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This page was generated on 2021-10-15 15:05:41 -0400 (Fri, 15 Oct 2021).

CHECK results for GeneAccord on nebbiolo1

To the developers/maintainers of the GeneAccord package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeneAccord.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 707/2041HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
GeneAccord 1.10.0  (landing page)
Ariane L. Moore
Snapshot Date: 2021-10-14 04:50:12 -0400 (Thu, 14 Oct 2021)
git_url: https://git.bioconductor.org/packages/GeneAccord
git_branch: RELEASE_3_13
git_last_commit: cfc8768
git_last_commit_date: 2021-05-19 12:37:11 -0400 (Wed, 19 May 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: GeneAccord
Version: 1.10.0
Command: /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:GeneAccord.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings GeneAccord_1.10.0.tar.gz
StartedAt: 2021-10-14 09:55:47 -0400 (Thu, 14 Oct 2021)
EndedAt: 2021-10-14 09:58:03 -0400 (Thu, 14 Oct 2021)
EllapsedTime: 135.8 seconds
RetCode: 0
Status:   OK  
CheckDir: GeneAccord.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:GeneAccord.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings GeneAccord_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/GeneAccord.Rcheck’
* using R version 4.1.1 (2021-08-10)
* 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 ‘1.10.0’
* 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  8.9Mb
  sub-directories of 1Mb or more:
    data      2.7Mb
    extdata   5.9Mb
* 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 LazyData ... 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-3.13-bioc/meat/GeneAccord.Rcheck/00check.log’
for details.



Installation output

GeneAccord.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL GeneAccord
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.13-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 4.1.1 (2021-08-10) -- "Kick Things"
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 (15)

[ FAIL 0 | WARN 1 | SKIP 15 | PASS 27 ]
> 
> 
> proc.time()
   user  system elapsed 
 13.962   1.007  14.954 

Example timings

GeneAccord.Rcheck/GeneAccord-Ex.timings

nameusersystemelapsed
GeneAccord1.9980.1242.123
build_null_test_statistic1.3290.0511.381
compute_rates_clon_excl0.2010.0070.209
compute_test_stat_avg_rate0.0300.0010.030
convert_ensembl_to_reactome_pw_tbl0.3280.0270.356
create_ensembl_gene_tbl_hg000
create_tbl_ent_clones0.0390.0030.043
create_tbl_tree_collection0.3510.0070.362
ecdf_lr_test_clon_excl_avg_rate0.5800.0040.585
ensembl_to_hgnc0.0000.0000.001
ensembl_to_reactome0.020.000.02
extract_num_clones_tbl0.0160.0000.017
generate_ecdf_test_stat0.4820.0070.489
generate_test_stat_hist0.6400.0200.659
get_hist_clon_excl0.5540.0170.570
get_hist_clon_excl_this_pat_this_pair0.0220.0030.025
get_rate_diff_branch_ent_pair0.3700.0030.374
heatmap_clones_gene_pat0.5400.0120.551
hgnc_to_ensembl000
is_diff_branch_ent_pair0.0130.0000.013
map_pairs_to_hgnc_symbols0.0000.0000.001
merge_clones_identical_ents0.0480.0000.049
pairs_in_patients_hist0.0490.0000.050
plot_ecdf_test_stat0.1900.0040.193
plot_rates_clon_excl0.1870.0000.187
take_pairs_and_get_patients0.210.000.21
vis_pval_distr_num_pat0.030.000.03
write_res_pairs_to_disk0.0040.0030.008