Back to Multiple platform build/check report for BioC 3.13 |
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This page was generated on 2021-10-15 15:06:45 -0400 (Fri, 15 Oct 2021).
To the developers/maintainers of the OmnipathR package: - Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/OmnipathR.git to reflect on this report. See How and When does the builder pull? When will my changes propagate? here for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
Package 1304/2041 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
OmnipathR 3.0.4 (landing page) Denes Turei
| nebbiolo1 | Linux (Ubuntu 20.04.2 LTS) / x86_64 | OK | OK | ERROR | |||||||||
tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | ERROR | OK | |||||||||
machv2 | macOS 10.14.6 Mojave / x86_64 | OK | OK | ERROR | OK | |||||||||
Package: OmnipathR |
Version: 3.0.4 |
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_3.0.4.tar.gz |
StartedAt: 2021-10-14 21:54:32 -0400 (Thu, 14 Oct 2021) |
EndedAt: 2021-10-14 22:08:04 -0400 (Thu, 14 Oct 2021) |
EllapsedTime: 812.4 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: OmnipathR.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### 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_3.0.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/Users/biocbuild/bbs-3.13-bioc/meat/OmnipathR.Rcheck’ * using R version 4.1.1 (2021-08-10) * 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 ‘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 22:06:49] [SUCCESS] [OmnipathR] Starting to build NicheNet signaling network [2021-10-14 22:06:54] [SUCCESS] [OmnipathR] Loaded 75524 interactions from cache. [2021-10-14 22:07:08] [SUCCESS] [OmnipathR] Harmonizome (maayanlab.cloud): loaded 6013 records from cache [2021-10-14 22:07:08] [SUCCESS] [OmnipathR] Harmonizome (maayanlab.cloud): loaded 12161 records from cache [2021-10-14 22:07:08] [SUCCESS] [OmnipathR] Harmonizome (maayanlab.cloud): loaded 819 records from cache Error in extractor(version$path, list = TRUE) : zip file '/Users/biocbuild/Library/Caches/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 ‘/Users/biocbuild/bbs-3.13-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/4.1/Resources/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)
OmnipathR.Rcheck/tests/testthat.Rout
R version 4.1.1 (2021-08-10) -- "Kick Things" 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 > # 2018-2021 > # 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 22:07:16] [SUCCESS] [OmnipathR] Loaded 11035 protein complexes from cache. [2021-10-14 22:07:19] [SUCCESS] [OmnipathR] Loaded 18486 enzyme-substrate relationships from cache. [2021-10-14 22:07:21] [SUCCESS] [OmnipathR] Loaded 16675 intercellular communication role records from cache. [2021-10-14 22:07:23] [SUCCESS] [OmnipathR] Loaded 47338 annotation records from cache. [2021-10-14 22:07:25] [SUCCESS] [OmnipathR] Loaded 2877 interactions from cache. [2021-10-14 22:07:27] [SUCCESS] [OmnipathR] Loaded 1343 interactions from cache. [2021-10-14 22:07:28] [SUCCESS] [OmnipathR] Loaded 2293 interactions from cache. [2021-10-14 22:07:30] [SUCCESS] [OmnipathR] Loaded 88 interactions from cache. [2021-10-14 22:07:31] [SUCCESS] [OmnipathR] Loaded 3006 interactions from cache. [2021-10-14 22:07:35] [SUCCESS] [OmnipathR] Loaded 41919 interactions from cache. [2021-10-14 22:07:38] [SUCCESS] [OmnipathR] Loaded 4960 interactions from cache. [2021-10-14 22:07:39] [SUCCESS] [OmnipathR] Loaded 8235 interactions from cache. [ FAIL 0 | WARN 0 | SKIP 0 | PASS 37 ] > > proc.time() user system elapsed 12.053 0.662 30.455
OmnipathR.Rcheck/OmnipathR-Ex.timings
name | user | system | elapsed | |
OmnipathR | 0 | 0 | 0 | |
all_uniprots | 0.290 | 0.012 | 0.302 | |
ancestors | 8.326 | 0.359 | 8.700 | |
annotated_network | 0.392 | 0.014 | 1.603 | |
annotation_categories | 30.622 | 0.047 | 30.696 | |
bioplex1 | 0.100 | 0.005 | 0.106 | |
bioplex2 | 0.174 | 0.005 | 0.181 | |
bioplex3 | 0.296 | 0.009 | 0.305 | |
bioplex_all | 26.753 | 1.131 | 27.905 | |
bioplex_hct116_1 | 0.264 | 0.004 | 0.268 | |
bma_motif_es | 0.143 | 0.004 | 0.729 | |
bma_motif_vs | 0.164 | 0.005 | 0.789 | |
