############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.19-bioc/R/site-library --timings OmnipathR_3.12.4.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/OmnipathR.Rcheck’ * using R version 4.4.1 (2024-06-14) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0 * running under: Ubuntu 22.04.5 LTS * using session charset: UTF-8 * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.12.4’ * 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 ... NOTE License stub is invalid DCF. * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code 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 whether startup messages can be suppressed ... NOTE [2024-10-17 03:14:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-17 03:14:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 03:14:44] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-10-17 03:14:44] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-10-17 03:14:44] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-10-17 03:14:44] [TRACE] [OmnipathR] Contains 1 files. [2024-10-17 03:14:44] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-10-17 03:14:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-17 03:14:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 03:14:44] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-10-17 03:14:44] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-10-17 03:14:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-10-17 03:14:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 03:14:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-10-17 03:14:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 03:14:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-10-17 03:14:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 03:14:44] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-10-17 03:14:44] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 03:14:44] [TRACE] [OmnipathR] Cache locked: FALSE It looks like this package (or a package it requires) has a startup message which cannot be suppressed: see ?packageStartupMessage. * 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 [2024-10-17 03:14:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-17 03:14:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 03:14:54] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-10-17 03:14:54] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-10-17 03:14:54] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-10-17 03:14:54] [TRACE] [OmnipathR] Contains 1 files. [2024-10-17 03:14:54] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-10-17 03:14:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-10-17 03:14:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 03:14:54] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-10-17 03:14:54] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-10-17 03:14:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-10-17 03:14:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 03:14:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-10-17 03:14:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 03:14:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-10-17 03:14:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 03:14:54] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.19-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-10-17 03:14:54] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-10-17 03:14:54] [TRACE] [OmnipathR] Cache locked: FALSE oma_organisms: no visible binding for global variable ‘ncbi_tax_id’ Undefined global functions or variables: ncbi_tax_id * 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 collectri 143.273 2.016 151.583 annotation_categories 85.846 0.070 89.068 dorothea 71.172 1.217 79.011 curated_ligrec_stats 45.217 3.260 146.122 static_table 10.455 12.436 118.918 nichenet_gr_network_omnipath 19.049 0.286 22.591 filter_extra_attrs 18.073 0.270 19.227 go_annot_download 15.978 1.114 28.783 extra_attr_values 16.084 0.736 21.734 pivot_annotations 15.385 1.292 50.717 with_extra_attrs 15.336 0.865 32.740 nichenet_signaling_network_omnipath 14.153 0.371 22.040 extra_attrs_to_cols 14.167 0.175 14.342 giant_component 13.133 0.231 21.543 pubmed_open 9.190 0.520 17.297 has_extra_attrs 9.538 0.129 10.098 print_interactions 9.085 0.443 21.162 filter_intercell 8.223 0.679 14.419 filter_by_resource 7.801 0.455 11.641 curated_ligand_receptor_interactions 6.490 0.795 22.303 resources_in 6.225 0.054 13.015 find_all_paths 5.927 0.075 6.003 get_signed_ptms 5.266 0.022 6.405 extra_attrs 5.108 0.047 5.154 hpo_download 3.741 0.383 29.891 import_transcriptional_interactions 3.555 0.317 8.288 print_path_vs 3.559 0.083 7.815 import_all_interactions 3.342 0.177 9.724 import_tf_target_interactions 2.259 0.187 5.122 enzsub_graph 2.257 0.072 5.187 intercell_consensus_filter 2.057 0.207 5.276 import_kinaseextra_interactions 1.659 0.286 7.155 ensembl_id_mapping_table 1.851 0.064 27.489 import_mirnatarget_interactions 1.801 0.085 5.251 annotated_network 1.664 0.115 7.712 biomart_query 1.059 0.068 9.032 kegg_picture 0.246 0.016 5.046 * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ OK * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/OmnipathR.Rcheck/00check.log’ for details.