Back to Multiple platform build/check report for BioC 3.19:   simplified   long
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This page was generated on 2024-06-14 14:37 -0400 (Fri, 14 Jun 2024).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 22.04.3 LTS)x86_644.4.0 (2024-04-24) -- "Puppy Cup" 4757
palomino3Windows Server 2022 Datacenterx644.4.0 (2024-04-24 ucrt) -- "Puppy Cup" 4491
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: 2024-06-12 14:00 -0400 (Wed, 12 Jun 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


CHECK results for cola on nebbiolo1

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: /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:cola.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings cola_2.10.0.tar.gz
StartedAt: 2024-06-12 21:50:44 -0400 (Wed, 12 Jun 2024)
EndedAt: 2024-06-12 21:53:42 -0400 (Wed, 12 Jun 2024)
EllapsedTime: 178.3 seconds
RetCode: 0
Status:   OK  
CheckDir: cola.Rcheck
Warnings: 0

Command output

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:cola.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings cola_2.10.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/cola.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* 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: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
* checking installed package size ... NOTE
  installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
* 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 18.557  0.404  18.961
* 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-3.19-bioc/meat/cola.Rcheck/00check.log’
for details.


Installation output

cola.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD INSTALL cola
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.19-bioc/R/site-library’
* installing *source* package ‘cola’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0’
g++ -std=gnu++17 -I"/home/biocbuild/bbs-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/include" -DNDEBUG  -I'/home/biocbuild/bbs-3.19-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-3.19-bioc/R/lib -L/usr/local/lib -o cola.so RcppExports.o atc.o cal_consensus_mat.o pdist.o -L/home/biocbuild/bbs-3.19-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.19-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 4.4.0 (2024-04-24) -- "Puppy Cup"
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 
  4.205   0.296   4.489 

