Alberto Valdeolivas Urbelz
| Snapshot Date: 2020-04-14 16:46:13 -0400 (Tue, 14 Apr 2020) |
| URL: https://git.bioconductor.org/packages/OmnipathR |
| Branch: RELEASE_3_10 |
| Last Commit: f0dd8eb |
| Last Changed Date: 2020-03-26 13:20:23 -0400 (Thu, 26 Mar 2020) |
| Back to Multiple platform build/check report for BioC 3.10 |
|
This page was generated on 2020-04-15 12:50:17 -0400 (Wed, 15 Apr 2020).
| Package 1184/1823 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||
| OmnipathR 1.0.1 Alberto Valdeolivas Urbelz
| malbec1 | Linux (Ubuntu 18.04.4 LTS) / x86_64 | OK | OK | OK | | ||||||
| tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||
| merida1 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | [ OK ] | OK | |
| Package: OmnipathR |
| Version: 1.0.1 |
| 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_1.0.1.tar.gz |
| StartedAt: 2020-04-15 04:20:43 -0400 (Wed, 15 Apr 2020) |
| EndedAt: 2020-04-15 04:24:02 -0400 (Wed, 15 Apr 2020) |
| EllapsedTime: 199.1 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_1.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/OmnipathR.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘1.0.1’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
get_signed_ptms 6.475 0.169 13.738
printPath_vs 4.321 0.075 9.152
OmnipathR 3.893 0.134 7.651
print_interactions 3.878 0.060 7.939
import_AllInteractions 3.410 0.075 7.114
get_intercell_categories 1.672 0.084 7.253
import_Omnipath_intercell 1.399 0.077 7.107
* 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
OmnipathR.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL OmnipathR ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/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)
OmnipathR.Rcheck/tests/testthat.Rout
R version 3.6.3 (2020-02-29) -- "Holding the Windsock"
Copyright (C) 2020 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: 9 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 0 ]
>
> proc.time()
user system elapsed
17.207 0.646 54.313
OmnipathR.Rcheck/OmnipathR-Ex.timings
| name | user | system | elapsed | |
| OmnipathR | 3.893 | 0.134 | 7.651 | |
| get_annotation_databases | 0.040 | 0.005 | 0.886 | |
| get_complex_genes | 0.708 | 0.028 | 2.107 | |
| get_complexes_databases | 0.284 | 0.012 | 1.919 | |
| get_interaction_databases | 1.359 | 0.043 | 3.412 | |
| get_intercell_categories | 1.672 | 0.084 | 7.253 | |
| get_ptms_databases | 0.681 | 0.024 | 2.273 | |
| get_signed_ptms | 6.475 | 0.169 | 13.738 | |
| import_AllInteractions | 3.410 | 0.075 | 7.114 | |
| import_KinaseExtra_Interactions | 0.700 | 0.019 | 1.785 | |
| import_LigrecExtra_Interactions | 0.144 | 0.004 | 0.830 | |
| import_Omnipath_Interactions | 1.611 | 0.030 | 4.105 | |
| import_Omnipath_PTMS | 1.619 | 0.032 | 3.677 | |
| import_Omnipath_annotations | 0.034 | 0.003 | 0.635 | |
| import_Omnipath_complexes | 0.595 | 0.016 | 2.155 | |
| import_Omnipath_intercell | 1.399 | 0.077 | 7.107 | |
| import_PathwayExtra_Interactions | 0.748 | 0.030 | 2.076 | |
| import_TFregulons_Interactions | 0.438 | 0.005 | 1.400 | |
| import_miRNAtarget_Interactions | 0.286 | 0.007 | 1.049 | |
| interaction_graph | 1.833 | 0.041 | 4.456 | |
| printPath_es | 1.932 | 0.044 | 4.715 | |
| printPath_vs | 4.321 | 0.075 | 9.152 | |
| print_interactions | 3.878 | 0.060 | 7.939 | |
| ptms_graph | 2.285 | 0.031 | 4.654 | |