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This page was generated on 2024-12-23 12:06 -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 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: 2.12.0
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_2.12.0.tar.gz
StartedAt: 2024-12-20 01:28:30 -0500 (Fri, 20 Dec 2024)
EndedAt: 2024-12-20 01:35:58 -0500 (Fri, 20 Dec 2024)
EllapsedTime: 447.8 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_2.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/cola.Rcheck’
* using R version 4.4.2 (2024-10-31)
* 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 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cola/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cola’ version ‘2.12.0’
* 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 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 ... 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                             50.396  0.529  56.469
get_signatures-ConsensusPartition-method        11.040  0.209  12.743
compare_signatures-HierarchicalPartition-method  8.564  0.308  10.456
collect_classes-ConsensusPartitionList-method    7.898  0.069   9.189
top_rows_heatmap-matrix-method                   5.538  0.350   6.933
collect_classes-ConsensusPartition-method        4.686  0.187   5.772
* 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-3.20-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 version 4.4.2 (2024-10-31) -- "Pile of Leaves"
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 
  9.076   0.614  10.489 

Example timings

cola.Rcheck/cola-Ex.timings

nameusersystemelapsed
ATC0.0550.0080.083
ATC_approx0.0000.0010.001
ConsensusPartition-class0.0000.0010.001
ConsensusPartitionList-class0.0000.0000.001
DownSamplingConsensusPartition-class0.0000.0000.001
Extract.ConsensusPartitionList0.9880.0391.193
Extract.HierarchicalPartition0.3830.0120.486
ExtractExtract.ConsensusPartitionList0.3020.0110.370
ExtractExtract.HierarchicalPartition000
FCC0.2940.0110.336
HierarchicalPartition-class0.0000.0000.001
PAC0.6350.0130.752
aPAC0.2470.0110.298
adjust_matrix0.0130.0040.022
adjust_outlier0.0020.0010.002
all_leaves-HierarchicalPartition-method0.2040.0060.235
all_nodes-HierarchicalPartition-method0.2160.0100.252
all_partition_methods0.0010.0010.003
all_top_value_methods0.0010.0000.001
cola0.1450.0030.158
cola_opt0.0500.0030.060
cola_report-ConsensusPartition-method0.0000.0000.001
cola_report-ConsensusPartitionList-method0.0010.0000.001
cola_report-HierarchicalPartition-method0.0000.0010.001
cola_report-dispatch0.0000.0010.002
cola_rl0.1380.0060.159
collect_classes-ConsensusPartition-method4.6860.1875.772
collect_classes-ConsensusPartitionList-method7.8980.0699.189
collect_classes-HierarchicalPartition-method3.1240.0643.730
collect_classes-dispatch0.0000.0000.001
collect_plots-ConsensusPartition-method0.0000.0000.001
collect_plots-ConsensusPartitionList-method0.0010.0000.000
collect_plots-dispatch0.0000.0010.002
collect_stats-ConsensusPartition-method0.0000.0010.000
collect_stats-ConsensusPartitionList-method0.9200.0171.085
collect_stats-dispatch0.0000.0000.001
colnames-ConsensusPartition-method000
colnames-ConsensusPartitionList-method0.0000.0000.001
colnames-DownSamplingConsensusPartition-method0.0000.0000.001
colnames-HierarchicalPartition-method0.0000.0000.002
colnames-dispatch0.0010.0010.000
compare_partitions-ConsensusPartition-method0.0000.0010.000
compare_signatures-ConsensusPartition-method0.0000.0010.000
compare_signatures-HierarchicalPartition-method 8.564 0.30810.456
compare_signatures-dispatch0.0010.0010.000
concordance0.2450.0080.292
config_ATC0.0020.0010.002
consensus_heatmap-ConsensusPartition-method1.2500.0201.437
consensus_partition50.396 0.52956.469
consensus_partition_by_down_sampling0.0000.0010.002
correspond_between_rankings0.1230.0050.146
correspond_between_two_rankings0.0540.0030.063
david_enrichment0.0000.0010.001
dim.ConsensusPartition000
dim.ConsensusPartitionList0.0000.0000.001
dim.DownSamplingConsensusPartition0.0010.0000.000
dim.HierarchicalPartition0.0000.0010.003
dimension_reduction-ConsensusPartition-method1.3930.0701.662
dimension_reduction-DownSamplingConsensusPartition-method3.1980.1143.704
dimension_reduction-HierarchicalPartition-method1.2110.0471.411
dimension_reduction-dispatch0.0000.0000.001
dimension_reduction-matrix-method000
find_best_km0.0000.0000.001
functional_enrichment-ANY-method000
functional_enrichment-ConsensusPartition-method0.0010.0010.000
functional_enrichment-ConsensusPartitionList-method0.0000.0010.001
functional_enrichment-HierarchicalPartition-method000
functional_enrichment-dispatch0.0010.0000.001
get_anno-ConsensusPartition-method0.0000.0010.001
get_anno-ConsensusPartitionList-method0.0000.0010.001
get_anno-DownSamplingConsensusPartition-method0.1290.0070.173
get_anno-HierarchicalPartition-method0.0010.0010.001