Example timings

cola.Rcheck/cola-Ex.timings

nameusersystemelapsed
ATC0.0250.0040.029
ATC_approx0.0010.0000.000
ConsensusPartition-class000
ConsensusPartitionList-class000
DownSamplingConsensusPartition-class0.0000.0000.001
Extract.ConsensusPartitionList0.4260.0180.444
Extract.HierarchicalPartition0.1500.0080.159
ExtractExtract.ConsensusPartitionList0.2520.0120.264
ExtractExtract.HierarchicalPartition000
FCC0.1710.0040.175
HierarchicalPartition-class000
PAC0.4930.0440.538
aPAC0.1460.0080.154
adjust_matrix0.0030.0040.008
adjust_outlier0.0000.0010.001
all_leaves-HierarchicalPartition-method0.1190.0100.130
all_nodes-HierarchicalPartition-method0.1310.0040.135
all_partition_methods0.0010.0000.001
all_top_value_methods000
cola0.0430.0000.043
cola_opt0.0250.0000.025
cola_report-ConsensusPartition-method000
cola_report-ConsensusPartitionList-method000
cola_report-HierarchicalPartition-method000
cola_report-dispatch000
cola_rl0.0670.0060.073
collect_classes-ConsensusPartition-method1.8820.0561.938
collect_classes-ConsensusPartitionList-method2.7140.0562.770
collect_classes-HierarchicalPartition-method1.2460.0241.270
collect_classes-dispatch0.0010.0000.000
collect_plots-ConsensusPartition-method000
collect_plots-ConsensusPartitionList-method000
collect_plots-dispatch000
collect_stats-ConsensusPartition-method0.0000.0010.000
collect_stats-ConsensusPartitionList-method0.4100.0330.444
collect_stats-dispatch0.0000.0000.001
colnames-ConsensusPartition-method000
colnames-ConsensusPartitionList-method000
colnames-DownSamplingConsensusPartition-method0.0000.0000.001
colnames-HierarchicalPartition-method000
colnames-dispatch000
compare_partitions-ConsensusPartition-method0.0000.0010.000
compare_signatures-ConsensusPartition-method000
compare_signatures-HierarchicalPartition-method4.2290.1514.382
compare_signatures-dispatch000
concordance0.1470.0080.155
config_ATC0.0010.0000.000
consensus_heatmap-ConsensusPartition-method0.5140.0120.525
consensus_partition18.557 0.40418.961
consensus_partition_by_down_sampling000
correspond_between_rankings0.0560.0000.056
correspond_between_two_rankings0.0260.0000.026
david_enrichment0.0010.0000.001
dim.ConsensusPartition000
dim.ConsensusPartitionList000
dim.DownSamplingConsensusPartition000
dim.HierarchicalPartition000
dimension_reduction-ConsensusPartition-method0.6410.0160.657
dimension_reduction-DownSamplingConsensusPartition-method1.6190.0361.655
dimension_reduction-HierarchicalPartition-method0.5330.0000.532
dimension_reduction-dispatch000
dimension_reduction-matrix-method000
find_best_km000
functional_enrichment-ANY-method000
functional_enrichment-ConsensusPartition-method000
functional_enrichment-ConsensusPartitionList-method000
functional_enrichment-HierarchicalPartition-method000
functional_enrichment-dispatch000
get_anno-ConsensusPartition-method0.0010.0000.000
get_anno-ConsensusPartitionList-method000
get_anno-DownSamplingConsensusPartition-method0.0860.0000.086
get_anno-HierarchicalPartition-method000
get_anno-dispatch000
get_anno_col-ConsensusPartition-method0.0000.0000.001
get_anno_col-ConsensusPartitionList-method000
get_anno_col-HierarchicalPartition-method000
get_anno_col-dispatch0.0000.0010.001
get_children_nodes-HierarchicalPartition-method000
get_classes-ConsensusPartition-method0.1350.0220.156
get_classes-ConsensusPartitionList-method0.1420.0080.150
get_classes-DownSamplingConsensusPartition-method0.0810.0070.088
get_classes-HierarchicalPartition-method0.140.000.14
get_classes-dispatch000
get_consensus-ConsensusPartition-method0.1450.0440.188
get_matrix-ConsensusPartition-method0.3490.6160.965
get_matrix-ConsensusPartitionList-method0.3740.6080.982
get_matrix-DownSamplingConsensusPartition-method0.0010.0000.001
get_matrix-HierarchicalPartition-method000
get_matrix-dispatch0.0000.0010.001
get_membership-ConsensusPartition-method0.1460.0310.176
get_membership-ConsensusPartitionList-method0.1460.0040.150
get_membership-dispatch000
get_param-ConsensusPartition-method0.1410.0230.164
get_signatures-ConsensusPartition-method3.9520.1364.089
get_signatures-DownSamplingConsensusPartition-method000
get_signatures-HierarchicalPartition-method0.0010.0000.000
get_signatures-dispatch000
get_stats-ConsensusPartition-method0.1730.0040.177
get_stats-ConsensusPartitionList-method0.1440.0100.154
get_stats-dispatch000
golub_cola0.1730.0080.182
golub_cola_ds0.1780.0160.194
golub_cola_rh0.1590.0080.167
hierarchical_partition000
is_best_k-ConsensusPartition-method0.1410.0080.149
is_best_k-ConsensusPartitionList-method0.1450.0080.153
is_best_k-dispatch000
is_leaf_node-HierarchicalPartition-method0.1310.0000.131
is_stable_k-ConsensusPartition-method0.170.000.17
is_stable_k-ConsensusPartitionList-method0.1620.0000.162
is_stable_k-dispatch000
knee_finder20.0350.0020.037
knitr_add_tab_item000
knitr_insert_tabs000
map_to_entrez_id000
max_depth-HierarchicalPartition-method0.120.010.13
membership_heatmap-ConsensusPartition-method0.4660.0030.469
merge_node-HierarchicalPartition-method000
merge_node_param0.0010.0000.001
ncol-ConsensusPartition-method000
ncol-ConsensusPartitionList-method000
ncol-DownSamplingConsensusPartition-method0.0010.0000.000
ncol-HierarchicalPartition-method000
ncol-dispatch000
node_info-HierarchicalPartition-method0.0010.0000.000
node_level-HierarchicalPartition-method0.0000.0000.001
nrow-ConsensusPartition-method000
nrow-ConsensusPartitionList-method000
nrow-HierarchicalPartition-method0.0000.0010.001
nrow-dispatch000
plot_ecdf-ConsensusPartition-method0.1480.0080.156
predict_classes-ConsensusPartition-method000
predict_classes-dispatch000
predict_classes-matrix-method000
print.hc_table_suggest_best_k0.0000.0000.001
recalc_stats000
register_NMF000
register_SOM0.0000.0010.001
register_partition_methods0.6810.0590.740
register_top_value_methods0.0010.0000.001
relabel_class0.0080.0000.009
remove_partition_methods000
remove_top_value_methods000
rownames-ConsensusPartition-method0.0010.0000.001
rownames-ConsensusPartitionList-method000
rownames-HierarchicalPartition-method000
rownames-dispatch0.0000.0000.001
run_all_consensus_partition_methods000
select_partition_number-ConsensusPartition-method0.1480.0120.160
show-ConsensusPartition-method000
show-ConsensusPartitionList-method0.0000.0000.001
show-DownSamplingConsensusPartition-method0.1060.0000.106
show-HierarchicalPartition-method0.1590.0040.163
show-dispatch000
split_node-HierarchicalPartition-method000
suggest_best_k-ConsensusPartition-method0.1440.0040.147
suggest_best_k-ConsensusPartitionList-method0.1540.0040.158
suggest_best_k-HierarchicalPartition-method0.1210.0150.136
suggest_best_k-dispatch000
test_between_factors0.0090.0000.010
test_to_known_factors-ConsensusPartition-method0.1620.0080.170
test_to_known_factors-ConsensusPartitionList-method0.2610.0080.269
test_to_known_factors-DownSamplingConsensusPartition-method0.1030.0030.106
test_to_known_factors-HierarchicalPartition-method0.1350.0080.143
test_to_known_factors-dispatch000
top_elements_overlap0.2100.0080.218
top_rows_heatmap-ConsensusPartition-method0.0000.0000.001
top_rows_heatmap-ConsensusPartitionList-method000
top_rows_heatmap-HierarchicalPartition-method000
top_rows_heatmap-dispatch0.0000.0010.001
top_rows_heatmap-matrix-method3.6350.0993.695
top_rows_overlap-ConsensusPartitionList-method0.7760.0080.784
top_rows_overlap-HierarchicalPartition-method0.4780.0040.482
top_rows_overlap-dispatch000
top_rows_overlap-matrix-method0.1180.0000.119