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CHECK report for GeneAccord on machv2

This page was generated on 2020-10-17 11:58:32 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE GeneAccord PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 673/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneAccord 1.6.0
Ariane L. Moore
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/GeneAccord
Branch: RELEASE_3_11
Last Commit: fbcd915
Last Changed Date: 2020-04-27 15:18:33 -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: GeneAccord
Version: 1.6.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneAccord.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneAccord_1.6.0.tar.gz
StartedAt: 2020-10-17 01:23:46 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 01:27:57 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 250.5 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneAccord.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:GeneAccord.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings GeneAccord_1.6.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/GeneAccord.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 ‘GeneAccord/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GeneAccord’ version ‘1.6.0’
* 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 ‘GeneAccord’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  9.9Mb
  sub-directories of 1Mb or more:
    data      3.0Mb
    extdata   6.5Mb
* 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
* 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: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/GeneAccord.Rcheck/00check.log’
for details.



Installation output

GeneAccord.Rcheck/00install.out

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


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘GeneAccord’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GeneAccord)

Tests output

GeneAccord.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("assertthat")
> 
> library("GeneAccord")
> # "When R CMD check runs tests, it sets R_TESTS. When the tests
> # themeselves run R CMD xxxx, as is the case with the tests in
> # devtools, having R_TESTS set causes errors because it confuses
> # the R subprocesses. Unsetting it here avoids those problems.
> #"R_TESTS" = "" "
> Sys.setenv("R_TESTS" = "")
> 
> test_check("GeneAccord")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 27 | SKIPPED: 6 | WARNINGS: 1 | FAILED: 0 ]
> 
> 
> proc.time()
   user  system elapsed 
 24.052   0.556  27.323 

Example timings

GeneAccord.Rcheck/GeneAccord-Ex.timings

nameusersystemelapsed
GeneAccord3.0930.0333.138
build_null_test_statistic2.6180.0172.644
compute_rates_clon_excl0.3300.0030.335
compute_test_stat_avg_rate0.0520.0010.053
convert_ensembl_to_reactome_pw_tbl0.6160.0110.628
create_ensembl_gene_tbl_hg0.0000.0000.001
create_tbl_ent_clones0.0800.0020.083
create_tbl_tree_collection0.5940.0120.611
ecdf_lr_test_clon_excl_avg_rate1.1820.0091.196
ensembl_to_hgnc000
ensembl_to_reactome0.0280.0030.031
extract_num_clones_tbl0.0340.0010.036
generate_ecdf_test_stat1.0060.0071.015
generate_test_stat_hist1.3160.0081.328
get_hist_clon_excl1.0410.0071.052
get_hist_clon_excl_this_pat_this_pair0.0330.0010.033
get_rate_diff_branch_ent_pair0.7210.0100.734
heatmap_clones_gene_pat0.9310.0140.949
hgnc_to_ensembl000
is_diff_branch_ent_pair0.0200.0010.020
map_pairs_to_hgnc_symbols0.0000.0010.000
merge_clones_identical_ents0.0790.0010.080
pairs_in_patients_hist0.1020.0010.102
plot_ecdf_test_stat0.3750.0030.379
plot_rates_clon_excl0.3420.0020.352
take_pairs_and_get_patients0.3820.0020.384
vis_pval_distr_num_pat0.0520.0020.054
write_res_pairs_to_disk0.0140.0020.016