Package: OmnipathR

Version: 1.1.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings OmnipathR_1.1.2.tar.gz

StartedAt: 2020-01-16 07:07:05 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 07:10:12 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 186.7 seconds

RetCode: 0

Status:  OK

CheckDir: OmnipathR.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:OmnipathR.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings OmnipathR_1.1.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/OmnipathR.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘1.1.2’
* 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 ‘OmnipathR’ 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 R/sysdata.rda ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                           user system elapsed
get_signed_ptms           8.782  0.350  12.864
import_AllInteractions    5.510  0.150   7.486
printPath_vs              5.075  0.133   7.565
OmnipathR                 4.748  0.278  10.184
get_interaction_databases 1.627  0.104   7.277
* 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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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL OmnipathR
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘OmnipathR’ ...
** 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 (OmnipathR)

R Under development (unstable) (2019-12-14 r77572) -- "Unsuffered Consequences"
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(OmnipathR)
Loading required package: igraph

Attaching package: 'igraph'

The following object is masked from 'package:testthat':

    compare

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

> 
> test_check("OmnipathR")
══ testthat results  ═══════════════════════════════════════════════════════════
[ OK: 10 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
> 
> proc.time()
   user  system elapsed 
 20.169   1.068  40.349 

name	user	system	elapsed
OmnipathR	4.748	0.278	10.184
get_annotation_databases	0.044	0.008	0.891
get_complex_genes	0.615	0.019	1.971
get_complexes_databases	0.324	0.017	1.845
get_interaction_databases	1.627	0.104	7.277
get_intercell_categories	0.817	0.081	3.817
get_ptms_databases	0.639	0.029	2.012
get_signed_ptms	8.782	0.350	12.864
import_AllInteractions	5.510	0.150	7.486
import_KinaseExtra_Interactions	0.963	0.045	3.282
import_LigrecExtra_Interactions	0.114	0.005	0.659
import_Omnipath_Interactions	2.153	0.090	3.459
import_Omnipath_PTMS	1.692	0.036	2.934
import_Omnipath_annotations	0.033	0.005	0.585
import_Omnipath_complexes	0.671	0.019	1.785
import_Omnipath_intercell	0.794	0.057	2.498
import_PathwayExtra_Interactions	1.754	0.066	4.837
import_TFregulons_Interactions	0.348	0.010	1.133
import_miRNAtarget_Interactions	0.369	0.007	0.973
interaction_graph	2.536	0.066	3.870
printPath_es	2.821	0.064	4.410
printPath_vs	5.075	0.133	7.565
print_interactions	2.548	0.083	4.894
ptms_graph	1.879	0.064	3.336