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This page was generated on 2023-04-12 11:05:44 -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 palomino4


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: F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OmnipathR.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings OmnipathR_3.6.6.tar.gz
StartedAt: 2023-04-11 04:07:34 -0400 (Tue, 11 Apr 2023)
EndedAt: 2023-04-11 04:47:35 -0400 (Tue, 11 Apr 2023)
EllapsedTime: 2400.7 seconds
RetCode: None
Status:   TIMEOUT  
CheckDir: OmnipathR.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OmnipathR.install-out.txt --library=F:\biocbuild\bbs-3.16-bioc\R\library --no-vignettes --timings OmnipathR_3.6.6.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'F:/biocbuild/bbs-3.16-bioc/meat/OmnipathR.Rcheck'
* using R version 4.2.3 (2023-03-15 ucrt)
* using platform: x86_64-w64-mingw32 (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 '3.6.6'
* 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 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 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
[2023-04-11 04:08:04] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2023-04-11 04:08:04] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-11 04:08:04] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2023-04-11 04:08:04] [TRACE]   [OmnipathR] Contains 1 files.
[2023-04-11 04:08:04] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-11 04:08:04] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2023-04-11 04:08:05] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-04-11 04:08:05] [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:
###
###   F:\biocbuild\bbs-3.16-bioc\R\bin\R.exe CMD INSTALL OmnipathR
###
##############################################################################
##############################################################################


* installing to library 'F:/biocbuild/bbs-3.16-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
[2023-04-10 16:04:57] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2023-04-10 16:04:57] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-10 16:04:57] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2023-04-10 16:04:57] [TRACE]   [OmnipathR] Contains 1 files.
[2023-04-10 16:04:57] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-10 16:04:57] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2023-04-10 16:04:57] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-04-10 16:04:57] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2023-04-10 16:04:59] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2023-04-10 16:04:59] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2023-04-10 16:04:59] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2023-04-10 16:04:59] [TRACE]   [OmnipathR] Contains 1 files.
[2023-04-10 16:04:59] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2023-04-10 16:04:59] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2023-04-10 16:04:59] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2023-04-10 16:04:59] [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
OmnipathR000
all_uniprot_acs 0.99 0.1612.42
all_uniprots0.140.097.44
ancestors8.910.389.56
annotated_network0.550.062.75
annotation_categories106.31 0.02107.08
biomart_query0.750.084.17
bioplex10.350.070.72
bioplex20.830.101.22
bioplex31.090.152.17
bioplex_all51.00 0.3652.08
bioplex_hct116_10.150.030.17
bma_motif_es0.250.071.16
bma_motif_vs0.150.000.61
common_name0.030.000.03
consensuspathdb_download000
consensuspathdb_raw_table14.39 0.4315.17
curated_ligand_receptor_interactions 5.51 0.3812.94
curated_ligrec_stats22.36 1.1977.37
descendants0.790.030.81
ensembl_dataset0.010.000.02
ensembl_id_mapping_table 0.75 0.0829.01
ensembl_id_type000
ensembl_name0.080.000.08
ensembl_organisms0.190.000.25
ensembl_organisms_raw0.170.010.19
ensembl_orthology000
enzsub_graph1.550.102.81
evex_download155.17 0.81164.36
extra_attr_values21.56 0.2222.31
extra_attrs17.84 0.0518.42
extra_attrs_to_cols11.85 0.0611.91
filter_by_resource5.200.145.89
filter_extra_attrs20.31 0.1621.01
filter_intercell5.600.376.02
filter_intercell_network202.86 0.96207.58
find_all_paths5.570.345.92
get_annotation_resources0.040.020.58
get_complex_genes1.140.042.03
get_complex_resources0.040.000.52
get_db0.360.070.45
get_enzsub_resources0.050.010.59
get_interaction_resources0.030.020.60
get_intercell_categories0.500.010.84
get_intercell_generic_categories0.030.020.05
get_intercell_resources0.030.000.57