consensuspathdb_download | 31.546 | 1.903 | 33.491 | |
consensuspathdb_raw_table | 1.186 | 0.010 | 1.197 | |
descendants | 1.514 | 0.045 | 1.564 | |
enzsub_graph | 1.558 | 0.021 | 2.165 | |
evex_download | 83.212 | 3.027 | 81.471 | |
filter_by_resource | 2.199 | 0.014 | 2.214 | |
filter_intercell_network | 32.683 | 0.707 | 33.433 | |
find_all_paths | 4.581 | 0.229 | 4.813 | |
get_annotation_resources | 0.054 | 0.002 | 0.641 | |
get_complex_genes | 0.637 | 0.005 | 0.644 | |
get_complex_resources | 0.070 | 0.003 | 0.653 | |
get_db | 0.143 | 0.003 | 0.188 | |
get_enzsub_resources | 0.075 | 0.003 | 0.678 | |
get_interaction_resources | 0.085 | 0.005 | 0.727 | |
get_intercell_categories | 0.032 | 0.014 | 0.045 | |
get_intercell_generic_categories | 0.027 | 0.003 | 0.029 | |
get_intercell_resources | 0.089 | 0.003 | 0.672 | |
get_ontology_db | 0.707 | 0.003 | 0.711 | |
get_resources | 0.086 | 0.004 | 0.688 | |
get_signed_ptms | 1.987 | 0.008 | 2.577 | |
giant_component | 4.416 | 0.028 | 4.449 | |
go_annot_download | 4.323 | 0.092 | 4.418 | |
go_annot_slim | 0 | 0 | 0 | |
go_ontology_download | 0.127 | 0.001 | 0.129 | |
guide2pharma_download | 0.868 | 0.037 | 0.906 | |
harmonizome_download | 0.098 | 0.006 | 0.104 | |
hpo_download | 1.475 | 0.016 | 1.492 | |
htridb_download | 0.116 | 0.002 | 0.119 | |
import_all_interactions | 0.769 | 0.007 | 1.804 | |
import_dorothea_interactions | 0.992 | 0.006 | 1.583 | |
import_intercell_network | 3.606 | 0.023 | 3.631 | |
import_kinaseextra_interactions | 0.673 | 0.006 | 1.261 | |
import_ligrecextra_interactions | 0.278 | 0.005 | 0.864 | |
import_lncrna_mrna_interactions | 0.122 | 0.004 | 0.709 | |
import_mirnatarget_interactions | 0.253 | 0.006 | 0.884 | |
import_omnipath_annotations | 0.099 | 0.005 | 0.685 | |
import_omnipath_complexes | 0.293 | 0.039 | 0.915 | |
import_omnipath_enzsub | 0.559 | 0.004 | 1.145 | |
import_omnipath_interactions | 0.226 | 0.004 | 0.811 | |
import_omnipath_intercell | 0.069 | 0.002 | 0.071 | |
import_pathwayextra_interactions | 0.203 | 0.004 | 0.790 | |
import_post_translational_interactions | 0.198 | 0.004 | 0.785 | |
import_tf_mirna_interactions | 0.223 | 0.004 | 0.809 | |
import_tf_target_interactions | 0.606 | 0.005 | 1.194 | |
import_transcriptional_interactions | 1.052 | 0.006 | 1.639 | |
inbiomap_download | 0.000 | 0.000 | 0.001 | |
inbiomap_raw | 0.000 | 0.000 | 0.001 | |
interaction_graph | 0.409 | 0.005 | 0.992 | |
intercell_categories | 0.039 | 0.002 | 0.041 | |
intercell_consensus_filter | 0.521 | 0.020 | 0.541 | |
is_ontology_id | 0.001 | 0.000 | 0.001 | |
kegg_info | 0.059 | 0.003 | 0.063 | |
kegg_open | 0.003 | 0.003 | 0.007 | |
kegg_pathway_download | 0.000 | 0.001 | 0.001 | |
kegg_pathway_list | 0.426 | 0.003 | 0.430 | |
kegg_pathways_download | 0 | 0 | 0 | |
kegg_picture | 0.256 | 0.017 | 1.409 | |
kegg_process | 0.001 | 0.001 | 0.001 | |
load_db | 0.223 | 0.003 | 0.226 | |
nichenet_build_model | 3.053 | 0.047 | 3.101 | |
nichenet_expression_data | 2.821 | 0.024 | 2.847 | |
nichenet_gr_network | 5.501 | 0.331 | 5.835 | |
nichenet_gr_network_evex | 87.095 | 2.682 | 84.443 | |
nichenet_gr_network_harmonizome | 4.735 | 0.517 | 5.150 | |
nichenet_gr_network_htridb | 0.060 | 0.002 | 0.061 | |
nichenet_gr_network_omnipath | 6.085 | 0.565 | 6.654 | |
nichenet_gr_network_pathwaycommons | 3.506 | 0.046 | 3.556 | |
nichenet_gr_network_regnetwork | 2.583 | 0.436 | 2.880 | |
nichenet_gr_network_remap | 0.000 | 0.000 | 0.001 | |
nichenet_gr_network_trrust | 0.205 | 0.007 | 0.213 | |
nichenet_ligand_activities | 0.000 | 0.001 | 0.001 | |
nichenet_ligand_target_links | 0.000 | 0.001 | 0.001 | |
nichenet_ligand_target_matrix | 0.000 | 0.001 | 0.001 | |
nichenet_lr_network | 117.320 | 1.347 | 130.622 | |
nichenet_lr_network_guide2pharma | 0.595 | 0.034 | 0.629 | |
nichenet_lr_network_omnipath | 43.525 | 0.477 | 45.835 | |
nichenet_lr_network_ramilowski | 0.152 | 0.009 | 0.162 | |
nichenet_main | 0.000 | 0.001 | 0.000 | |
nichenet_networks | 55.830 | 1.203 | 68.878 | |
nichenet_optimization | 0.000 | 0.001 | 0.000 | |
nichenet_remove_orphan_ligands | 34.474 | 0.418 | 35.877 | |
nichenet_results_dir | 0.000 | 0.000 | 0.001 | |