Back to Multiple platform build/check report for BioC 3.20:   simplified   long
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This page was generated on 2024-12-23 12:03 -0500 (Mon, 23 Dec 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.1 LTS)x86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4744
palomino8Windows Server 2022 Datacenterx644.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" 4487
merida1macOS 12.7.5 Montereyx86_644.4.2 (2024-10-31) -- "Pile of Leaves" 4515
kjohnson1macOS 13.6.6 Venturaarm644.4.2 (2024-10-31) -- "Pile of Leaves" 4467
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: 2024-12-19 13:00 -0500 (Thu, 19 Dec 2024)
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 -0500 (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


CHECK results for cola on nebbiolo2

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: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:cola.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings cola_2.12.0.tar.gz
StartedAt: 2024-12-19 21:48:50 -0500 (Thu, 19 Dec 2024)
EndedAt: 2024-12-19 21:55:11 -0500 (Thu, 19 Dec 2024)
EllapsedTime: 381.2 seconds
RetCode: 0
Status:   OK  
CheckDir: cola.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:cola.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings cola_2.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.20-bioc/meat/cola.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
    GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* 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 ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... NOTE
  installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data      3.2Mb
    extdata   1.0Mb
    libs      2.0Mb
* 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 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 ... 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 17.621   0.42  18.042
* 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 re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.20-bioc/meat/cola.Rcheck/00check.log’
for details.


Installation output

cola.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL cola
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.20-bioc/R/site-library’
* installing *source* package ‘cola’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c atc.cpp -o atc.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c cal_consensus_mat.cpp -o cal_consensus_mat.o
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.20-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.20-bioc/R/site-library/Rcpp/include' -I/usr/local/include    -fpic  -g -O2  -Wall  -c pdist.cpp -o pdist.o
g++ -std=gnu++17 -shared -L/home/biocbuild/bbs-3.20-bioc/R/lib -L/usr/local/lib -o cola.so RcppExports.o atc.o cal_consensus_mat.o pdist.o -L/home/biocbuild/bbs-3.20-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.20-bioc/R/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 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 
  3.682   0.247   3.915 

