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This page was generated on 2024-10-18 20:40 -0400 (Fri, 18 Oct 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.1 (2024-06-14) -- "Race for Your Life" 4763
palomino7Windows Server 2022 Datacenterx644.4.1 (2024-06-14 ucrt) -- "Race for Your Life" 4500
merida1macOS 12.7.5 Montereyx86_644.4.1 (2024-06-14) -- "Race for Your Life" 4530
kjohnson1macOS 13.6.6 Venturaarm644.4.1 (2024-06-14) -- "Race for Your Life" 4480
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 410/2300HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cola 2.10.0  (landing page)
Zuguang Gu
Snapshot Date: 2024-10-16 14:00 -0400 (Wed, 16 Oct 2024)
git_url: https://git.bioconductor.org/packages/cola
git_branch: RELEASE_3_19
git_last_commit: cb0cd6e
git_last_commit_date: 2024-04-30 11:12:03 -0400 (Tue, 30 Apr 2024)
nebbiolo1Linux (Ubuntu 22.04.3 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
palomino7Windows 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: 2.10.0
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_2.10.0.tar.gz
StartedAt: 2024-10-17 03:06:57 -0400 (Thu, 17 Oct 2024)
EndedAt: 2024-10-17 03:15:11 -0400 (Thu, 17 Oct 2024)
EllapsedTime: 494.3 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_2.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/cola.Rcheck’
* using R version 4.4.1 (2024-06-14)
* 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 ‘2.10.0’
* 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                             52.244  0.642  64.340
get_signatures-ConsensusPartition-method        11.280  0.275  13.729
compare_signatures-HierarchicalPartition-method  8.913  0.324  11.092
collect_classes-ConsensusPartitionList-method    8.069  0.077  10.000
top_rows_heatmap-matrix-method                   6.455  0.390   8.126
collect_classes-ConsensusPartition-method        4.692  0.172   6.454
* 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 version 4.4.1 (2024-06-14) -- "Race for Your Life"
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 
  9.464   0.654  11.731 

Example timings

cola.Rcheck/cola-Ex.timings

nameusersystemelapsed
ATC0.0540.0070.081
ATC_approx0.0000.0010.001
ConsensusPartition-class0.0010.0010.002
ConsensusPartitionList-class000
DownSamplingConsensusPartition-class0.0000.0000.001
Extract.ConsensusPartitionList1.0200.0401.296
Extract.HierarchicalPartition0.2700.0090.334
ExtractExtract.ConsensusPartitionList0.4200.0120.537
ExtractExtract.HierarchicalPartition000
FCC0.3010.0110.400
HierarchicalPartition-class000
PAC0.6360.0150.894
aPAC0.2550.0110.360
adjust_matrix0.0130.0050.023
adjust_outlier0.0010.0010.006
all_leaves-HierarchicalPartition-method0.2120.0080.301
all_nodes-HierarchicalPartition-method0.2190.0110.302
all_partition_methods0.0020.0010.004
all_top_value_methods0.0010.0000.001
cola0.1490.0030.203
cola_opt0.0490.0020.073
cola_report-ConsensusPartition-method0.0000.0010.002
cola_report-ConsensusPartitionList-method0.0010.0000.001
cola_report-HierarchicalPartition-method000
cola_report-dispatch0.0000.0000.001
cola_rl0.1430.0070.197
collect_classes-ConsensusPartition-method4.6920.1726.454
collect_classes-ConsensusPartitionList-method 8.069 0.07710.000
collect_classes-HierarchicalPartition-method3.1370.0743.960
collect_classes-dispatch0.0000.0000.001
collect_plots-ConsensusPartition-method0.0000.0010.001
