############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings OmnipathR_3.10.1.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/OmnipathR.Rcheck’ * using R version 4.3.2 Patched (2023-11-13 r85521) * using platform: x86_64-pc-linux-gnu (64-bit) * 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 22.04.4 LTS * using session charset: UTF-8 * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.10.1’ * 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 ... 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 loading without being on the library search path ... OK * checking startup messages can be suppressed ... NOTE [2024-03-06 00:44:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-06 00:44:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-06 00:44:15] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-03-06 00:44:15] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-06 00:44:15] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-03-06 00:44:15] [TRACE] [OmnipathR] Contains 1 files. [2024-03-06 00:44:15] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-06 00:44:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-06 00:44:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-06 00:44:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-03-06 00:44:15] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-03-06 00:44:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-06 00:44:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-06 00:44:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-06 00:44:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-06 00:44:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-06 00:44:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-06 00:44:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-06 00:44:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-06 00:44:15] [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 [2024-03-06 00:44:25] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-06 00:44:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-06 00:44:25] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-03-06 00:44:25] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-03-06 00:44:25] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-03-06 00:44:25] [TRACE] [OmnipathR] Contains 1 files. [2024-03-06 00:44:25] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-03-06 00:44:25] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-03-06 00:44:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-06 00:44:25] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-03-06 00:44:25] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2024-03-06 00:44:25] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-03-06 00:44:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-06 00:44:25] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-03-06 00:44:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-06 00:44:25] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-03-06 00:44:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-06 00:44:25] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.18-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-03-06 00:44:25] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-03-06 00:44:25] [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 collectri 113.298 1.656 119.103 dorothea 68.430 1.356 75.753 annotation_categories 64.911 0.076 66.580 curated_ligrec_stats 43.734 3.923 135.598 filter_extra_attrs 28.527 0.884 33.598 nichenet_signaling_network_omnipath 27.109 0.425 47.532 nichenet_gr_network_omnipath 19.825 0.423 25.728 go_annot_download 17.982 0.821 33.470 pivot_annotations 16.718 0.584 41.189 with_extra_attrs 15.756 0.472 33.352 extra_attrs_to_cols 16.057 0.170 16.619 giant_component 11.825 0.336 18.606 extra_attr_values 11.026 0.085 15.035 static_table 9.440 0.795 78.362 pubmed_open 8.963 0.727 12.377 curated_ligand_receptor_interactions 8.319 0.829 25.386 filter_intercell 8.799 0.335 14.393 print_interactions 8.393 0.354 24.654 has_extra_attrs 7.853 0.199 8.058 get_signed_ptms 7.639 0.248 9.613 filter_by_resource 5.752 0.162 7.840 extra_attrs 5.409 0.038 5.446 import_transcriptional_interactions 4.885 0.376 9.593 print_path_vs 4.118 0.132 12.783 hpo_download 3.108 0.349 6.617 enzsub_graph 3.264 0.050 6.901 import_all_interactions 2.892 0.211 8.945 import_tf_target_interactions 2.794 0.214 6.591 database_summary 2.295 0.132 5.076 import_kinaseextra_interactions 2.282 0.113 7.196 annotated_network 1.808 0.261 8.047 import_post_translational_interactions 1.484 0.116 6.176 import_pathwayextra_interactions 1.428 0.148 6.644 ensembl_id_mapping_table 1.230 0.045 34.431 kegg_picture 0.237 0.015 5.003 * 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 ... ‘bioc_workshop.Rmd’ using ‘UTF-8’... OK ‘db_manager.Rmd’ using ‘UTF-8’... OK ‘drug_targets.Rmd’ using ‘UTF-8’... OK ‘extra_attrs.Rmd’ using ‘UTF-8’... OK ‘nichenet.Rmd’ using ‘UTF-8’... OK ‘omnipath_intro.Rmd’ using ‘UTF-8’... OK ‘paths.Rmd’ using ‘UTF-8’... OK NONE * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 NOTEs See ‘/home/biocbuild/bbs-3.18-bioc/meat/OmnipathR.Rcheck/00check.log’ for details.