Back to Multiple platform build/check report for BioC 3.12 |
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This page was generated on 2021-05-06 12:36:01 -0400 (Thu, 06 May 2021).
To the developers/maintainers of the OmnipathR package: Please make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1260/1974 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
OmnipathR 2.0.0 (landing page) Denes Turei
| malbec1 | Linux (Ubuntu 18.04.5 LTS) / x86_64 | OK | OK | OK | |||||||||
tokay1 | Windows Server 2012 R2 Standard / x64 | OK | OK | OK | OK | |||||||||
merida1 | macOS 10.14.6 Mojave / x86_64 | OK | OK | OK | OK | |||||||||
Package: OmnipathR |
Version: 2.0.0 |
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_2.0.0.tar.gz |
StartedAt: 2021-05-06 04:22:40 -0400 (Thu, 06 May 2021) |
EndedAt: 2021-05-06 04:25:38 -0400 (Thu, 06 May 2021) |
EllapsedTime: 178.3 seconds |
RetCode: 0 |
Status: OK |
CheckDir: OmnipathR.Rcheck |
Warnings: 0 |
############################################################################## ############################################################################## ### ### Running 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_2.0.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.12-bioc/meat/OmnipathR.Rcheck’ * using R version 4.0.5 (2021-03-31) * using platform: x86_64-apple-darwin17.0 (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 ‘2.0.0’ * 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 ‘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 ... NOTE pivot_annotations: no visible binding for global variable ‘record_id’ Undefined global functions or variables: record_id * 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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed OmnipathR 7.685 0.353 11.422 get_signed_ptms 4.331 0.065 7.336 import_intercell_network 3.905 0.054 7.177 print_path_vs 2.138 0.037 5.392 * 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-3.12-bioc/meat/OmnipathR.Rcheck/00check.log’ for details.
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/4.0/Resources/library’ * installing *source* package ‘OmnipathR’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading Note: wrong number of arguments to '>' ** help *** installing help indices *** copying figures ** 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 4.0.5 (2021-03-31) -- "Shake and Throw" Copyright (C) 2021 The R Foundation for Statistical Computing Platform: x86_64-apple-darwin17.0 (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. > #!/usr/bin/env Rscript > > # > # This file is part of the `OmnipathR` R package > # > # Copyright > # 2018-2020 > # Saez Lab, Uniklinik RWTH Aachen, Heidelberg University > # > # File author(s): Alberto Valdeolivas > # Dénes Türei (turei.denes@gmail.com) > # Attila Gábor > # > # Distributed under the MIT (Expat) License. > # See accompanying file `LICENSE` or find a copy at > # https://directory.fsf.org/wiki/License:Expat > # > # Website: https://saezlab.github.io/omnipathr > # Git repo: https://github.com/saezlab/OmnipathR > # > > > 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 Loading required package: jsonlite > > test_check("OmnipathR") [ FAIL 0 | WARN 0 | SKIP 0 | PASS 24 ] > > proc.time() user system elapsed 12.595 0.623 39.821
OmnipathR.Rcheck/OmnipathR-Ex.timings
name | user | system | elapsed | |
OmnipathR | 7.685 | 0.353 | 11.422 | |
get_annotation_resources | 0.055 | 0.002 | 0.593 | |
get_complex_genes | 0.614 | 0.016 | 1.759 | |
get_complex_resources | 0.055 | 0.003 | 0.595 | |
get_enzsub_resources | 0.065 | 0.003 | 0.604 | |
get_interaction_resources | 0.090 | 0.010 | 0.637 | |
get_intercell_categories | 0.031 | 0.017 | 0.604 | |
get_intercell_generic_categories | 0.016 | 0.002 | 0.610 | |
get_intercell_resources | 0.076 | 0.004 | 0.615 | |
get_resources | 0.079 | 0.006 | 0.621 | |
get_signed_ptms | 4.331 | 0.065 | 7.336 | |
import_all_interactions | 1.406 | 0.029 | 3.510 | |
import_dorothea_interactions | 0.186 | 0.005 | 1.577 | |
import_intercell_network | 3.905 | 0.054 | 7.177 | |
import_kinaseextra_interactions | 0.998 | 0.021 | 2.712 | |
import_ligrecextra_interactions | 0.309 | 0.008 | 1.904 | |
import_lncrna_mrna_interactions | 0.094 | 0.004 | 1.097 | |
import_mirnatarget_interactions | 0.476 | 0.010 | 1.968 | |
import_omnipath_annotations | 0.075 | 0.004 | 1.085 | |
import_omnipath_complexes | 0.140 | 0.006 | 1.685 | |
import_omnipath_enzsub | 0.973 | 0.018 | 2.678 | |
import_omnipath_interactions | 0.274 | 0.008 | 1.873 | |
import_omnipath_intercell | 0.045 | 0.004 | 0.931 | |
import_pathwayextra_interactions | 0.318 | 0.009 | 1.892 | |
import_post_translational_interactions | 0.323 | 0.008 | 1.904 | |
import_tf_mirna_interactions | 0.247 | 0.005 | 1.686 | |
import_tf_target_interactions | 0.105 | 0.004 | 1.193 | |
import_transcriptional_interactions | 0.462 | 0.010 | 3.292 | |
interaction_graph | 0.458 | 0.010 | 1.965 | |
print_interactions | 2.138 | 0.030 | 3.356 | |
print_path_es | 0.467 | 0.008 | 2.009 | |
print_path_vs | 2.138 | 0.037 | 5.392 | |
ptms_graph | 1.773 | 0.022 | 3.485 | |