Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-05-04 11:39:01 -0400 (Sat, 04 May 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4753
palomino3Windows Server 2022 Datacenterx644.4.0 beta (2024-04-15 r86425 ucrt) -- "Puppy Cup" 4486
lconwaymacOS 12.7.1 Montereyx86_644.4.0 beta (2024-04-14 r86421) -- "Puppy Cup" 4519
kunpeng2Linux (openEuler 22.03 LTS-SP1)aarch644.4.0 beta (2024-04-15 r86425) -- "Puppy Cup" 4479
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: 2024-05-03 14:00:19 -0400 (Fri, 03 May 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
palomino3Windows 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
kunpeng2Linux (openEuler 22.03 LTS-SP1) / aarch64  OK    OK    OK  
kjohnson3macOS 13.6.5 Ventura / arm64see weekly results here

CHECK results for cola on lconway


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: 2024-05-03 21:00:10 -0400 (Fri, 03 May 2024)
EndedAt: 2024-05-03 21:03:51 -0400 (Fri, 03 May 2024)
EllapsedTime: 221.5 seconds
RetCode: 0
Status:   OK  
CheckDir: cola.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### 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 4.4.0 beta (2024-04-14 r86421)
* 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 ‘2.10.0’
* 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                             21.359  0.359  22.043
get_signatures-ConsensusPartition-method         5.058  0.195   5.345
compare_signatures-HierarchicalPartition-method  4.925  0.230   5.404
* 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 4.4.0 beta (2024-04-14 r86421) -- "Puppy Cup"
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 
  5.103   0.420   5.642 

