############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OmnipathR.install-out.txt --library=F:\biocbuild\bbs-3.15-bioc\R\library --no-vignettes --timings OmnipathR_3.4.7.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.15-bioc/meat/OmnipathR.Rcheck' * using R version 4.2.1 (2022-06-23 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 '3.4.7' * 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 'build' directory ... OK * checking DESCRIPTION meta-information ... NOTE Package listed in more than one of Depends, Imports, Suggests, Enhances: 'rmarkdown' A package should be listed in only one of these fields. * 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 [2022-10-19 02:33:23] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2022-10-19 02:33:23] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2022-10-19 02:33:23] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2022-10-19 02:33:24] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2022-10-19 02:33:24] [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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed nichenet_lr_network 161.09 0.74 163.45 nichenet_networks 67.13 0.58 68.89 filter_intercell_network 64.99 1.57 74.67 simplify_intercell_network 58.19 0.69 61.86 evex_download 58.03 0.84 75.00 nichenet_gr_network_evex 57.24 0.77 58.30 unique_intercell_network 54.85 0.28 55.14 nichenet_signaling_network 37.95 1.48 46.21 nichenet_lr_network_omnipath 37.33 1.17 45.16 annotation_categories 32.28 0.10 33.53 pivot_annotations 25.35 1.44 29.18 bioplex_all 23.72 0.75 25.43 consensuspathdb_raw_table 21.73 1.19 22.88 curated_ligrec_stats 20.11 2.45 84.05 go_annot_download 15.27 1.29 33.68 filter_intercell 12.95 0.68 13.65 nichenet_gr_network_pathwaycommons 9.27 0.61 9.78 filter_extra_attrs 9.80 0.07 10.44 nichenet_gr_network_omnipath 8.86 0.26 10.11 pathwaycommons_download 7.67 0.66 8.19 nichenet_signaling_network_evex 7.78 0.45 8.75 ancestors 7.28 0.53 12.30 preppi_filter 6.76 0.79 6.21 extra_attr_values 7.11 0.22 10.82 preppi_download 6.39 0.93 8.04 extra_attrs_to_cols 6.86 0.07 6.94 nichenet_gr_network 6.31 0.45 7.91 with_extra_attrs 5.75 0.22 7.11 import_intercell_network 4.96 0.57 8.70 curated_ligand_receptor_interactions 4.77 0.67 15.25 nichenet_signaling_network_omnipath 5.23 0.04 5.28 giant_component 4.92 0.26 6.40 kegg_pathway_download 3.44 0.10 21.86 print_interactions 2.40 0.19 5.71 import_transcriptional_interactions 1.67 0.20 9.54 nichenet_gr_network_trrust 1.61 0.03 6.38 all_uniprots 1.52 0.09 14.61 uniprot_full_id_mapping_table 1.21 0.05 13.32 translate_ids 1.16 0.08 13.13 trrust_download 0.95 0.01 5.59 import_omnipath_intercell 0.65 0.17 6.17 uniprot_id_mapping_table 0.54 0.02 5.86 remap_dorothea_download 0.30 0.03 5.58 * 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: 2 NOTEs See 'F:/biocbuild/bbs-3.15-bioc/meat/OmnipathR.Rcheck/00check.log' for details.