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CHECK report for GeneAccord on malbec1

This page was generated on 2021-05-06 12:27:40 -0400 (Thu, 06 May 2021).

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 681/1974HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneAccord 1.8.0  (landing page)
Ariane L. Moore
Snapshot Date: 2021-05-05 14:51:38 -0400 (Wed, 05 May 2021)
URL: https://git.bioconductor.org/packages/GeneAccord
Branch: RELEASE_3_12
Last Commit: 0413942
Last Changed Date: 2020-10-27 11:37:41 -0400 (Tue, 27 Oct 2020)
malbec1Linux (Ubuntu 18.04.5 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
tokay1Windows Server 2012 R2 Standard / x64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version exists in internal repository

Summary

Package: GeneAccord
Version: 1.8.0
Command: /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:GeneAccord.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings GeneAccord_1.8.0.tar.gz
StartedAt: 2021-05-06 01:46:48 -0400 (Thu, 06 May 2021)
EndedAt: 2021-05-06 01:49:57 -0400 (Thu, 06 May 2021)
EllapsedTime: 188.6 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneAccord.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD check --install=check:GeneAccord.install-out.txt --library=/home/biocbuild/bbs-3.12-bioc/R/library --no-vignettes --timings GeneAccord_1.8.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.12-bioc/meat/GeneAccord.Rcheck’
* using R version 4.0.5 (2021-03-31)
* 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 ‘1.8.0’
* 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-3.12-bioc/meat/GeneAccord.Rcheck/00check.log’
for details.



Installation output

GeneAccord.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.12-bioc/R/bin/R CMD INSTALL GeneAccord
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.12-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 4.0.5 (2021-03-31) -- "Shake and Throw"
Copyright (C) 2021 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")
══ Skipped tests ═══════════════════════════════════════════════════════════════
• empty test (6)

[ FAIL 0 | WARN 1 | SKIP 6 | PASS 27 ]
> 
> 
> proc.time()
   user  system elapsed 
 20.160   0.260  22.034 

Example timings

GeneAccord.Rcheck/GeneAccord-Ex.timings

nameusersystemelapsed
GeneAccord3.2520.0003.256
build_null_test_statistic2.2840.0042.291
compute_rates_clon_excl0.3680.0000.371
compute_test_stat_avg_rate0.0480.0000.050
convert_ensembl_to_reactome_pw_tbl0.5880.0080.600
create_ensembl_gene_tbl_hg000
create_tbl_ent_clones0.0520.0000.105
create_tbl_tree_collection0.4920.0040.551
ecdf_lr_test_clon_excl_avg_rate1.100.001.11
ensembl_to_hgnc000
ensembl_to_reactome0.0280.0000.030
extract_num_clones_tbl0.0360.0000.035
generate_ecdf_test_stat0.8160.0000.817
generate_test_stat_hist1.0800.0041.091
get_hist_clon_excl0.8320.0000.837
get_hist_clon_excl_this_pat_this_pair0.0480.0000.051
get_rate_diff_branch_ent_pair0.6800.0040.686
heatmap_clones_gene_pat0.8080.0000.810
hgnc_to_ensembl000
is_diff_branch_ent_pair0.0200.0000.019
map_pairs_to_hgnc_symbols000
merge_clones_identical_ents0.0600.0000.058
pairs_in_patients_hist0.0560.0000.056
plot_ecdf_test_stat0.2120.0000.212
plot_rates_clon_excl0.3160.0040.322
take_pairs_and_get_patients0.3760.0000.380
vis_pval_distr_num_pat0.0600.0000.058
write_res_pairs_to_disk0.0160.0000.016