############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.15-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.15-bioc/R/library --no-vignettes --timings OmnipathR_3.4.7.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.15-bioc/meat/OmnipathR.Rcheck’ * using R version 4.2.1 (2022-06-23) * using platform: x86_64-pc-linux-gnu (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 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 ... 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 [2022-10-18 20:57:05] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2022-10-18 20:57:05] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2022-10-18 20:57:05] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2022-10-18 20:57:05] [TRACE] [OmnipathR] Pandoc version: `2.5`. [2022-10-18 20:57:05] [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 ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed nichenet_lr_network 161.559 1.360 164.310 evex_download 97.772 2.428 147.902 nichenet_networks 67.066 1.103 75.467 simplify_intercell_network 55.529 1.270 66.020 nichenet_gr_network_evex 52.667 1.019 52.828 filter_intercell_network 50.290 0.997 62.613 unique_intercell_network 50.347 0.285 50.633 nichenet_signaling_network 40.603 2.391 49.801 nichenet_lr_network_omnipath 35.992 1.748 49.147 annotation_categories 35.609 0.046 38.084 bioplex_all 23.142 0.813 25.284 curated_ligrec_stats 20.625 2.798 107.218 consensuspathdb_raw_table 20.156 1.521 44.745 go_annot_download 13.726 1.332 14.804 pivot_annotations 13.106 1.272 45.799 preppi_download 10.659 2.080 52.807 preppi_filter 10.422 1.610 7.141 nichenet_signaling_network_evex 8.160 0.628 7.943 nichenet_gr_network_pathwaycommons 7.822 0.588 10.902 filter_intercell 6.781 0.885 14.330 pathwaycommons_download 6.719 0.515 9.523 extra_attr_values 6.893 0.300 11.345 filter_extra_attrs 6.890 0.297 7.810 ancestors 5.975 0.641 14.271 nichenet_gr_network 5.593 0.128 8.713 curated_ligand_receptor_interactions 4.782 0.652 22.643 with_extra_attrs 5.050 0.339 9.540 nichenet_gr_network_omnipath 5.101 0.136 8.371 import_intercell_network 4.726 0.261 11.509 nichenet_gr_network_harmonizome 4.292 0.209 6.033 hpo_download 4.019 0.449 7.825 giant_component 3.924 0.301 8.934 guide2pharma_download 2.828 0.308 7.957 filter_by_resource 2.171 0.347 6.323 kegg_pathway_download 2.443 0.040 18.779 print_interactions 2.222 0.235 10.451 enzsub_graph 2.052 0.159 6.168 pubmed_open 1.954 0.218 5.996 htridb_download 1.453 0.132 5.691 print_path_vs 1.371 0.123 5.471 nichenet_gr_network_trrust 1.394 0.064 10.749 import_all_interactions 1.122 0.122 5.633 all_uniprots 1.138 0.035 13.702 uniprot_full_id_mapping_table 0.961 0.004 13.031 translate_ids 0.833 0.057 13.266 annotated_network 0.608 0.097 5.501 trrust_download 0.576 0.015 10.428 kegg_info 0.422 0.016 5.418 uniprot_id_mapping_table 0.352 0.012 5.430 ramilowski_download 0.257 0.032 5.353 * 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 ‘/home/biocbuild/bbs-3.15-bioc/meat/OmnipathR.Rcheck/00check.log’ for details.