############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.17-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:OmnipathR.install-out.txt --library=F:\biocbuild\bbs-3.17-bioc\R\library --no-vignettes --timings OmnipathR_3.7.0.tar.gz ### ############################################################################## ############################################################################## * using log directory 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/OmnipathR.Rcheck' * using R Under development (unstable) (2022-12-25 r83502 ucrt) * using platform: x86_64-w64-mingw32 (64-bit) * R was compiled by gcc.exe (GCC) 10.4.0 GNU Fortran (GCC) 10.4.0 * running under: Windows Server x64 (build 20348) * using session charset: UTF-8 * using option '--no-vignettes' * checking for file 'OmnipathR/DESCRIPTION' ... OK * checking extension type ... Package * this is package 'OmnipathR' version '3.7.0' * 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 ... 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 [2022-12-29 01:59:29] [INFO] [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2022-12-29 01:59:29] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2022-12-29 01:59:29] [TRACE] [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2022-12-29 01:59:29] [TRACE] [OmnipathR] Contains 1 files. [2022-12-29 01:59:29] [TRACE] [OmnipathR] Cache is locked: FALSE. [2022-12-29 01:59:29] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`. [2022-12-29 01:59:29] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2022-12-29 01:59:29] [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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed nichenet_lr_network 136.80 0.79 138.58 nichenet_networks 57.09 0.52 58.30 nichenet_gr_network_evex 49.72 0.81 55.67 simplify_intercell_network 43.89 0.31 45.93 filter_intercell_network 42.18 0.87 45.48 unique_intercell_network 42.12 0.08 42.20 evex_download 37.14 0.57 48.62 nichenet_signaling_network 33.53 1.37 40.45 nichenet_lr_network_omnipath 33.02 0.78 37.98 curated_ligrec_stats 19.35 1.58 75.00 bioplex_all 17.26 0.28 18.19 annotation_categories 17.17 0.00 17.80 consensuspathdb_raw_table 12.03 0.48 12.86 pivot_annotations 9.59 0.59 11.97 nichenet_gr_network 8.09 0.33 9.14 filter_extra_attrs 7.37 0.08 8.00 extra_attr_values 7.22 0.05 7.85 preppi_download 6.19 0.89 7.19 nichenet_signaling_network_omnipath 6.86 0.14 7.00 nichenet_gr_network_omnipath 6.61 0.26 7.45 go_annot_download 6.12 0.55 5.54 preppi_filter 5.92 0.64 4.81 with_extra_attrs 6.34 0.12 7.09 filter_intercell 5.79 0.30 6.42 nichenet_signaling_network_evex 5.49 0.39 6.22 extra_attrs_to_cols 5.56 0.06 5.62 giant_component 5.33 0.19 6.15 ancestors 5.06 0.36 5.48 curated_ligand_receptor_interactions 4.17 0.47 11.86 import_intercell_network 4.06 0.35 6.04 homologene_uniprot_orthology 2.27 0.10 11.78 kegg_pathway_download 1.87 0.11 9.75 import_mirnatarget_interactions 1.25 0.16 7.91 all_uniprot_acs 1.06 0.14 13.46 uniprot_full_id_mapping_table 0.97 0.04 7.03 is_trembl 0.92 0.07 40.24 translate_ids 0.82 0.06 7.98 ensembl_id_mapping_table 0.56 0.05 60.22 all_uniprots 0.22 0.02 5.95 * 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 NOTE See 'F:/biocbuild/bbs-3.17-bioc-rtools43/meat/OmnipathR.Rcheck/00check.log' for details.