1
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_2.13.1.tar.gz
StartedAt: 2025-03-16 18:43:39 -0400 (Sun, 16 Mar 2025)
EndedAt: 2025-03-16 18:44:51 -0400 (Sun, 16 Mar 2025)
EllapsedTime: 71.8 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_2.13.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/cola.Rcheck’
* using R Under development (unstable) (2025-03-02 r87868)
* using platform: aarch64-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 Ventura 13.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cola/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cola’ version ‘2.13.1’
* 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 15.0.0 (clang-1500.1.0.2.5)’
* 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
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 5.324  0.159   5.512
* 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-3.21-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/4.5-arm64/Resources/library’
* installing *source* package ‘cola’ ...
** this is package ‘cola’ version ‘2.13.1’
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 15.0.0 (clang-1500.1.0.2.5)’
using SDK: ‘MacOSX11.3.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c RcppExports.cpp -o RcppExports.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c atc.cpp -o atc.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c cal_consensus_mat.cpp -o cal_consensus_mat.o
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2   -c pdist.cpp -o pdist.o
clang++ -arch arm64 -std=gnu++17 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/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/4.5-arm64/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 Under development (unstable) (2025-03-02 r87868) -- "Unsuffered Consequences"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: aarch64-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 
  1.594   0.130   1.733 

