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This page was generated on 2024-03-04 11:39:01 -0500 (Mon, 04 Mar 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4676
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2024-01-14 r85805 ucrt) -- "Unsuffered Consequences" 4414
merida1macOS 12.7.1 Montereyx86_64R Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences" 4441
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch64R Under development (unstable) (2024-01-16 r85812) -- "Unsuffered Consequences" 4417
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 406/2251HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cola 2.9.1  (landing page)
Zuguang Gu
Snapshot Date: 2024-03-01 14:00:22 -0500 (Fri, 01 Mar 2024)
git_url: https://git.bioconductor.org/packages/cola
git_branch: devel
git_last_commit: 1456cfb
git_last_commit_date: 2024-02-26 08:40:57 -0500 (Mon, 26 Feb 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino3Windows Server 2022 Datacenter / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
merida1macOS 12.7.1 Monterey / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published
kunpeng2Linux (openEuler 22.03 LTS-SP1) / 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: 2.9.1
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_2.9.1.tar.gz
StartedAt: 2024-03-02 01:59:13 -0500 (Sat, 02 Mar 2024)
EndedAt: 2024-03-02 02:07:00 -0500 (Sat, 02 Mar 2024)
EllapsedTime: 466.9 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_2.9.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/cola.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* 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 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cola/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cola’ version ‘2.9.1’
* 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 R 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                             47.421  0.714  57.015
get_signatures-ConsensusPartition-method        10.637  0.312  13.083
compare_signatures-HierarchicalPartition-method  8.057  0.330  10.067
collect_classes-ConsensusPartitionList-method    7.176  0.081   8.981
top_rows_heatmap-matrix-method                   6.080  0.408   7.916
collect_classes-ConsensusPartition-method        4.219  0.169   5.469
* 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-3.19-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 Under development (unstable) (2024-01-16 r85808) -- "Unsuffered Consequences"
Copyright (C) 2024 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 
  8.899   0.718  11.767 

Example timings

cola.Rcheck/cola-Ex.timings

nameusersystemelapsed
ATC0.0480.0100.077
ATC_approx0.0010.0000.001
ConsensusPartition-class0.0000.0000.001
ConsensusPartitionList-class0.0000.0010.001
DownSamplingConsensusPartition-class0.0000.0010.000
Extract.ConsensusPartitionList1.0470.0401.323
Extract.HierarchicalPartition0.2600.0100.329
ExtractExtract.ConsensusPartitionList0.6180.0150.773
ExtractExtract.HierarchicalPartition000
FCC0.2580.0120.323
HierarchicalPartition-class0.0000.0000.002
PAC0.2620.0120.332
aPAC0.2570.0130.333
adjust_matrix0.0130.0040.019
adjust_outlier0.0020.0010.003
all_leaves-HierarchicalPartition-method0.2020.0090.262
all_nodes-HierarchicalPartition-method0.2010.0070.248
all_partition_methods0.0020.0010.002
all_top_value_methods0.0000.0010.001
cola0.1360.0040.169
cola_opt0.0470.0040.063
cola_report-ConsensusPartition-method000
cola_report-ConsensusPartitionList-method000
cola_report-HierarchicalPartition-method000
cola_report-dispatch0.0010.0010.001
