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CHECK report for GeneAccord on malbec1

This page was generated on 2020-04-15 12:14:34 -0400 (Wed, 15 Apr 2020).

Package 646/1823HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneAccord 1.4.0
Ariane L. Moore
Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020)
URL: https://git.bioconductor.org/packages/GeneAccord
Branch: RELEASE_3_10
Last Commit: ad6ab9d
Last Changed Date: 2019-10-29 13:11:18 -0400 (Tue, 29 Oct 2019)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: GeneAccord
Version: 1.4.0
Command: /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:GeneAccord.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings GeneAccord_1.4.0.tar.gz
StartedAt: 2020-04-15 05:56:19 -0400 (Wed, 15 Apr 2020)
EndedAt: 2020-04-15 05:58:30 -0400 (Wed, 15 Apr 2020)
EllapsedTime: 130.6 seconds
RetCode: 0
Status:  OK 
CheckDir: GeneAccord.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD check --install=check:GeneAccord.install-out.txt --library=/home/biocbuild/bbs-3.10-bioc/R/library --no-vignettes --timings GeneAccord_1.4.0.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.10-bioc/meat/GeneAccord.Rcheck’
* using R version 3.6.3 (2020-02-29)
* using platform: x86_64-pc-linux-gnu (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 ‘1.4.0’
* 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 10.0Mb
  sub-directories of 1Mb or more:
    data      3.0Mb
    extdata   6.6Mb
* 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
  ‘/home/biocbuild/bbs-3.10-bioc/meat/GeneAccord.Rcheck/00check.log’
for details.



Installation output

GeneAccord.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.10-bioc/R/bin/R CMD INSTALL GeneAccord
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.10-bioc/R/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 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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: 0 | FAILED: 0 ]
> 
> 
> proc.time()
   user  system elapsed 
 15.116   0.160  15.384 

Example timings

GeneAccord.Rcheck/GeneAccord-Ex.timings

nameusersystemelapsed
GeneAccord2.2320.0082.252
build_null_test_statistic2.0400.0002.049
compute_rates_clon_excl0.2480.0000.250
compute_test_stat_avg_rate0.0440.0000.041
convert_ensembl_to_reactome_pw_tbl0.4600.0080.471
create_ensembl_gene_tbl_hg0.0000.0000.001
create_tbl_ent_clones0.0720.0000.101
create_tbl_tree_collection0.4560.0000.668
ecdf_lr_test_clon_excl_avg_rate0.6800.0000.709
ensembl_to_hgnc000
ensembl_to_reactome0.0240.0000.024
extract_num_clones_tbl0.0360.0000.035
generate_ecdf_test_stat0.6200.0040.624
generate_test_stat_hist0.9640.0000.991
get_hist_clon_excl0.6960.0000.702
get_hist_clon_excl_this_pat_this_pair0.0240.0000.044
get_rate_diff_branch_ent_pair0.4080.0000.470
heatmap_clones_gene_pat0.9400.0000.963
hgnc_to_ensembl000
is_diff_branch_ent_pair0.0120.0000.011
map_pairs_to_hgnc_symbols000
merge_clones_identical_ents0.0520.0000.051
pairs_in_patients_hist0.0400.0000.041
plot_ecdf_test_stat0.2400.0000.241
plot_rates_clon_excl0.2920.0000.292
take_pairs_and_get_patients0.1680.0000.167
vis_pval_distr_num_pat0.0400.0000.041
write_res_pairs_to_disk0.0120.0000.011