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CHECK report for clustifyr on machv2

This page was generated on 2020-10-17 11:58:15 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE clustifyr PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 323/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
clustifyr 1.0.0
Rui Fu
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/clustifyr
Branch: RELEASE_3_11
Last Commit: bede830
Last Changed Date: 2020-04-27 15:33:56 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: clustifyr
Version: 1.0.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings clustifyr_1.0.0.tar.gz
StartedAt: 2020-10-16 23:49:24 -0400 (Fri, 16 Oct 2020)
EndedAt: 2020-10-16 23:57:45 -0400 (Fri, 16 Oct 2020)
EllapsedTime: 501.2 seconds
RetCode: 0
Status:  OK 
CheckDir: clustifyr.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:clustifyr.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings clustifyr_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/clustifyr.Rcheck’
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘clustifyr/DESCRIPTION’ ... OK
* this is package ‘clustifyr’ version ‘1.0.0’
* package encoding: UTF-8
* 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 ‘clustifyr’ can be installed ... OK
* checking installed package size ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                         user system elapsed
overcluster_test       13.254  0.093  13.667
calculate_pathway_gsea  5.877  0.141   6.124
plot_pathway_gsea       5.942  0.031   6.023
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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: OK


Installation output

clustifyr.Rcheck/00install.out

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL clustifyr
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘clustifyr’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (clustifyr)

Tests output

clustifyr.Rcheck/tests/testthat.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 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)
> library(clustifyr)
> 
> test_check("clustifyr")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 159 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
180.827   4.803 186.032 

Example timings

clustifyr.Rcheck/clustifyr-Ex.timings

nameusersystemelapsed
average_clusters0.1640.0180.192
binarize_expr0.0530.0030.062
calculate_pathway_gsea5.8770.1416.124
call_consensus0.2770.0100.289
call_to_metadata0.0000.0010.000
clustify0.2940.0310.327
clustify_lists0.2090.0170.227
clustify_nudge1.3500.0121.399
collapse_to_cluster2.5020.0882.679
compare_lists0.2160.0040.234
cor_to_call0.1100.0020.115
cor_to_call_rank0.1060.0060.115
cor_to_call_topn0.1070.0040.110
downsample_matrix0.7420.0070.776
feature_select_PCA0.0150.0030.019
file_marker_parse0.0030.0020.004
find_rank_bias0.1390.0140.162
gene_pct_markerm0.6940.0030.746
get_vargenes0.0010.0010.002
gmt_to_list0.2910.0230.328
insert_meta_object0.0000.0000.001
marker_select0.0350.0030.042
matrixize_markers0.0580.0110.071
object_data0.0860.0020.091
object_ref0.0080.0090.018
overcluster2.6240.1402.792
overcluster_test13.254 0.09313.667
parse_loc_object0.0010.0000.002
plot_best_call0.7190.0190.742
plot_cor0.6650.0180.684
plot_cor_heatmap1.1150.0241.141
plot_dims0.4040.0070.410
plot_gene0.6140.0140.630
plot_pathway_gsea5.9420.0316.023
pos_neg_marker0.0160.0010.016
pos_neg_select0.1470.0030.150
ref_feature_select0.0440.0010.045
ref_marker_select0.4390.0030.442
reverse_marker_matrix0.0120.0100.022
run_gsea0.3730.0050.378
seurat_meta0.0000.0000.001
seurat_ref0.0090.0000.011
write_meta0.1620.0030.168