Example timings

cola.Rcheck/cola-Ex.timings

nameusersystemelapsed
ATC0.0170.0030.020
ATC_approx000
ConsensusPartition-class000
ConsensusPartitionList-class0.0000.0010.000
DownSamplingConsensusPartition-class0.0000.0000.001
Extract.ConsensusPartitionList0.1550.0070.162
Extract.HierarchicalPartition0.0650.0020.067
ExtractExtract.ConsensusPartitionList0.0680.0030.071
ExtractExtract.HierarchicalPartition0.0010.0000.000
FCC0.0720.0040.088
HierarchicalPartition-class000
PAC0.1080.0040.118
aPAC0.0630.0020.066
adjust_matrix0.0020.0000.003
adjust_outlier000
all_leaves-HierarchicalPartition-method0.0580.0010.061
all_nodes-HierarchicalPartition-method0.0610.0010.062
all_partition_methods000
all_top_value_methods000
cola0.0160.0000.017
cola_opt0.0090.0010.010
cola_report-ConsensusPartition-method000
cola_report-ConsensusPartitionList-method000
cola_report-HierarchicalPartition-method000
cola_report-dispatch000
cola_rl0.0290.0010.030
collect_classes-ConsensusPartition-method0.5560.0110.578
collect_classes-ConsensusPartitionList-method1.1140.0321.178
collect_classes-HierarchicalPartition-method0.3910.0120.411
collect_classes-dispatch000
collect_plots-ConsensusPartition-method000
collect_plots-ConsensusPartitionList-method000
collect_plots-dispatch000
collect_stats-ConsensusPartition-method000
collect_stats-ConsensusPartitionList-method0.1450.0040.149
collect_stats-dispatch000
colnames-ConsensusPartition-method000
colnames-ConsensusPartitionList-method000
colnames-DownSamplingConsensusPartition-method000
colnames-HierarchicalPartition-method000
colnames-dispatch0.0010.0000.000
compare_partitions-ConsensusPartition-method000
compare_signatures-ConsensusPartition-method000
compare_signatures-HierarchicalPartition-method1.7440.0781.837
compare_signatures-dispatch000
concordance0.0640.0010.065
config_ATC0.0010.0000.000
consensus_heatmap-ConsensusPartition-method0.1770.0080.186
consensus_partition5.3240.1595.512
consensus_partition_by_down_sampling000
correspond_between_rankings0.0200.0010.021
correspond_between_two_rankings0.0110.0010.012
david_enrichment000
dim.ConsensusPartition000
dim.ConsensusPartitionList000
dim.DownSamplingConsensusPartition000
dim.HierarchicalPartition0.0000.0010.000
dimension_reduction-ConsensusPartition-method0.2660.0170.287
dimension_reduction-DownSamplingConsensusPartition-method0.6730.0210.695
dimension_reduction-HierarchicalPartition-method0.2380.0180.258
dimension_reduction-dispatch000
dimension_reduction-matrix-method000
find_best_km000
functional_enrichment-ANY-method0.0000.0010.000
functional_enrichment-ConsensusPartition-method000
functional_enrichment-ConsensusPartitionList-method0.0000.0000.001
functional_enrichment-HierarchicalPartition-method000
functional_enrichment-dispatch000
get_anno-ConsensusPartition-method0.0000.0000.001
get_anno-ConsensusPartitionList-method000
get_anno-DownSamplingConsensusPartition-method0.0400.0020.043
get_anno-HierarchicalPartition-method000
get_anno-dispatch000
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-method0.0640.0030.066
get_classes-ConsensusPartitionList-method0.0630.0030.066
get_classes-DownSamplingConsensusPartition-method0.0400.0020.043
get_classes-HierarchicalPartition-method0.0630.0020.065
get_classes-dispatch000
get_consensus-ConsensusPartition-method0.0700.0110.080
get_matrix-ConsensusPartition-method0.1300.1750.309
get_matrix-ConsensusPartitionList-method0.1290.1630.293
get_matrix-DownSamplingConsensusPartition-method000
get_matrix-HierarchicalPartition-method0.0000.0000.001
get_matrix-dispatch000
get_membership-ConsensusPartition-method0.0640.0080.073
get_membership-ConsensusPartitionList-method0.0670.0030.072
get_membership-dispatch000
get_param-ConsensusPartition-method0.0650.0040.069
get_signatures-ConsensusPartition-method1.6440.0771.752
get_signatures-DownSamplingConsensusPartition-method000
get_signatures-HierarchicalPartition-method000
get_signatures-dispatch000
get_stats-ConsensusPartition-method0.0660.0020.069
get_stats-ConsensusPartitionList-method0.0760.0030.080
get_stats-dispatch0.0000.0000.001
golub_cola0.0710.0030.074
golub_cola_ds0.0470.0010.049
golub_cola_rh0.0710.0020.073
hierarchical_partition000
is_best_k-ConsensusPartition-method0.0700.0030.073
is_best_k-ConsensusPartitionList-method0.0660.0020.068
is_best_k-dispatch000
is_leaf_node-HierarchicalPartition-method0.0810.0060.087
is_stable_k-ConsensusPartition-method0.0640.0020.067
is_stable_k-ConsensusPartitionList-method0.0660.0020.067
is_stable_k-dispatch000
knee_finder20.0100.0010.011
knitr_add_tab_item000
knitr_insert_tabs000
map_to_entrez_id0.0010.0000.000
max_depth-HierarchicalPartition-method0.0600.0020.062
membership_heatmap-ConsensusPartition-method0.1760.0050.183
merge_node-HierarchicalPartition-method0.0010.0000.001
merge_node_param000
ncol-ConsensusPartition-method000
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-method0.0000.0010.000
nrow-HierarchicalPartition-method000
nrow-dispatch000
plot_ecdf-ConsensusPartition-method0.0680.0030.077
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_methods0.2830.0060.298
register_top_value_methods0.0010.0000.001
relabel_class0.0020.0010.003
remove_partition_methods0.0010.0000.000
remove_top_value_methods000
rownames-ConsensusPartition-method000
rownames-ConsensusPartitionList-method000
rownames-HierarchicalPartition-method000
rownames-dispatch000
run_all_consensus_partition_methods000
select_partition_number-ConsensusPartition-method0.0680.0030.072
show-ConsensusPartition-method000
show-ConsensusPartitionList-method000
show-DownSamplingConsensusPartition-method0.0470.0020.048
show-HierarchicalPartition-method0.0690.0010.070
show-dispatch000
split_node-HierarchicalPartition-method000
suggest_best_k-ConsensusPartition-method0.0620.0020.067
suggest_best_k-ConsensusPartitionList-method0.0640.0030.068
suggest_best_k-HierarchicalPartition-method0.0600.0020.062
suggest_best_k-dispatch0.0000.0000.001
test_between_factors0.0030.0000.003
test_to_known_factors-ConsensusPartition-method0.0680.0030.071
test_to_known_factors-ConsensusPartitionList-method0.0930.0020.096
test_to_known_factors-DownSamplingConsensusPartition-method0.0460.0020.047
test_to_known_factors-HierarchicalPartition-method0.0620.0010.064
test_to_known_factors-dispatch000
top_elements_overlap0.0730.0090.082
top_rows_heatmap-ConsensusPartition-method000
top_rows_heatmap-ConsensusPartitionList-method000
top_rows_heatmap-HierarchicalPartition-method000
top_rows_heatmap-dispatch000
top_rows_heatmap-matrix-method1.5410.0871.634
top_rows_overlap-ConsensusPartitionList-method0.2910.0170.309
top_rows_overlap-HierarchicalPartition-method0.2250.0050.238
top_rows_overlap-dispatch000
top_rows_overlap-matrix-method0.0470.0010.049