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This page was generated on 2021-10-15 15:06:32 -0400 (Fri, 15 Oct 2021).

CHECK results for cola on machv2

To the developers/maintainers of the cola package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/cola.git to
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raw results

Package 364/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
cola 1.8.1  (landing page)
Zuguang Gu
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/cola
git_branch: RELEASE_3_13
git_last_commit: ffd39a8
git_last_commit_date: 2021-07-15 09:45:48 -0400 (Thu, 15 Jul 2021)
nebbiolo1Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: cola
Version: 1.8.1
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cola.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cola_1.8.1.tar.gz
StartedAt: 2021-10-14 17:40:04 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 17:44:21 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 257.3 seconds
RetCode: 0
Status:   OK  
CheckDir: cola.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:cola.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings cola_1.8.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/cola.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘cola/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘cola’ version ‘1.8.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .git_fetch_output.txt
  .git_merge_output.txt
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘cola’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data      3.5Mb
    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 R 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 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                             32.233  0.260  32.516
get_signatures-ConsensusPartition-method         7.713  0.154   7.886
compare_signatures-HierarchicalPartition-method  6.075  0.185   6.267
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘test-all.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.13-bioc/meat/cola.Rcheck/00check.log’
for details.



Installation output

cola.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL cola
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.1/Resources/library’
* installing *source* package ‘cola’ ...
** using staged installation
** libs
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c RcppExports.cpp -o RcppExports.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c atc.cpp -o atc.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c cal_consensus_mat.cpp -o cal_consensus_mat.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.1/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  -Wall -g -O2  -c pdist.cpp -o pdist.o
clang++ -mmacosx-version-min=10.13 -std=gnu++14 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/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/4.1/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 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin17.0 (64-bit)