cola_rl0.1470.0080.189
collect_classes-ConsensusPartition-method4.2190.1695.469
collect_classes-ConsensusPartitionList-method7.1760.0818.981
collect_classes-HierarchicalPartition-method2.8990.0753.616
collect_classes-dispatch0.0000.0000.001
collect_plots-ConsensusPartition-method0.0000.0010.000
collect_plots-ConsensusPartitionList-method0.0000.0010.000
collect_plots-dispatch0.0000.0000.001
collect_stats-ConsensusPartition-method0.0000.0000.002
collect_stats-ConsensusPartitionList-method0.8810.0191.100
collect_stats-dispatch0.0000.0000.001
colnames-ConsensusPartition-method0.0000.0000.001
colnames-ConsensusPartitionList-method0.0010.0000.002
colnames-DownSamplingConsensusPartition-method000
colnames-HierarchicalPartition-method000
colnames-dispatch0.0000.0010.001
compare_partitions-ConsensusPartition-method0.0000.0010.001
compare_signatures-ConsensusPartition-method0.0010.0000.001
compare_signatures-HierarchicalPartition-method 8.057 0.33010.067
compare_signatures-dispatch0.0000.0000.001
concordance0.2590.0120.325
config_ATC0.0010.0010.001
consensus_heatmap-ConsensusPartition-method1.1470.0211.395
consensus_partition47.421 0.71457.015
consensus_partition_by_down_sampling0.0000.0010.001
correspond_between_rankings0.1170.0050.141
correspond_between_two_rankings0.0500.0030.062
david_enrichment0.0000.0000.001
dim.ConsensusPartition000
dim.ConsensusPartitionList0.0000.0010.001
dim.DownSamplingConsensusPartition000
dim.HierarchicalPartition0.0000.0000.001
dimension_reduction-ConsensusPartition-method1.3580.0601.715
dimension_reduction-DownSamplingConsensusPartition-method2.9990.1213.818
dimension_reduction-HierarchicalPartition-method1.1580.0481.517
dimension_reduction-dispatch0.0000.0000.001
dimension_reduction-matrix-method0.0000.0000.001
find_best_km000
functional_enrichment-ANY-method000
functional_enrichment-ConsensusPartition-method0.0010.0010.000
functional_enrichment-ConsensusPartitionList-method0.0000.0010.000
functional_enrichment-HierarchicalPartition-method0.0000.0010.001
functional_enrichment-dispatch0.0000.0000.001
get_anno-ConsensusPartition-method0.0010.0000.000
get_anno-ConsensusPartitionList-method0.0000.0000.001
get_anno-DownSamplingConsensusPartition-method0.1310.0070.160
get_anno-HierarchicalPartition-method0.0000.0010.001
get_anno-dispatch0.0000.0010.001
get_anno_col-ConsensusPartition-method0.0010.0000.000
get_anno_col-ConsensusPartitionList-method000
get_anno_col-HierarchicalPartition-method0.0000.0000.001
get_anno_col-dispatch0.0000.0010.001
get_children_nodes-HierarchicalPartition-method0.0010.0010.001
get_classes-ConsensusPartition-method0.2480.0170.330
get_classes-ConsensusPartitionList-method0.2410.0130.313
get_classes-DownSamplingConsensusPartition-method0.1340.0140.196
get_classes-HierarchicalPartition-method0.2330.0100.311
get_classes-dispatch0.0000.0010.000
get_consensus-ConsensusPartition-method0.2640.0830.412
get_matrix-ConsensusPartition-method0.8641.5872.949
get_matrix-ConsensusPartitionList-method0.8491.7523.166
get_matrix-DownSamplingConsensusPartition-method0.0010.0010.001
get_matrix-HierarchicalPartition-method0.0000.0010.001
get_matrix-dispatch0.0000.0000.001
get_membership-ConsensusPartition-method0.2540.0630.369
get_membership-ConsensusPartitionList-method0.2390.0100.292
get_membership-dispatch0.0000.0000.001
get_param-ConsensusPartition-method0.2550.0250.335
get_signatures-ConsensusPartition-method10.637 0.31213.083
get_signatures-DownSamplingConsensusPartition-method0.0010.0010.000
get_signatures-HierarchicalPartition-method0.0000.0000.001
get_signatures-dispatch0.0000.0010.001
get_stats-ConsensusPartition-method0.2420.0080.298