get_ontology_db0.140.000.15
get_resources0.070.000.51
get_signed_ptms4.150.054.75
giant_component7.940.258.83
go_annot_download7.970.537.36
go_annot_slim000
go_ontology_download0.080.000.08
guide2pharma_download2.030.123.29
harmonizome_download0.360.000.46
has_extra_attrs12.64 0.0612.70
homologene_download2.450.162.59
homologene_raw0.880.020.89
homologene_uniprot_orthology 3.92 0.1715.77
homology_translate000
hpo_download1.590.081.83
htridb_download0.700.111.69
import_all_interactions1.970.063.59
import_dorothea_interactions2.580.043.69
import_intercell_network21.86 0.1523.79
import_kinaseextra_interactions1.780.063.02
import_ligrecextra_interactions0.990.041.98
import_lncrna_mrna_interactions0.530.021.36
import_mirnatarget_interactions1.220.032.30
import_omnipath_annotations0.620.031.48
import_omnipath_complexes0.520.071.66
import_omnipath_enzsub1.330.001.78
import_omnipath_interactions0.250.000.80
import_omnipath_intercell0.650.041.17
import_pathwayextra_interactions0.830.042.04
import_post_translational_interactions0.810.102.06
import_small_molecule_protein_interactions1.510.091.94
import_tf_mirna_interactions0.500.101.51
import_tf_target_interactions1.250.072.44
import_transcriptional_interactions1.880.073.10
inbiomap_download000
inbiomap_raw000
interaction_graph0.370.030.85
intercell_categories0.070.000.07
intercell_consensus_filter1.580.092.25
is_ontology_id000
is_swissprot0.090.020.11
is_trembl 0.74 0.0418.17
is_uniprot0.200.000.21
kegg_info0.530.052.78
kegg_open000
kegg_pathway_annotations000
kegg_pathway_download1.710.179.36
kegg_pathway_list0.460.001.32
kegg_pathways_download000
kegg_picture0.110.001.12
kegg_process0.210.000.20
latin_name0.040.020.06
load_db0.180.000.17
ncbi_taxid0.060.000.05
nichenet_build_model000
nichenet_expression_data000
nichenet_gr_network5.700.186.50
nichenet_gr_network_evex153.27 0.82154.67
nichenet_gr_network_harmonizome3.230.213.66
nichenet_gr_network_htridb0.040.000.06
nichenet_gr_network_omnipath11.13 0.2115.23
nichenet_gr_network_pathwaycommons5.250.295.08
nichenet_gr_network_regnetwork2.080.142.31
nichenet_gr_network_remap000
nichenet_gr_network_trrust0.590.043.00
nichenet_ligand_activities000
nichenet_ligand_target_links000
nichenet_ligand_target_matrix000
nichenet_lr_network561.42 1.95564.84
nichenet_lr_network_guide2pharma0.450.000.46
nichenet_lr_network_omnipath106.67 0.44111.43
nichenet_lr_network_ramilowski0.080.040.13
nichenet_main000
nichenet_networks192.66 0.67193.83
nichenet_optimization000
nichenet_remove_orphan_ligands000
nichenet_results_dir000
nichenet_signaling_network56.18 1.5262.28
nichenet_signaling_network_cpdb000
nichenet_signaling_network_evex14.96 0.1815.86
nichenet_signaling_network_harmonizome0.150.020.16
nichenet_signaling_network_inbiomap000
nichenet_signaling_network_omnipath8.070.038.09
nichenet_signaling_network_pathwaycommons1.640.021.66
nichenet_signaling_network_vinayagam0.540.070.72
nichenet_test000
nichenet_workarounds000
obo_parser0.100.000.15
omnipath_cache_autoclean000
omnipath_cache_clean0.030.000.04
omnipath_cache_clean_db0.190.040.21
omnipath_cache_download_ready0.730.090.89
omnipath_cache_filter_versions0.060.020.11
omnipath_cache_get0.030.010.05
omnipath_cache_key000
omnipath_cache_latest_or_new0.030.020.04
omnipath_cache_load0.380.001.27
omnipath_cache_move_in0.170.030.26
omnipath_cache_remove0.060.000.11
omnipath_cache_save0.080.030.14
omnipath_cache_search000
omnipath_cache_set_ext0.050.020.09
omnipath_cache_update_status0.030.030.08
omnipath_cache_wipe000
omnipath_get_config_path000
omnipath_load_config000
omnipath_log000
omnipath_logfile000
omnipath_msg0.010.000.02
omnipath_reset_config000
omnipath_save_config000
omnipath_set_cachedir000
omnipath_set_console_loglevel000
omnipath_set_logfile_loglevel000
omnipath_set_loglevel000
omnipath_show_db0.090.000.10
omnipath_unlock_cache_db000
ontology_ensure_id0.020.000.01
ontology_ensure_name000
ontology_name_id0.030.000.03
pathwaycommons_download4.040.414.14
pivot_annotations 9.57 0.5812.21
preppi_download6.360.896.92
preppi_filter6.790.925.69
print_bma_motif_es0.210.011.00
print_bma_motif_vs0.090.000.56
print_interactions4.830.136.75
print_path_es0.420.061.59
print_path_vs1.700.003.42
pubmed_open3.770.114.53
ramilowski_download0.140.081.21
regnetwork_directions0.220.030.39
regnetwork_download0.980.141.05
relations_list_to_table0.050.020.10
relations_table_to_graph0.160.010.18
relations_table_to_list0.070.020.12
remap_dorothea_download0.180.010.47
remap_filtered000
remap_tf_target_download0.000.020.02
resources_colname0.560.051.36