collect_plots-ConsensusPartitionList-method0.0000.0010.001
collect_plots-dispatch0.0010.0000.001
collect_stats-ConsensusPartition-method0.0010.0000.001
collect_stats-ConsensusPartitionList-method0.9510.0151.173
collect_stats-dispatch0.0000.0010.000
colnames-ConsensusPartition-method0.0000.0010.001
colnames-ConsensusPartitionList-method0.0000.0000.002
colnames-DownSamplingConsensusPartition-method0.0010.0000.001
colnames-HierarchicalPartition-method000
colnames-dispatch000
compare_partitions-ConsensusPartition-method0.0010.0010.003
compare_signatures-ConsensusPartition-method0.0000.0010.000
compare_signatures-HierarchicalPartition-method 8.913 0.32411.092
compare_signatures-dispatch0.0000.0000.001
concordance0.2580.0100.346
config_ATC0.0010.0000.001
consensus_heatmap-ConsensusPartition-method1.2250.0231.627
consensus_partition52.244 0.64264.340
consensus_partition_by_down_sampling0.0000.0000.001
correspond_between_rankings0.1300.0040.159
correspond_between_two_rankings0.0580.0030.104
david_enrichment0.0000.0010.001
dim.ConsensusPartition0.0010.0010.001
dim.ConsensusPartitionList0.0000.0010.001
dim.DownSamplingConsensusPartition0.0000.0010.000
dim.HierarchicalPartition0.0000.0010.001
dimension_reduction-ConsensusPartition-method1.4180.0641.825
dimension_reduction-DownSamplingConsensusPartition-method3.2380.1214.227
dimension_reduction-HierarchicalPartition-method1.2040.0381.510
dimension_reduction-dispatch0.0000.0010.001
dimension_reduction-matrix-method0.0000.0000.001
find_best_km0.0000.0000.001
functional_enrichment-ANY-method0.0000.0010.001
functional_enrichment-ConsensusPartition-method000
functional_enrichment-ConsensusPartitionList-method0.0000.0000.001
functional_enrichment-HierarchicalPartition-method0.0000.0010.001
functional_enrichment-dispatch0.0000.0000.001
get_anno-ConsensusPartition-method0.0010.0010.001
get_anno-ConsensusPartitionList-method0.0000.0010.002
get_anno-DownSamplingConsensusPartition-method0.1330.0080.171
get_anno-HierarchicalPartition-method0.0000.0010.000
get_anno-dispatch0.0000.0000.001
get_anno_col-ConsensusPartition-method000
get_anno_col-ConsensusPartitionList-method0.0010.0010.001
get_anno_col-HierarchicalPartition-method0.0000.0000.001
get_anno_col-dispatch0.0000.0010.000
get_children_nodes-HierarchicalPartition-method0.0010.0010.001
get_classes-ConsensusPartition-method0.2570.0220.326
get_classes-ConsensusPartitionList-method0.2500.0110.306
get_classes-DownSamplingConsensusPartition-method0.1360.0170.175
get_classes-HierarchicalPartition-method0.2370.0090.286
get_classes-dispatch0.0010.0010.001
get_consensus-ConsensusPartition-method0.2760.1030.447
get_matrix-ConsensusPartition-method0.8631.5612.845
get_matrix-ConsensusPartitionList-method0.8851.5892.949
get_matrix-DownSamplingConsensusPartition-method0.0000.0000.001
get_matrix-HierarchicalPartition-method0.0010.0000.001
get_matrix-dispatch0.0000.0010.001
get_membership-ConsensusPartition-method0.2610.0580.368
get_membership-ConsensusPartitionList-method0.2480.0090.306
get_membership-dispatch0.0010.0010.000
get_param-ConsensusPartition-method0.2640.0240.362
get_signatures-ConsensusPartition-method11.280 0.27513.729
get_signatures-DownSamplingConsensusPartition-method0.0000.0010.000
get_signatures-HierarchicalPartition-method000
get_signatures-dispatch0.0010.0010.000
get_stats-ConsensusPartition-method0.2490.0110.292
