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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.13-bioc/R/library --no-vignettes --timings OmnipathR_3.0.4.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.13-bioc/meat/OmnipathR.Rcheck’
* using R version 4.1.1 (2021-08-10)
* using platform: x86_64-pc-linux-gnu (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 ‘3.0.4’
* 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 files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OmnipathR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: nichenet_signaling_network
> ### Title: Builds a NicheNet signaling network
> ### Aliases: nichenet_signaling_network
> 
> ### ** Examples
> 
> # load everything with the default parameters:
> # we don't load inBio Map due to the - hopefully
> # temporary - issues of their server
> sig_network <- nichenet_signaling_network(inbiomap = NULL)
[2021-10-14 11:01:07] [SUCCESS] [OmnipathR] Starting to build NicheNet signaling network
[2021-10-14 11:01:09] [SUCCESS] [OmnipathR] Loaded 75524 interactions from cache.
[2021-10-14 11:01:14] [SUCCESS] [OmnipathR] Harmonizome (maayanlab.cloud): loaded 6013 records from cache
[2021-10-14 11:01:14] [SUCCESS] [OmnipathR] Harmonizome (maayanlab.cloud): loaded 12161 records from cache
[2021-10-14 11:01:14] [SUCCESS] [OmnipathR] Harmonizome (maayanlab.cloud): loaded 819 records from cache
Error in extractor(version$path, list = TRUE) : 
  zip file '/var/cache/biocbuild_cache/OmnipathR/4943bf5eda7fdb771649a2148f63ecd4355cc539-1.zip' cannot be opened
Calls: nichenet_signaling_network ... archive_extractor -> archive_downloader -> extractor
Execution halted
* 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 ERROR
See
  ‘/home/biocbuild/bbs-3.13-bioc/meat/OmnipathR.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.13-bioc/R/bin/R CMD INSTALL OmnipathR
###
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* installing to library ‘/home/biocbuild/bbs-3.13-bioc/R/library’
* installing *source* package ‘OmnipathR’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** 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)

R version 4.1.1 (2021-08-10) -- "Kick Things"
Copyright (C) 2021 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.

> #!/usr/bin/env Rscript
> 
> #
> #  This file is part of the `OmnipathR` R package
> #
> #  Copyright
> #  2018-2021
> #  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)
> 
> test_check('OmnipathR')
[2021-10-14 11:01:19] [SUCCESS] [OmnipathR] Loaded 11035 protein complexes from cache.
[2021-10-14 11:01:21] [SUCCESS] [OmnipathR] Loaded 18486 enzyme-substrate relationships from cache.
[2021-10-14 11:01:22] [SUCCESS] [OmnipathR] Loaded 16675 intercellular communication role records from cache.
[2021-10-14 11:01:24] [SUCCESS] [OmnipathR] Loaded 47338 annotation records from cache.
[2021-10-14 11:01:25] [SUCCESS] [OmnipathR] Loaded 2877 interactions from cache.
[2021-10-14 11:01:26] [SUCCESS] [OmnipathR] Loaded 1343 interactions from cache.
[2021-10-14 11:01:28] [SUCCESS] [OmnipathR] Loaded 2293 interactions from cache.
[2021-10-14 11:01:29] [SUCCESS] [OmnipathR] Loaded 88 interactions from cache.
[2021-10-14 11:01:30] [SUCCESS] [OmnipathR] Loaded 3006 interactions from cache.
[2021-10-14 11:01:32] [SUCCESS] [OmnipathR] Loaded 41919 interactions from cache.
[2021-10-14 11:01:34] [SUCCESS] [OmnipathR] Loaded 4960 interactions from cache.
[2021-10-14 11:01:36] [SUCCESS] [OmnipathR] Loaded 8235 interactions from cache.
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 37 ]
> 
> proc.time()
   user  system elapsed 
  6.858   0.332  21.437