Package: nanotatoR

Version: 1.0.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:nanotatoR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings nanotatoR_1.0.0.tar.gz

StartedAt: 2019-10-16 03:29:33 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:33:31 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 237.2 seconds

RetCode: 0

Status:  OK

CheckDir: nanotatoR.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:nanotatoR.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings nanotatoR_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/nanotatoR.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘nanotatoR/DESCRIPTION’ ... OK
* this is package ‘nanotatoR’ 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 ‘nanotatoR’ can be installed ... OK
* checking installed package size ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
gene_list_generation 3.21  0.027   7.045
* 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: OK

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL nanotatoR
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘nanotatoR’ ...
** using staged installation
** R
** 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 (nanotatoR)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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(nanotatoR)

> 
> test_check("nanotatoR")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 11.449   0.436  12.612 

name	user	system	elapsed
DGV_extraction	0.001	0.000	0.000
Decipher_extraction	0.57	0.04	0.63
buildrunBNBedFiles	0.129	0.000	0.158
clinvar_gene	3.162	0.112	4.682
cohortFrequency	0.464	0.000	0.484
compSmapbed	0.561	0.015	0.808
gene_extraction	0.331	0.009	0.760
gene_list_generation	3.210	0.027	7.045
gtr_gene	0.246	0.000	0.663
internalFrequency	0.896	0.008	0.915
makeMergedSVData	0.230	0.000	0.735
makeMergedSmapData	0.002	0.000	0.002
nanotatoR	0.001	0.000	0.001
nonOverlapGenes	0.548	0.008	0.630
omim_gene	0.279	0.000	1.041
overlapGenes	0.556	0.004	0.641
readBNBedFiles	0.006	0.000	0.007
readSMap	0.053	0.020	0.073
run_bionano_filter	0	0	0