Package: GeneAccord

Version: 1.0.0

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_1.0.0.tar.gz

StartedAt: 2019-04-16 00:06:39 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 00:09:06 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 147.1 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_1.0.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/GeneAccord.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.0.0’
* 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-3.8-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/3.5/Resources/library’
* installing *source* package ‘GeneAccord’ ...
** 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
* DONE (GeneAccord)

R version 3.5.3 (2019-03-11) -- "Great Truth"
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 FAILED: 0
> 
> 
> proc.time()
   user  system elapsed 
 18.515   0.373  18.941 

name	user	system	elapsed
GeneAccord	2.141	0.033	2.200
build_null_test_statistic	4.041	0.006	4.107
compute_rates_clon_excl	0.158	0.000	0.162
compute_test_stat_avg_rate	0.076	0.000	0.078
convert_ensembl_to_reactome_pw_tbl	0.330	0.013	0.349
create_ensembl_gene_tbl_hg	0	0	0
create_tbl_ent_clones	0.201	0.003	0.208
create_tbl_tree_collection	0.411	0.006	0.426
ecdf_lr_test_clon_excl_avg_rate	0.903	0.003	0.921
ensembl_to_hgnc	0.000	0.000	0.001
ensembl_to_reactome	0.024	0.004	0.028
extract_num_clones_tbl	0.017	0.000	0.018
generate_ecdf_test_stat	0.811	0.026	0.840
generate_test_stat_hist	1.192	0.003	1.203
get_hist_clon_excl	0.424	0.001	0.428
get_hist_clon_excl_this_pat_this_pair	0.014	0.000	0.015
get_rate_diff_branch_ent_pair	0.252	0.002	0.256
heatmap_clones_gene_pat	0.904	0.007	0.918
hgnc_to_ensembl	0	0	0
is_diff_branch_ent_pair	0.007	0.001	0.007
map_pairs_to_hgnc_symbols	0	0	0
merge_clones_identical_ents	0.088	0.001	0.089
pairs_in_patients_hist	0.051	0.001	0.051
plot_ecdf_test_stat	0.604	0.002	0.612
plot_rates_clon_excl	0.253	0.001	0.255
take_pairs_and_get_patients	0.157	0.001	0.160
vis_pval_distr_num_pat	0.022	0.001	0.024
write_res_pairs_to_disk	0.010	0.001	0.010