############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:OmnipathR.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings OmnipathR_3.7.15.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/OmnipathR.Rcheck’ * using R version 4.3.0 alpha (2023-04-03 r84154) * using platform: x86_64-pc-linux-gnu (64-bit) * R was compiled by gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0 * running under: Ubuntu 22.04.2 LTS * using session charset: UTF-8 * checking for file ‘OmnipathR/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘OmnipathR’ version ‘3.7.15’ * 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 [2023-04-11 22:06:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-11 22:06:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 22:06:15] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2023-04-11 22:06:15] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-04-11 22:06:15] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2023-04-11 22:06:15] [TRACE] [OmnipathR] Contains 1 files. [2023-04-11 22:06:15] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-04-11 22:06:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-11 22:06:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 22:06:15] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2023-04-11 22:06:15] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-04-11 22:06:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-04-11 22:06:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 22:06:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-04-11 22:06:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 22:06:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-04-11 22:06:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 22:06:15] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-04-11 22:06:15] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 22:06:15] [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 [2023-04-11 22:06:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-11 22:06:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 22:06:24] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2023-04-11 22:06:24] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2023-04-11 22:06:24] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2023-04-11 22:06:24] [TRACE] [OmnipathR] Contains 1 files. [2023-04-11 22:06:24] [TRACE] [OmnipathR] Cache is locked: FALSE. [2023-04-11 22:06:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2023-04-11 22:06:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 22:06:24] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2023-04-11 22:06:24] [TRACE] [OmnipathR] Pandoc version: `2.7.3`. [2023-04-11 22:06:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2023-04-11 22:06:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 22:06:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2023-04-11 22:06:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 22:06:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2023-04-11 22:06:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 22:06:24] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/bbs-3.17-bioc/R/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2023-04-11 22:06:24] [TRACE] [OmnipathR] JSON validation successful: TRUE [2023-04-11 22:06:24] [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 annotation_categories 65.143 0.076 66.660 curated_ligrec_stats 34.484 1.579 111.639 extra_attrs_to_cols 32.840 0.052 37.548 filter_extra_attrs 31.392 0.280 37.606 extra_attr_values 26.131 0.312 30.136 with_extra_attrs 24.587 0.499 41.532 go_annot_download 20.076 1.192 33.236 giant_component 19.603 0.989 31.496 has_extra_attrs 19.901 0.169 31.165 pivot_annotations 17.280 1.644 42.469 nichenet_gr_network_omnipath 17.306 0.534 21.776 extra_attrs 14.376 0.111 16.150 get_signed_ptms 12.614 0.202 24.519 nichenet_signaling_network_omnipath 10.390 0.803 26.226 print_interactions 9.932 0.462 19.328 filter_intercell 9.539 0.600 15.078 pubmed_open 8.698 0.561 18.925 filter_by_resource 8.427 0.272 11.372 find_all_paths 6.120 0.091 6.211 curated_ligand_receptor_interactions 5.634 0.281 16.096 omnipath 4.675 0.384 6.187 print_path_vs 4.459 0.340 11.195 import_all_interactions 3.844 0.207 8.669 collectri 3.909 0.111 5.779 import_transcriptional_interactions 3.799 0.198 10.158 omnipath_cache_download_ready 0.651 3.002 6.299 database_summary 1.760 1.291 5.538 import_kinaseextra_interactions 2.663 0.259 5.815 hpo_download 2.618 0.214 6.125 omnipath_cache_load 0.704 1.787 12.748 import_mirnatarget_interactions 2.113 0.205 5.889 intercell_consensus_filter 2.121 0.159 5.512 obo_parser 0.169 1.264 19.885 annotated_network 1.214 0.147 5.140 ensembl_id_mapping_table 1.217 0.037 15.624 biomart_query 1.175 0.045 5.893 * 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-3.17-bioc/meat/OmnipathR.Rcheck/00check.log’ for details.