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 11:40:23 -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 kunpeng2


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.
- See Martin Grigorov's blog post for how to debug Linux ARM64 related issues on a x86_64 host.

raw results


Summary

Package: cola
Version: 2.10.0
Command: /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:cola.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings cola_2.10.0.tar.gz
StartedAt: 2024-05-04 06:10:58 -0000 (Sat, 04 May 2024)
EndedAt: 2024-05-04 06:14:53 -0000 (Sat, 04 May 2024)
EllapsedTime: 235.4 seconds
RetCode: 0
Status:   OK  
CheckDir: cola.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:cola.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings cola_2.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/cola.Rcheck’
* using R version 4.4.0 beta (2024-04-15 r86425)
* using platform: aarch64-unknown-linux-gnu
* R was compiled by
    gcc (GCC) 10.3.1
    GNU Fortran (GCC) 10.3.1
* running under: openEuler 22.03 (LTS-SP1)
* 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: ‘g++ (GCC) 10.3.1’
* checking installed package size ... NOTE
  installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data      3.2Mb
    extdata   1.0Mb
    libs      2.3Mb
* 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                             30.199  1.260  31.542
get_signatures-ConsensusPartition-method         6.210  0.064   6.285
compare_signatures-HierarchicalPartition-method  5.827  0.255   6.104
* 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
  ‘/home/biocbuild/bbs-3.19-bioc/meat/cola.Rcheck/00check.log’
for details.


Installation output

cola.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD INSTALL cola
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library’
* installing *source* package ‘cola’ ...
** using staged installation
** libs
using C++ compiler: ‘g++ (GCC) 10.3.1’
g++ -std=gnu++17 -I"/home/biocbuild/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/include" -DNDEBUG  -I'/home/biocbuild/R/R-beta-2024-04-15_r86425/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/R/R-beta-2024-04-15_r86425/lib -L/usr/local/lib -o cola.so RcppExports.o atc.o cal_consensus_mat.o pdist.o -L/home/biocbuild/R/R-beta-2024-04-15_r86425/lib -lR
installing to /home/biocbuild/R/R-beta-2024-04-15_r86425/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 beta (2024-04-15 r86425) -- "Puppy Cup"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-unknown-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 
  6.666   0.595   7.260 