get_anno-dispatch0.0000.0000.001
get_anno_col-ConsensusPartition-method0.0000.0000.001
get_anno_col-ConsensusPartitionList-method0.0010.0010.000
get_anno_col-HierarchicalPartition-method0.0000.0000.001
get_anno_col-dispatch0.0010.0000.001
get_children_nodes-HierarchicalPartition-method0.0000.0000.001
get_classes-ConsensusPartition-method0.2440.0150.282
get_classes-ConsensusPartitionList-method0.2380.0080.266
get_classes-DownSamplingConsensusPartition-method0.1310.0140.157
get_classes-HierarchicalPartition-method0.2320.0080.260
get_classes-dispatch0.0010.0000.001
get_consensus-ConsensusPartition-method0.2670.0850.365
get_matrix-ConsensusPartition-method0.8521.5822.637
get_matrix-ConsensusPartitionList-method0.8601.5652.650
get_matrix-DownSamplingConsensusPartition-method0.0000.0000.001
get_matrix-HierarchicalPartition-method0.0000.0000.001
get_matrix-dispatch000
get_membership-ConsensusPartition-method0.2550.0590.335
get_membership-ConsensusPartitionList-method0.2370.0090.269
get_membership-dispatch0.0000.0010.001
get_param-ConsensusPartition-method0.2590.0240.316
get_signatures-ConsensusPartition-method11.040 0.20912.743
get_signatures-DownSamplingConsensusPartition-method0.0000.0000.001
get_signatures-HierarchicalPartition-method000
get_signatures-dispatch0.0000.0010.000
get_stats-ConsensusPartition-method0.2400.0090.270
get_stats-ConsensusPartitionList-method0.2390.0100.271
get_stats-dispatch0.0000.0000.002
golub_cola0.3200.0080.356
golub_cola_ds0.1940.0070.224
golub_cola_rh0.2970.0070.334
hierarchical_partition0.0000.0020.001
is_best_k-ConsensusPartition-method0.2390.0060.269
is_best_k-ConsensusPartitionList-method0.2670.0090.301
is_best_k-dispatch000
is_leaf_node-HierarchicalPartition-method0.2070.0060.237
is_stable_k-ConsensusPartition-method0.2900.0090.325
is_stable_k-ConsensusPartitionList-method0.2590.0080.293
is_stable_k-dispatch0.0000.0000.001
knee_finder20.0380.0080.050
knitr_add_tab_item0.0000.0000.001
knitr_insert_tabs0.0010.0010.001
map_to_entrez_id0.0000.0000.001
max_depth-HierarchicalPartition-method0.2050.0060.232
membership_heatmap-ConsensusPartition-method1.0120.0111.117
merge_node-HierarchicalPartition-method0.0000.0000.001
merge_node_param000
ncol-ConsensusPartition-method0.0000.0010.001
ncol-ConsensusPartitionList-method0.0010.0000.001
ncol-DownSamplingConsensusPartition-method0.0010.0000.001
ncol-HierarchicalPartition-method0.0000.0010.000
ncol-dispatch0.0000.0000.001
node_info-HierarchicalPartition-method000
node_level-HierarchicalPartition-method0.0000.0010.001
nrow-ConsensusPartition-method0.0000.0010.001
nrow-ConsensusPartitionList-method0.0010.0000.001
nrow-HierarchicalPartition-method0.0000.0010.001
nrow-dispatch0.0000.0000.001
plot_ecdf-ConsensusPartition-method0.2730.0090.343
predict_classes-ConsensusPartition-method000
predict_classes-dispatch0.0000.0000.001
predict_classes-matrix-method0.0010.0010.001
print.hc_table_suggest_best_k000
recalc_stats0.0000.0010.002
register_NMF000
register_SOM0.0000.0000.001
register_partition_methods0.6900.0380.879
register_top_value_methods0.0020.0010.004
relabel_class0.0180.0060.030
remove_partition_methods0.0010.0010.001
remove_top_value_methods0.0000.0010.001
rownames-ConsensusPartition-method0.0000.0000.001
rownames-ConsensusPartitionList-method0.0010.0010.001
rownames-HierarchicalPartition-method0.0000.0000.001
rownames-dispatch0.0000.0010.005
run_all_consensus_partition_methods0.0000.0010.001
select_partition_number-ConsensusPartition-method0.2610.0080.322
show-ConsensusPartition-method000
show-ConsensusPartitionList-method0.0010.0010.006
show-DownSamplingConsensusPartition-method0.1830.0060.234
show-HierarchicalPartition-method0.2980.0090.348
show-dispatch000
split_node-HierarchicalPartition-method0.0000.0010.001
suggest_best_k-ConsensusPartition-method0.2360.0060.273
suggest_best_k-ConsensusPartitionList-method0.2600.0090.286
suggest_best_k-HierarchicalPartition-method0.2190.0090.272
suggest_best_k-dispatch0.0010.0010.000
test_between_factors0.0180.0020.023
test_to_known_factors-ConsensusPartition-method0.2900.0110.331
test_to_known_factors-ConsensusPartitionList-method0.5560.0140.659
test_to_known_factors-DownSamplingConsensusPartition-method0.1900.0060.226
test_to_known_factors-HierarchicalPartition-method0.2330.0060.264
test_to_known_factors-dispatch0.0000.0010.000
top_elements_overlap0.4650.0270.530
top_rows_heatmap-ConsensusPartition-method0.0000.0010.001
top_rows_heatmap-ConsensusPartitionList-method0.0000.0010.000
top_rows_heatmap-HierarchicalPartition-method0.0000.0010.000
top_rows_heatmap-dispatch0.0000.0000.001
top_rows_heatmap-matrix-method5.5380.3506.933
top_rows_overlap-ConsensusPartitionList-method1.4950.0631.675
top_rows_overlap-HierarchicalPartition-method0.9440.0400.994
top_rows_overlap-dispatch0.0010.0000.001
top_rows_overlap-matrix-method0.3100.0030.320