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This page was generated on 2023-04-12 11:05:13 -0400 (Wed, 12 Apr 2023).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.5 LTS)x86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4502
palomino4Windows Server 2022 Datacenterx644.2.3 (2023-03-15 ucrt) -- "Shortstop Beagle" 4282
lconwaymacOS 12.5.1 Montereyx86_644.2.3 (2023-03-15) -- "Shortstop Beagle" 4310
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

CHECK results for OmnipathR on nebbiolo2


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? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1393/2183HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OmnipathR 3.6.6  (landing page)
Denes Turei
Snapshot Date: 2023-04-10 14:00:05 -0400 (Mon, 10 Apr 2023)
git_url: https://git.bioconductor.org/packages/OmnipathR
git_branch: RELEASE_3_16
git_last_commit: 27bb65f
git_last_commit_date: 2023-03-21 11:32:02 -0400 (Tue, 21 Mar 2023)
nebbiolo2Linux (Ubuntu 20.04.5 LTS) / x86_64  OK    OK    TIMEOUT  
palomino4Windows Server 2022 Datacenter / x64  OK    OK    TIMEOUT    OK  
lconwaymacOS 12.5.1 Monterey / x86_64  OK    OK    TIMEOUT    OK  

Summary

Package: OmnipathR
Version: 3.6.6
Command: /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings OmnipathR_3.6.6.tar.gz
StartedAt: 2023-04-10 22:28:04 -0400 (Mon, 10 Apr 2023)
EndedAt: 2023-04-10 23:08:04 -0400 (Mon, 10 Apr 2023)
EllapsedTime: 2400.6 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: OmnipathR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.16-bioc/R/site-library --timings OmnipathR_3.6.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.16-bioc/meat/OmnipathR.Rcheck’
* using R version 4.2.3 (2023-03-15)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.6.6’
* 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 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 loading without being on the library search path ... 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
[2023-04-10 22:28:29] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-04-10 22:28:29] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-10 22:28:29] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-04-10 22:28:29] [TRACE]   [OmnipathR] Contains 1 files.
[2023-04-10 22:28:29] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-10 22:28:29] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-04-10 22:28:29] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-04-10 22:28:29] [TRACE]   [OmnipathR] Cache locked: FALSE
* 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 ...

Installation output

OmnipathR.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.16-bioc/R/bin/R CMD INSTALL OmnipathR
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.16-bioc/R/site-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
[2023-04-10 15:24:11] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-04-10 15:24:11] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-10 15:24:11] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-04-10 15:24:11] [TRACE]   [OmnipathR] Contains 6 files.
[2023-04-10 15:24:11] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-10 15:24:11] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-04-10 15:24:11] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-04-10 15:24:11] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2023-04-10 15:24:12] [INFO]    [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`.
[2023-04-10 15:24:12] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-10 15:24:12] [TRACE]   [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`.
[2023-04-10 15:24:12] [TRACE]   [OmnipathR] Contains 1 files.
[2023-04-10 15:24:12] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-10 15:24:12] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`.
[2023-04-10 15:24:12] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-04-10 15:24:12] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (OmnipathR)