Example timings

cola.Rcheck/cola-Ex.timings

nameusersystemelapsed
ATC0.0310.0050.036
ATC_approx000
ConsensusPartition-class000
ConsensusPartitionList-class000
DownSamplingConsensusPartition-class0.0000.0000.001
Extract.ConsensusPartitionList0.5030.0180.529
Extract.HierarchicalPartition0.2550.0070.266
ExtractExtract.ConsensusPartitionList0.1820.0050.190
ExtractExtract.HierarchicalPartition000
FCC0.1720.0080.183
HierarchicalPartition-class000
PAC0.4530.0070.464
aPAC0.1500.0050.158
adjust_matrix0.0060.0020.009
adjust_outlier0.0010.0000.001
all_leaves-HierarchicalPartition-method0.1250.0030.134
all_nodes-HierarchicalPartition-method0.1360.0060.145
all_partition_methods0.0020.0000.002
all_top_value_methods0.0000.0010.001
cola0.0570.0020.059
cola_opt0.0230.0010.025
cola_report-ConsensusPartition-method000
cola_report-ConsensusPartitionList-method0.0000.0010.000
cola_report-HierarchicalPartition-method0.0000.0000.001
cola_report-dispatch000
cola_rl0.0690.0030.073
collect_classes-ConsensusPartition-method2.2210.0802.340
collect_classes-ConsensusPartitionList-method3.4970.0523.613
collect_classes-HierarchicalPartition-method1.5180.0621.600
collect_classes-dispatch0.0000.0000.001
collect_plots-ConsensusPartition-method0.0000.0000.001
collect_plots-ConsensusPartitionList-method000
collect_plots-dispatch0.0000.0010.001
collect_stats-ConsensusPartition-method000
collect_stats-ConsensusPartitionList-method0.5350.0160.567
collect_stats-dispatch0.0010.0000.000
colnames-ConsensusPartition-method000
colnames-ConsensusPartitionList-method000
colnames-DownSamplingConsensusPartition-method000
colnames-HierarchicalPartition-method0.0000.0010.001
colnames-dispatch000
compare_partitions-ConsensusPartition-method000
compare_signatures-ConsensusPartition-method000
compare_signatures-HierarchicalPartition-method4.9250.2305.404
compare_signatures-dispatch0.0000.0000.001
concordance0.1610.0070.169
config_ATC0.0010.0000.000
consensus_heatmap-ConsensusPartition-method0.6300.0160.654
consensus_partition21.359 0.35922.043
consensus_partition_by_down_sampling0.0000.0000.001
correspond_between_rankings0.0650.0030.069
correspond_between_two_rankings0.0330.0020.035
david_enrichment0.0000.0000.001
dim.ConsensusPartition0.0000.0000.001
dim.ConsensusPartitionList000
dim.DownSamplingConsensusPartition0.0010.0000.000
dim.HierarchicalPartition0.0000.0000.001
dimension_reduction-ConsensusPartition-method0.7230.0400.769
dimension_reduction-DownSamplingConsensusPartition-method1.8430.0891.963
dimension_reduction-HierarchicalPartition-method0.6370.0380.692
dimension_reduction-dispatch0.0000.0010.000
dimension_reduction-matrix-method0.0000.0000.001
find_best_km000
functional_enrichment-ANY-method0.0000.0000.001
functional_enrichment-ConsensusPartition-method000
functional_enrichment-ConsensusPartitionList-method0.0010.0010.001
functional_enrichment-HierarchicalPartition-method0.0000.0010.001
functional_enrichment-dispatch0.0000.0010.000
get_anno-ConsensusPartition-method0.0000.0010.000
get_anno-ConsensusPartitionList-method0.0000.0000.001
get_anno-DownSamplingConsensusPartition-method0.0890.0060.096
get_anno-HierarchicalPartition-method0.0000.0000.001
get_anno-dispatch0.0000.0000.001
get_anno_col-ConsensusPartition-method000
get_anno_col-ConsensusPartitionList-method0.0010.0000.001
get_anno_col-HierarchicalPartition-method000
get_anno_col-dispatch0.0000.0010.001
get_children_nodes-HierarchicalPartition-method000
get_classes-ConsensusPartition-method0.1630.0120.181
get_classes-ConsensusPartitionList-method0.1580.0080.177
get_classes-DownSamplingConsensusPartition-method0.0940.0110.106
get_classes-HierarchicalPartition-method0.1510.0050.157
get_classes-dispatch000
get_consensus-ConsensusPartition-method0.1650.0430.208
get_matrix-ConsensusPartition-method0.3930.5140.917
get_matrix-ConsensusPartitionList-method0.3900.5580.957
get_matrix-DownSamplingConsensusPartition-method000
get_matrix-HierarchicalPartition-method0.0010.0000.000
get_matrix-dispatch0.0000.0010.000
get_membership-ConsensusPartition-method0.1620.0200.184
get_membership-ConsensusPartitionList-method0.1540.0060.162
get_membership-dispatch000
get_param-ConsensusPartition-method0.1610.0090.170
get_signatures-ConsensusPartition-method5.0580.1955.345
get_signatures-DownSamplingConsensusPartition-method000
get_signatures-HierarchicalPartition-method0.0000.0000.001
get_signatures-dispatch000
get_stats-ConsensusPartition-method0.1600.0040.167
get_stats-ConsensusPartitionList-method0.1720.0050.178
get_stats-dispatch0.0000.0010.000
golub_cola0.1900.0050.197
golub_cola_ds0.1270.0060.136
golub_cola_rh0.1830.0050.190
hierarchical_partition0.0010.0000.000
is_best_k-ConsensusPartition-method0.2260.0170.249
is_best_k-ConsensusPartitionList-method0.1500.0050.158
is_best_k-dispatch000
is_leaf_node-HierarchicalPartition-method0.1320.0050.145
is_stable_k-ConsensusPartition-method0.8090.0250.848
is_stable_k-ConsensusPartitionList-method0.1570.0040.164
is_stable_k-dispatch0.0000.0000.001
knee_finder20.0220.0050.029
knitr_add_tab_item0.0000.0000.001
knitr_insert_tabs000
map_to_entrez_id000
max_depth-HierarchicalPartition-method0.1360.0030.141
membership_heatmap-ConsensusPartition-method0.5220.0100.537
merge_node-HierarchicalPartition-method000
merge_node_param0.0000.0000.001
ncol-ConsensusPartition-method0.0000.0010.000
ncol-ConsensusPartitionList-method000
ncol-DownSamplingConsensusPartition-method0.0000.0000.001
ncol-HierarchicalPartition-method0.0010.0000.000
ncol-dispatch000
node_info-HierarchicalPartition-method0.0000.0010.000
node_level-HierarchicalPartition-method0.0010.0000.000
nrow-ConsensusPartition-method000
nrow-ConsensusPartitionList-method000
nrow-HierarchicalPartition-method0.0000.0000.001
nrow-dispatch000
plot_ecdf-ConsensusPartition-method0.1490.0040.155
predict_classes-ConsensusPartition-method000
predict_classes-dispatch0.0000.0010.000
predict_classes-matrix-method000
print.hc_table_suggest_best_k000
recalc_stats0.0000.0000.001
register_NMF000
register_SOM000
register_partition_methods0.6030.0150.623
register_top_value_methods0.0010.0000.001
relabel_class0.0090.0010.011
remove_partition_methods000
remove_top_value_methods000
rownames-ConsensusPartition-method000
rownames-ConsensusPartitionList-method000
rownames-HierarchicalPartition-method0.0000.0000.001
rownames-dispatch0.0000.0000.001
run_all_consensus_partition_methods0.0000.0010.000
select_partition_number-ConsensusPartition-method0.1630.0050.170
show-ConsensusPartition-method000
show-ConsensusPartitionList-method0.0000.0010.000
show-DownSamplingConsensusPartition-method0.1200.0030.124
show-HierarchicalPartition-method0.1750.0050.181
show-dispatch000
split_node-HierarchicalPartition-method000
suggest_best_k-ConsensusPartition-method0.1580.0050.165
suggest_best_k-ConsensusPartitionList-method0.1560.0040.163
suggest_best_k-HierarchicalPartition-method0.1420.0050.148
suggest_best_k-dispatch000
test_between_factors0.0090.0010.010
test_to_known_factors-ConsensusPartition-method0.1700.0040.175
test_to_known_factors-ConsensusPartitionList-method0.2830.0070.294
test_to_known_factors-DownSamplingConsensusPartition-method0.1070.0030.111
test_to_known_factors-HierarchicalPartition-method0.1460.0040.152
test_to_known_factors-dispatch000
top_elements_overlap0.2480.0220.277
top_rows_heatmap-ConsensusPartition-method000
top_rows_heatmap-ConsensusPartitionList-method0.0000.0010.000
top_rows_heatmap-HierarchicalPartition-method0.0000.0000.001
top_rows_heatmap-dispatch000
top_rows_heatmap-matrix-method3.8390.2744.187
top_rows_overlap-ConsensusPartitionList-method0.7900.0480.857
top_rows_overlap-HierarchicalPartition-method0.5790.0170.607
top_rows_overlap-dispatch0.0000.0010.001
top_rows_overlap-matrix-method0.1560.0040.163