get_stats-ConsensusPartitionList-method0.2700.0090.328
get_stats-dispatch0.0000.0000.001
golub_cola0.3080.0080.365
golub_cola_ds0.1960.0070.225
golub_cola_rh0.3070.0080.345
hierarchical_partition000
is_best_k-ConsensusPartition-method0.3160.0240.408
is_best_k-ConsensusPartitionList-method0.2570.0080.324
is_best_k-dispatch0.0000.0010.009
is_leaf_node-HierarchicalPartition-method0.2110.0060.244
is_stable_k-ConsensusPartition-method0.9310.0241.043
is_stable_k-ConsensusPartitionList-method0.2670.0080.315
is_stable_k-dispatch0.0000.0010.001
knee_finder20.0380.0070.053
knitr_add_tab_item0.0010.0010.003
knitr_insert_tabs000
map_to_entrez_id0.0010.0010.000
max_depth-HierarchicalPartition-method0.2060.0060.244
membership_heatmap-ConsensusPartition-method1.0390.0141.193
merge_node-HierarchicalPartition-method0.0010.0000.001
merge_node_param0.0000.0000.001
ncol-ConsensusPartition-method0.0000.0010.001
ncol-ConsensusPartitionList-method0.0010.0000.001
ncol-DownSamplingConsensusPartition-method0.0000.0010.001
ncol-HierarchicalPartition-method0.0000.0010.001
ncol-dispatch0.0010.0010.001
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-method0.0010.0000.001
nrow-dispatch0.0000.0000.001
plot_ecdf-ConsensusPartition-method0.2640.0080.307
predict_classes-ConsensusPartition-method0.0000.0010.001
predict_classes-dispatch0.0000.0000.002
predict_classes-matrix-method0.0000.0010.000
print.hc_table_suggest_best_k0.0000.0010.001
recalc_stats0.0010.0000.001
register_NMF0.0000.0010.001
register_SOM0.0000.0000.001
register_partition_methods0.6910.0170.819
register_top_value_methods0.0030.0010.006
relabel_class0.0190.0060.030
remove_partition_methods0.0010.0000.001
remove_top_value_methods0.0000.0010.001
rownames-ConsensusPartition-method0.0000.0000.001
rownames-ConsensusPartitionList-method0.0010.0010.000
rownames-HierarchicalPartition-method0.0000.0010.001
rownames-dispatch000
run_all_consensus_partition_methods0.0000.0010.001
select_partition_number-ConsensusPartition-method0.2700.0070.317
show-ConsensusPartition-method0.0000.0010.001
show-ConsensusPartitionList-method0.0000.0000.001
show-DownSamplingConsensusPartition-method0.1900.0070.221
show-HierarchicalPartition-method0.3050.0110.360
show-dispatch0.0000.0000.001
split_node-HierarchicalPartition-method0.0000.0010.000
suggest_best_k-ConsensusPartition-method0.2430.0060.281
suggest_best_k-ConsensusPartitionList-method0.2680.0090.309
suggest_best_k-HierarchicalPartition-method0.2220.0090.260
suggest_best_k-dispatch0.0000.0010.001
test_between_factors0.0200.0020.024
test_to_known_factors-ConsensusPartition-method0.2990.0100.365
test_to_known_factors-ConsensusPartitionList-method0.5840.0170.701
test_to_known_factors-DownSamplingConsensusPartition-method0.1910.0060.241
test_to_known_factors-HierarchicalPartition-method0.2410.0070.293
test_to_known_factors-dispatch0.0010.0000.001
top_elements_overlap0.4820.0280.610
top_rows_heatmap-ConsensusPartition-method0.0000.0010.001
top_rows_heatmap-ConsensusPartitionList-method0.0000.0000.001
top_rows_heatmap-HierarchicalPartition-method0.0010.0010.001
top_rows_heatmap-dispatch000
top_rows_heatmap-matrix-method6.4550.3908.126
top_rows_overlap-ConsensusPartitionList-method1.5330.0731.907
top_rows_overlap-HierarchicalPartition-method0.9990.0251.196
top_rows_overlap-dispatch0.0010.0010.001
top_rows_overlap-matrix-method0.3270.0030.390