Tests output

Example timings

OmnipathR.Rcheck/OmnipathR-Ex.timings

nameusersystemelapsed
OmnipathR0.0010.0000.000
all_uniprot_acs 0.896 0.06313.570
all_uniprots0.1990.0246.915
ancestors8.7090.3819.822
annotated_network0.8140.1314.167
annotation_categories97.650 0.09199.238
biomart_query0.6130.0333.821
bioplex10.3550.0480.786
bioplex20.8040.0591.276
bioplex31.4090.0782.258
bioplex_all48.129 1.01349.628
bioplex_hct116_10.1460.0000.146
bma_motif_es0.2890.0281.488
bma_motif_vs0.1180.0000.829
common_name0.0340.0000.034
consensuspathdb_download0.0010.0000.000
consensuspathdb_raw_table15.484 0.64643.225
curated_ligand_receptor_interactions 8.863 0.27122.089
curated_ligrec_stats 34.072 1.641117.490
descendants0.8120.0240.836
ensembl_dataset0.0090.0000.009
ensembl_id_mapping_table 1.107 0.09330.680
ensembl_id_type0.0070.0040.011
ensembl_name0.1210.0080.128
ensembl_organisms0.5080.0040.512
ensembl_organisms_raw0.3120.0040.316
ensembl_orthology000
enzsub_graph2.0340.1204.209
evex_download279.347 10.439516.561
extra_attr_values23.033 0.54534.293
extra_attrs13.417 0.07515.776
extra_attrs_to_cols17.542 0.15517.953
filter_by_resource5.3240.0907.874
filter_extra_attrs36.597 0.58544.945
filter_intercell 8.383 0.33715.723
filter_intercell_network295.858 2.556344.116
find_all_paths6.4020.0406.446
get_annotation_resources0.0890.0000.808
get_complex_genes1.0700.0243.329
get_complex_resources0.0680.0040.867
get_db0.4110.0120.523
get_enzsub_resources0.0850.0000.838
get_interaction_resources0.1010.0000.814
get_intercell_categories0.4660.0080.895
get_intercell_generic_categories0.0480.0000.047
get_intercell_resources0.0950.0000.831
get_ontology_db0.6050.0000.834
get_resources0.0940.0000.763
get_signed_ptms10.105 0.04710.955
giant_component11.368 0.20614.252
go_annot_download7.9180.4657.435
go_annot_slim000
go_ontology_download0.0810.0040.086
guide2pharma_download1.5040.1534.556
harmonizome_download0.3710.0200.596
has_extra_attrs20.950 0.67621.654
homologene_download2.7570.1334.417
homologene_raw0.9320.0080.940
homologene_uniprot_orthology 4.793 0.16820.078
homology_translate000
hpo_download2.0180.0775.464
htridb_download1.4060.0426.140
import_all_interactions3.8560.0598.377
import_dorothea_interactions2.6810.0415.068
import_intercell_network26.143 0.33631.813
import_kinaseextra_interactions2.3300.2016.786
import_ligrecextra_interactions0.9890.1023.145
import_lncrna_mrna_interactions1.0320.0532.214
import_mirnatarget_interactions1.9410.0904.168
import_omnipath_annotations0.8560.0652.267
import_omnipath_complexes1.2960.0643.669
import_omnipath_enzsub1.7690.0612.546
import_omnipath_interactions0.3060.0040.950
import_omnipath_intercell1.0760.0372.430
import_pathwayextra_interactions1.4760.1415.091
import_post_translational_interactions1.1020.0703.906
import_small_molecule_protein_interactions1.0920.0322.490
import_tf_mirna_interactions2.2140.1824.052
import_tf_target_interactions2.2810.2034.640
import_transcriptional_interactions3.3430.2686.368
inbiomap_download000
inbiomap_raw000
interaction_graph0.5270.0081.436
intercell_categories0.0780.0040.114
intercell_consensus_filter2.2600.1818.721
is_ontology_id0.0000.0000.001
is_swissprot0.1880.0240.212
is_trembl 1.551 0.10976.518
is_uniprot0.1560.0080.164
kegg_info0.9060.0285.081
kegg_open0.0030.0000.003
kegg_pathway_annotations000
kegg_pathway_download 3.594 0.19715.314
kegg_pathway_list1.1460.0283.460
kegg_pathways_download000
kegg_picture0.1320.0042.298
kegg_process0.2290.0120.241
latin_name0.1130.0040.117
load_db0.3460.0080.355
ncbi_taxid0.0980.0030.101
nichenet_build_model000
nichenet_expression_data0.0010.0000.000
nichenet_gr_network10.311 0.20912.319
nichenet_gr_network_evex223.325 1.717235.290
nichenet_gr_network_harmonizome 4.740 0.25311.244
nichenet_gr_network_htridb0.0580.0000.058
nichenet_gr_network_omnipath6.4160.1938.359
nichenet_gr_network_pathwaycommons5.0450.2865.868
nichenet_gr_network_regnetwork 0.342 0.03610.778
nichenet_gr_network_remap000
nichenet_gr_network_trrust0.4830.0246.300
nichenet_ligand_activities0.0000.0000.001
nichenet_ligand_target_links000
nichenet_ligand_target_matrix000