Package: GeneAccord

Version: 1.2.0

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_1.2.0.tar.gz

StartedAt: 2019-10-16 03:02:15 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:05:08 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 172.7 seconds

RetCode: 0

Status:  OK

CheckDir: GeneAccord.Rcheck

Warnings: 0

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### Running command:
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###   /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_1.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/GeneAccord.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘1.2.0’
* 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-3.9-bioc/meat/GeneAccord.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL GeneAccord
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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: 0 | FAILED: 0 ]
> 
> 
> proc.time()
   user  system elapsed 
 17.685   0.862  18.496 

name	user	system	elapsed
GeneAccord	2.249	0.028	2.287
build_null_test_statistic	2.261	0.010	2.272
compute_rates_clon_excl	0.149	0.001	0.151
compute_test_stat_avg_rate	0.032	0.000	0.033
convert_ensembl_to_reactome_pw_tbl	0.331	0.014	0.347
create_ensembl_gene_tbl_hg	0.000	0.000	0.001
create_tbl_ent_clones	0.073	0.001	0.074
create_tbl_tree_collection	0.364	0.009	0.383
ecdf_lr_test_clon_excl_avg_rate	0.583	0.002	0.585
ensembl_to_hgnc	0.000	0.000	0.001
ensembl_to_reactome	0.018	0.004	0.022
extract_num_clones_tbl	0.013	0.001	0.013
generate_ecdf_test_stat	0.659	0.004	0.663
generate_test_stat_hist	0.785	0.004	0.788
get_hist_clon_excl	0.385	0.002	0.387
get_hist_clon_excl_this_pat_this_pair	0.023	0.000	0.024
get_rate_diff_branch_ent_pair	0.344	0.001	0.345
heatmap_clones_gene_pat	0.964	0.013	0.978
hgnc_to_ensembl	0	0	0
is_diff_branch_ent_pair	0.011	0.000	0.011
map_pairs_to_hgnc_symbols	0.001	0.000	0.000
merge_clones_identical_ents	0.066	0.001	0.067
pairs_in_patients_hist	0.055	0.000	0.056
plot_ecdf_test_stat	0.351	0.001	0.352
plot_rates_clon_excl	0.321	0.008	0.330
take_pairs_and_get_patients	0.199	0.001	0.200
vis_pval_distr_num_pat	0.032	0.002	0.035
write_res_pairs_to_disk	0.012	0.001	0.013