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 
  6.009   0.352   6.350 

Example timings

cola.Rcheck/cola-Ex.timings

nameusersystemelapsed
ATC0.0400.0040.044
ATC_approx0.0000.0010.001
ConsensusPartition-class0.0000.0010.000
ConsensusPartitionList-class0.0000.0010.000
DownSamplingConsensusPartition-class000
Extract.ConsensusPartitionList0.7290.0300.759
Extract.HierarchicalPartition0.3090.0070.315
ExtractExtract.ConsensusPartitionList0.3040.0090.313
ExtractExtract.HierarchicalPartition0.0000.0010.001
FCC0.2950.0110.306
HierarchicalPartition-class0.0010.0000.001
PAC0.2670.0080.275
aPAC0.5240.0060.530
adjust_matrix0.0110.0030.014
adjust_outlier0.0010.0010.002
all_leaves-HierarchicalPartition-method0.1840.0030.187
all_nodes-HierarchicalPartition-method0.2040.0040.208
all_partition_methods0.0010.0000.002
all_top_value_methods0.0000.0000.001
cola0.0960.0020.098
cola_opt0.0370.0020.039
cola_report-ConsensusPartition-method0.0000.0010.000
cola_report-ConsensusPartitionList-method0.0010.0000.000
cola_report-HierarchicalPartition-method0.0010.0000.001
cola_report-dispatch000
cola_rl0.1710.0070.178
collect_classes-ConsensusPartition-method3.3270.0803.410
collect_classes-ConsensusPartitionList-method4.7460.0334.782
collect_classes-HierarchicalPartition-method2.3160.0512.373
collect_classes-dispatch0.0000.0000.001
collect_plots-ConsensusPartition-method0.0000.0000.001
collect_plots-ConsensusPartitionList-method0.0010.0010.000
collect_plots-dispatch0.0010.0000.000
collect_stats-ConsensusPartition-method000
collect_stats-ConsensusPartitionList-method0.6940.0070.701
collect_stats-dispatch000
colnames-ConsensusPartition-method0.0010.0000.001
colnames-ConsensusPartitionList-method000
colnames-DownSamplingConsensusPartition-method000
colnames-HierarchicalPartition-method000
colnames-dispatch000
compare_partitions-ConsensusPartition-method000
compare_signatures-ConsensusPartition-method000
compare_signatures-HierarchicalPartition-method6.0750.1856.267
compare_signatures-dispatch0.0000.0000.001
concordance0.2320.0050.237
config_ATC0.0010.0010.002
consensus_heatmap-ConsensusPartition-method0.8160.0140.831
consensus_partition32.233 0.26032.516
consensus_partition_by_down_sampling0.0000.0000.001
correspond_between_rankings0.0800.0020.082
correspond_between_two_rankings0.0380.0020.040
david_enrichment000
dim.ConsensusPartition000
dim.ConsensusPartitionList0.0010.0000.000
dim.DownSamplingConsensusPartition0.0010.0000.000
dim.HierarchicalPartition0.0000.0000.001
dimension_reduction-ConsensusPartition-method0.9920.0401.032
dimension_reduction-DownSamplingConsensusPartition-method1.7930.0711.866
dimension_reduction-HierarchicalPartition-method0.7330.0260.760
dimension_reduction-dispatch000
dimension_reduction-matrix-method000
find_best_km0.0010.0000.000
functional_enrichment-ANY-method0.0000.0000.001
functional_enrichment-ConsensusPartition-method0.0000.0010.000
functional_enrichment-ConsensusPartitionList-method000
functional_enrichment-HierarchicalPartition-method000
functional_enrichment-dispatch0.0010.0000.000
get_anno-ConsensusPartition-method0.0010.0000.000
get_anno-ConsensusPartitionList-method0.0010.0000.000
get_anno-DownSamplingConsensusPartition-method0.1030.0050.109
get_anno-HierarchicalPartition-method0.0010.0010.000
get_anno-dispatch0.0000.0010.000
get_anno_col-ConsensusPartition-method0.0000.0000.001
get_anno_col-ConsensusPartitionList-method0.0000.0000.001
get_anno_col-HierarchicalPartition-method0.0000.0010.000
get_anno_col-dispatch000
get_children_nodes-HierarchicalPartition-method0.0000.0000.001
get_classes-ConsensusPartition-method0.2050.0090.214
get_classes-ConsensusPartitionList-method0.2740.0070.281
get_classes-DownSamplingConsensusPartition-method0.1320.0120.145
get_classes-HierarchicalPartition-method0.2020.0050.208
get_classes-dispatch0.0000.0000.001
get_consensus-ConsensusPartition-method0.2220.0440.266
get_matrix-ConsensusPartition-method0.6470.8251.497
get_matrix-ConsensusPartitionList-method0.6870.8621.572
get_matrix-HierarchicalPartition-method0.0010.0000.000
get_matrix-dispatch000
get_membership-ConsensusPartition-method0.1980.0240.222
get_membership-ConsensusPartitionList-method0.2640.0050.269
get_membership-dispatch000
get_param-ConsensusPartition-method0.2930.0170.311
get_signatures-ConsensusPartition-method7.7130.1547.886
get_signatures-DownSamplingConsensusPartition-method000
get_signatures-HierarchicalPartition-method0.0000.0000.001
get_signatures-dispatch000
get_stats-ConsensusPartition-method0.2680.0060.274
get_stats-ConsensusPartitionList-method0.2690.0060.274
get_stats-dispatch0.0000.0000.001
golub_cola0.3050.0040.309
golub_cola_ds0.1360.0030.140
golub_cola_rh0.2170.0030.220
hierarchical_partition0.0000.0000.001
is_best_k-ConsensusPartition-method0.1950.0050.199
is_best_k-ConsensusPartitionList-method0.2400.0030.243
is_best_k-dispatch000
is_leaf_node-HierarchicalPartition-method0.1880.0040.192
is_stable_k-ConsensusPartition-method0.2480.0160.264
is_stable_k-ConsensusPartitionList-method0.2340.0030.237
is_stable_k-dispatch000
knee_finder20.0310.0040.034
knitr_add_tab_item0.0000.0010.000
knitr_insert_tabs000
map_to_entrez_id0.0000.0000.001
max_depth-HierarchicalPartition-method0.1910.0040.196
membership_heatmap-ConsensusPartition-method0.6950.0060.702
merge_node-HierarchicalPartition-method0.0000.0000.001
merge_node_param0.0010.0000.000
ncol-ConsensusPartition-method0.0010.0010.000
ncol-ConsensusPartitionList-method000
ncol-DownSamplingConsensusPartition-method0.0000.0000.001
ncol-HierarchicalPartition-method0.0000.0000.001
ncol-dispatch0.0000.0000.001
node_info-HierarchicalPartition-method0.0000.0010.000
node_level-HierarchicalPartition-method0.0010.0000.000
nrow-ConsensusPartition-method0.0000.0010.001
nrow-ConsensusPartitionList-method0.0000.0000.001
nrow-HierarchicalPartition-method0.0000.0010.000
nrow-dispatch0.0000.0010.000
plot_ecdf-ConsensusPartition-method0.2750.0050.281
predict_classes-ConsensusPartition-method0.0000.0010.000
predict_classes-dispatch000
predict_classes-matrix-method000
print.hc_table_suggest_best_k000
recalc_stats0.0000.0000.001
register_NMF0.0000.0010.001
register_SOM000
register_partition_methods0.5400.0130.554
register_top_value_methods0.0020.0000.002
relabel_class0.0150.0030.018
remove_partition_methods0.0000.0010.000
remove_top_value_methods0.0000.0000.001
rownames-ConsensusPartition-method000
rownames-ConsensusPartitionList-method0.0000.0000.001
rownames-HierarchicalPartition-method0.0010.0000.000
rownames-dispatch0.0000.0010.000
run_all_consensus_partition_methods000
select_partition_number-ConsensusPartition-method0.2480.0040.253
show-ConsensusPartition-method0.0010.0000.001
show-ConsensusPartitionList-method0.0010.0000.001
show-DownSamplingConsensusPartition-method0.1700.0030.174
show-HierarchicalPartition-method0.2590.0050.265
show-dispatch0.0010.0010.001
split_node-HierarchicalPartition-method0.0000.0000.001
suggest_best_k-ConsensusPartition-method0.2250.0030.228
suggest_best_k-ConsensusPartitionList-method0.2810.0060.287
suggest_best_k-HierarchicalPartition-method0.2010.0050.206
suggest_best_k-dispatch000
test_between_factors0.0160.0000.017
test_to_known_factors-ConsensusPartition-method0.2420.0040.246
test_to_known_factors-ConsensusPartitionList-method0.4900.0060.497
test_to_known_factors-DownSamplingConsensusPartition-method0.1700.0030.173
test_to_known_factors-HierarchicalPartition-method0.2040.0040.207
test_to_known_factors-dispatch0.0000.0010.000
top_elements_overlap0.2930.0100.304
top_rows_heatmap-ConsensusPartition-method0.0010.0000.000
top_rows_heatmap-ConsensusPartitionList-method000
top_rows_heatmap-HierarchicalPartition-method0.0000.0000.001
top_rows_heatmap-dispatch0.0000.0010.000
top_rows_heatmap-matrix-method4.4680.2634.740
top_rows_overlap-ConsensusPartitionList-method1.0120.0361.049
top_rows_overlap-HierarchicalPartition-method0.7960.0120.812
top_rows_overlap-dispatch0.0000.0000.001
top_rows_overlap-matrix-method0.2340.0040.238