get_stats-ConsensusPartitionList-method0.2420.0120.307
get_stats-dispatch0.0000.0010.001
golub_cola0.3220.0120.399
golub_cola_ds0.1880.0090.250
golub_cola_rh0.3000.0110.367
hierarchical_partition0.0010.0010.001
is_best_k-ConsensusPartition-method0.2410.0080.308
is_best_k-ConsensusPartitionList-method0.2690.0100.336
is_best_k-dispatch0.0000.0010.001
is_leaf_node-HierarchicalPartition-method0.2060.0070.258
is_stable_k-ConsensusPartition-method0.2430.0060.294
is_stable_k-ConsensusPartitionList-method0.3180.0320.400
is_stable_k-dispatch0.0000.0010.001
knee_finder20.0380.0080.052
knitr_add_tab_item0.0010.0000.001
knitr_insert_tabs0.0000.0010.002
map_to_entrez_id0.0000.0000.001
max_depth-HierarchicalPartition-method0.2040.0080.246
membership_heatmap-ConsensusPartition-method0.9800.0181.162
merge_node-HierarchicalPartition-method0.0000.0010.003
merge_node_param0.0000.0010.001
ncol-ConsensusPartition-method0.0000.0010.002
ncol-ConsensusPartitionList-method0.0010.0010.001
ncol-DownSamplingConsensusPartition-method0.0000.0010.001
ncol-HierarchicalPartition-method000
ncol-dispatch0.0000.0010.001
node_info-HierarchicalPartition-method0.0010.0000.001
node_level-HierarchicalPartition-method0.0000.0010.001
nrow-ConsensusPartition-method0.0000.0000.001
nrow-ConsensusPartitionList-method0.0000.0010.001
nrow-HierarchicalPartition-method0.0010.0010.000
nrow-dispatch0.0000.0010.003
plot_ecdf-ConsensusPartition-method0.2740.0130.346
predict_classes-ConsensusPartition-method0.0000.0000.001
predict_classes-dispatch0.0010.0010.001
predict_classes-matrix-method0.0000.0010.001
print.hc_table_suggest_best_k0.0000.0010.001
recalc_stats0.0000.0000.001
register_NMF0.0010.0010.001
register_SOM0.0000.0000.001
register_partition_methods0.6210.0210.750
register_top_value_methods0.0030.0010.007
relabel_class0.0170.0060.025
remove_partition_methods0.0010.0000.001
remove_top_value_methods0.0000.0010.000
rownames-ConsensusPartition-method0.0000.0010.002
rownames-ConsensusPartitionList-method0.0000.0000.001
rownames-HierarchicalPartition-method0.0000.0010.001
rownames-dispatch0.0010.0000.001
run_all_consensus_partition_methods0.0000.0010.001
select_partition_number-ConsensusPartition-method0.2610.0090.346
show-ConsensusPartition-method0.0000.0010.001
show-ConsensusPartitionList-method0.0010.0000.000
show-DownSamplingConsensusPartition-method0.1830.0070.217
show-HierarchicalPartition-method0.2960.0090.357
show-dispatch0.0000.0010.001
split_node-HierarchicalPartition-method0.0010.0000.001
suggest_best_k-ConsensusPartition-method0.2370.0080.293
suggest_best_k-ConsensusPartitionList-method0.2620.0110.342
suggest_best_k-HierarchicalPartition-method0.2160.0100.268
suggest_best_k-dispatch0.0000.0000.002
test_between_factors0.0180.0020.022
test_to_known_factors-ConsensusPartition-method0.2840.0130.351
test_to_known_factors-ConsensusPartitionList-method0.5410.0190.641
test_to_known_factors-DownSamplingConsensusPartition-method0.1830.0070.232
test_to_known_factors-HierarchicalPartition-method0.2310.0060.256
test_to_known_factors-dispatch0.0010.0000.001
top_elements_overlap0.4350.0300.570
top_rows_heatmap-ConsensusPartition-method0.0000.0010.000
top_rows_heatmap-ConsensusPartitionList-method0.0000.0010.000
top_rows_heatmap-HierarchicalPartition-method0.0000.0010.001
top_rows_heatmap-dispatch0.0000.0000.001
top_rows_heatmap-matrix-method6.0800.4087.916
top_rows_overlap-ConsensusPartitionList-method1.4620.0821.868
top_rows_overlap-HierarchicalPartition-method0.9550.0311.208
top_rows_overlap-dispatch0.0000.0010.001
top_rows_overlap-matrix-method0.3050.0060.430