Example timings

cola.Rcheck/cola-Ex.timings

nameusersystemelapsed
ATC0.0230.0020.025
ATC_approx0.0000.0000.001
ConsensusPartition-class000
ConsensusPartitionList-class000
DownSamplingConsensusPartition-class0.0000.0000.001
Extract.ConsensusPartitionList0.4060.0060.411
Extract.HierarchicalPartition0.2160.0050.220
ExtractExtract.ConsensusPartitionList0.1580.0070.166
ExtractExtract.HierarchicalPartition000
FCC0.1610.0060.167
HierarchicalPartition-class000
PAC0.4040.0080.411
aPAC0.1430.0050.149
adjust_matrix0.0050.0000.006
adjust_outlier0.0000.0010.000
all_leaves-HierarchicalPartition-method0.1180.0090.128
all_nodes-HierarchicalPartition-method0.1280.0030.131
all_partition_methods0.0000.0000.001
all_top_value_methods000
cola0.0410.0010.041
cola_opt0.0200.0010.020
cola_report-ConsensusPartition-method000
cola_report-ConsensusPartitionList-method000
cola_report-HierarchicalPartition-method000
cola_report-dispatch000
cola_rl0.0670.0050.073
collect_classes-ConsensusPartition-method1.7270.0571.784
collect_classes-ConsensusPartitionList-method2.6130.0502.662
collect_classes-HierarchicalPartition-method1.1290.0541.182
collect_classes-dispatch000
collect_plots-ConsensusPartition-method000
collect_plots-ConsensusPartitionList-method0.0000.0000.001
collect_plots-dispatch000
collect_stats-ConsensusPartition-method000
collect_stats-ConsensusPartitionList-method0.3850.0100.396
collect_stats-dispatch000
colnames-ConsensusPartition-method0.0000.0000.001
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-method3.6520.2073.862
compare_signatures-dispatch000
concordance0.1390.0100.148
config_ATC000
consensus_heatmap-ConsensusPartition-method0.4920.0050.496
consensus_partition17.621 0.42018.042
consensus_partition_by_down_sampling0.0000.0010.001
correspond_between_rankings0.0480.0020.050
correspond_between_two_rankings0.0230.0000.023
david_enrichment000
dim.ConsensusPartition000
dim.ConsensusPartitionList0.0000.0010.001
dim.DownSamplingConsensusPartition000
dim.HierarchicalPartition000
dimension_reduction-ConsensusPartition-method0.5920.0170.608
dimension_reduction-DownSamplingConsensusPartition-method1.4590.0211.480
dimension_reduction-HierarchicalPartition-method0.5200.0040.523
dimension_reduction-dispatch000
dimension_reduction-matrix-method000
find_best_km0.0000.0010.000
functional_enrichment-ANY-method000
functional_enrichment-ConsensusPartition-method000
functional_enrichment-ConsensusPartitionList-method0.0010.0000.000
functional_enrichment-HierarchicalPartition-method000
functional_enrichment-dispatch000
get_anno-ConsensusPartition-method000
get_anno-ConsensusPartitionList-method000
get_anno-DownSamplingConsensusPartition-method0.0810.0020.082
get_anno-HierarchicalPartition-method0.0000.0000.001
get_anno-dispatch000
get_anno_col-ConsensusPartition-method000
get_anno_col-ConsensusPartitionList-method000
get_anno_col-HierarchicalPartition-method000
get_anno_col-dispatch000
get_children_nodes-HierarchicalPartition-method000
get_classes-ConsensusPartition-method0.1390.0080.147
get_classes-ConsensusPartitionList-method0.1370.0070.144
get_classes-DownSamplingConsensusPartition-method0.0810.0020.083
get_classes-HierarchicalPartition-method0.1350.0010.136
get_classes-dispatch000
get_consensus-ConsensusPartition-method0.1440.0080.151
get_matrix-ConsensusPartition-method0.2800.0750.354
get_matrix-ConsensusPartitionList-method0.2940.0680.362
get_matrix-DownSamplingConsensusPartition-method0.0000.0010.000
get_matrix-HierarchicalPartition-method000
get_matrix-dispatch000
get_membership-ConsensusPartition-method0.1380.0100.148
get_membership-ConsensusPartitionList-method0.1360.0060.142
get_membership-dispatch000
get_param-ConsensusPartition-method0.1450.0040.149
get_signatures-ConsensusPartition-method3.5940.0493.644
get_signatures-DownSamplingConsensusPartition-method000
get_signatures-HierarchicalPartition-method000
get_signatures-dispatch000
get_stats-ConsensusPartition-method0.1410.0040.146
get_stats-ConsensusPartitionList-method0.1350.0090.144
get_stats-dispatch0.0000.0010.000
golub_cola0.1800.0130.193
golub_cola_ds0.1040.0010.105
golub_cola_rh0.1550.0060.162
hierarchical_partition000
is_best_k-ConsensusPartition-method0.1360.0080.143
is_best_k-ConsensusPartitionList-method0.1430.0040.147
is_best_k-dispatch000
is_leaf_node-HierarchicalPartition-method0.1290.0070.135
is_stable_k-ConsensusPartition-method0.1380.0080.145
is_stable_k-ConsensusPartitionList-method0.1390.0110.150
is_stable_k-dispatch000
knee_finder20.0300.0020.032
knitr_add_tab_item0.0000.0000.001
knitr_insert_tabs000
map_to_entrez_id000
max_depth-HierarchicalPartition-method0.1250.0010.126
membership_heatmap-ConsensusPartition-method0.4790.0080.487
merge_node-HierarchicalPartition-method0.0010.0000.000
merge_node_param000
ncol-ConsensusPartition-method000
ncol-ConsensusPartitionList-method000
ncol-DownSamplingConsensusPartition-method0.0000.0000.001
ncol-HierarchicalPartition-method000
ncol-dispatch000
node_info-HierarchicalPartition-method000
node_level-HierarchicalPartition-method000
nrow-ConsensusPartition-method0.0000.0010.001
nrow-ConsensusPartitionList-method000
nrow-HierarchicalPartition-method000
nrow-dispatch000
plot_ecdf-ConsensusPartition-method0.1440.0080.153
predict_classes-ConsensusPartition-method000
predict_classes-dispatch000
predict_classes-matrix-method000
print.hc_table_suggest_best_k000
recalc_stats000
register_NMF0.0000.0000.001
register_SOM000
register_partition_methods0.5540.0440.598
register_top_value_methods0.0020.0000.001
relabel_class0.0070.0000.006
remove_partition_methods000
remove_top_value_methods000
rownames-ConsensusPartition-method000
rownames-ConsensusPartitionList-method000
rownames-HierarchicalPartition-method000
rownames-dispatch000
run_all_consensus_partition_methods000
select_partition_number-ConsensusPartition-method0.1460.0100.155
show-ConsensusPartition-method000
show-ConsensusPartitionList-method0.0010.0000.000
show-DownSamplingConsensusPartition-method0.1020.0010.103
show-HierarchicalPartition-method0.1550.0040.159
show-dispatch000
split_node-HierarchicalPartition-method000
suggest_best_k-ConsensusPartition-method0.1360.0080.143
suggest_best_k-ConsensusPartitionList-method0.1440.0070.151
suggest_best_k-HierarchicalPartition-method0.1300.0010.131
suggest_best_k-dispatch000
test_between_factors0.0070.0000.007
test_to_known_factors-ConsensusPartition-method0.1560.0050.161
test_to_known_factors-ConsensusPartitionList-method0.2480.0060.255
test_to_known_factors-DownSamplingConsensusPartition-method0.0990.0030.102
test_to_known_factors-HierarchicalPartition-method0.1350.0030.137
test_to_known_factors-dispatch0.0010.0000.000
top_elements_overlap0.1810.0050.187
top_rows_heatmap-ConsensusPartition-method0.0000.0000.001
top_rows_heatmap-ConsensusPartitionList-method000
top_rows_heatmap-HierarchicalPartition-method000
top_rows_heatmap-dispatch000
top_rows_heatmap-matrix-method3.1100.1213.217
top_rows_overlap-ConsensusPartitionList-method0.7190.0120.731
top_rows_overlap-HierarchicalPartition-method0.4720.0020.474
top_rows_overlap-dispatch000
top_rows_overlap-matrix-method0.1170.0010.118