Example timings

cola.Rcheck/cola-Ex.timings

nameusersystemelapsed
ATC0.1680.0040.172
ATC_approx000
ConsensusPartition-class000
ConsensusPartitionList-class000
DownSamplingConsensusPartition-class000
Extract.ConsensusPartitionList0.5690.0040.574
Extract.HierarchicalPartition0.2740.0000.274
ExtractExtract.ConsensusPartitionList0.1720.0040.176
ExtractExtract.HierarchicalPartition000
FCC0.1770.0200.197
HierarchicalPartition-class000
PAC0.5490.0200.570
aPAC0.1400.0080.149
adjust_matrix0.0080.0000.007
adjust_outlier0.0010.0000.001
all_leaves-HierarchicalPartition-method0.1080.0160.123
all_nodes-HierarchicalPartition-method0.1300.0000.131
all_partition_methods0.0010.0000.001
all_top_value_methods000
cola0.0760.0040.080
cola_opt0.0310.0000.032
cola_report-ConsensusPartition-method000
cola_report-ConsensusPartitionList-method000
cola_report-HierarchicalPartition-method000
cola_report-dispatch000
cola_rl0.0650.0200.084
collect_classes-ConsensusPartition-method2.6860.0522.743
collect_classes-ConsensusPartitionList-method4.4150.1004.523
collect_classes-HierarchicalPartition-method1.7840.0361.825
collect_classes-dispatch000
collect_plots-ConsensusPartition-method000
collect_plots-ConsensusPartitionList-method000
collect_plots-dispatch000
collect_stats-ConsensusPartition-method000
collect_stats-ConsensusPartitionList-method0.5490.0000.550
collect_stats-dispatch000
colnames-ConsensusPartition-method000
colnames-ConsensusPartitionList-method000
colnames-DownSamplingConsensusPartition-method0.0000.0000.001
colnames-HierarchicalPartition-method0.0010.0000.000
colnames-dispatch000
compare_partitions-ConsensusPartition-method000
compare_signatures-ConsensusPartition-method000
compare_signatures-HierarchicalPartition-method5.8270.2556.104
compare_signatures-dispatch000
concordance0.1400.0040.145
config_ATC0.0010.0000.000
consensus_heatmap-ConsensusPartition-method0.7440.0320.779
consensus_partition30.199 1.26031.542
consensus_partition_by_down_sampling0.0010.0000.001
correspond_between_rankings0.0820.0040.086
correspond_between_two_rankings0.0380.0000.037
david_enrichment000
dim.ConsensusPartition000
dim.ConsensusPartitionList000
dim.DownSamplingConsensusPartition000
dim.HierarchicalPartition000
dimension_reduction-ConsensusPartition-method0.8870.0080.897
dimension_reduction-DownSamplingConsensusPartition-method2.2250.0562.284
dimension_reduction-HierarchicalPartition-method0.7660.0000.768
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-method0.0000.0000.001
functional_enrichment-dispatch000
get_anno-ConsensusPartition-method000
get_anno-ConsensusPartitionList-method0.0010.0000.000
get_anno-DownSamplingConsensusPartition-method0.0700.0040.074
get_anno-HierarchicalPartition-method000
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-method0.1330.0120.145
get_classes-ConsensusPartitionList-method0.1440.0080.152
get_classes-DownSamplingConsensusPartition-method0.0720.0040.075
get_classes-HierarchicalPartition-method0.1380.0000.141
get_classes-dispatch000
get_consensus-ConsensusPartition-method0.1340.0160.151
get_matrix-ConsensusPartition-method0.2910.1000.392
get_matrix-ConsensusPartitionList-method0.3320.0750.412
get_matrix-DownSamplingConsensusPartition-method000
get_matrix-HierarchicalPartition-method000
get_matrix-dispatch0.0000.0000.001
get_membership-ConsensusPartition-method0.1420.0040.146
get_membership-ConsensusPartitionList-method0.1300.0080.139
get_membership-dispatch000
get_param-ConsensusPartition-method0.1470.0000.147
get_signatures-ConsensusPartition-method6.2100.0646.285
get_signatures-DownSamplingConsensusPartition-method000
get_signatures-HierarchicalPartition-method000
get_signatures-dispatch000
get_stats-ConsensusPartition-method0.1630.0040.168
get_stats-ConsensusPartitionList-method0.140.000.14
get_stats-dispatch000
golub_cola0.1570.0200.177
golub_cola_ds0.1770.0000.176
golub_cola_rh0.1740.0040.178
hierarchical_partition000
is_best_k-ConsensusPartition-method0.1300.0080.138
is_best_k-ConsensusPartitionList-method0.1400.0040.144
is_best_k-dispatch000
is_leaf_node-HierarchicalPartition-method0.1190.0000.118
is_stable_k-ConsensusPartition-method0.1500.0050.154
is_stable_k-ConsensusPartitionList-method0.1430.0070.150
is_stable_k-dispatch000
knee_finder20.0310.0000.031
knitr_add_tab_item000
knitr_insert_tabs000
map_to_entrez_id000
max_depth-HierarchicalPartition-method0.1080.0080.117
membership_heatmap-ConsensusPartition-method0.6070.0160.625
merge_node-HierarchicalPartition-method000
merge_node_param000
ncol-ConsensusPartition-method000
ncol-ConsensusPartitionList-method000
ncol-DownSamplingConsensusPartition-method000
ncol-HierarchicalPartition-method000
ncol-dispatch000
node_info-HierarchicalPartition-method000
node_level-HierarchicalPartition-method000
nrow-ConsensusPartition-method000
nrow-ConsensusPartitionList-method000
nrow-HierarchicalPartition-method000
nrow-dispatch000
plot_ecdf-ConsensusPartition-method0.1510.0080.158
predict_classes-ConsensusPartition-method000
predict_classes-dispatch000
predict_classes-matrix-method000
print.hc_table_suggest_best_k000
recalc_stats000
register_NMF0.0010.0000.000
register_SOM000
register_partition_methods0.7210.0390.761
register_top_value_methods0.0020.0000.001
relabel_class0.0110.0000.010
remove_partition_methods000
remove_top_value_methods000
rownames-ConsensusPartition-method0.0010.0000.000
rownames-ConsensusPartitionList-method000
rownames-HierarchicalPartition-method000
rownames-dispatch000
run_all_consensus_partition_methods000
select_partition_number-ConsensusPartition-method0.1470.0080.155
show-ConsensusPartition-method000
show-ConsensusPartitionList-method000
show-DownSamplingConsensusPartition-method0.0990.0080.107
show-HierarchicalPartition-method0.1690.0040.174
show-dispatch000
split_node-HierarchicalPartition-method0.0000.0000.001
suggest_best_k-ConsensusPartition-method0.1350.0040.139
suggest_best_k-ConsensusPartitionList-method0.1470.0040.151
suggest_best_k-HierarchicalPartition-method0.1220.0040.127
suggest_best_k-dispatch000
test_between_factors0.0110.0000.012
test_to_known_factors-ConsensusPartition-method0.1590.0080.167
test_to_known_factors-ConsensusPartitionList-method0.3190.0080.328
test_to_known_factors-DownSamplingConsensusPartition-method0.1000.0040.105
test_to_known_factors-HierarchicalPartition-method0.1350.0000.136
test_to_known_factors-dispatch000
top_elements_overlap0.2900.0040.295
top_rows_heatmap-ConsensusPartition-method000
top_rows_heatmap-ConsensusPartitionList-method0.0000.0000.001
top_rows_heatmap-HierarchicalPartition-method0.0010.0000.000
top_rows_heatmap-dispatch000
top_rows_heatmap-matrix-method4.2230.0884.308
top_rows_overlap-ConsensusPartitionList-method0.9300.0120.944
top_rows_overlap-HierarchicalPartition-method0.5280.0160.545
top_rows_overlap-dispatch000
top_rows_overlap-matrix-method0.1820.0000.183