############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R-beta-2024-04-15_r86425/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library --no-vignettes --timings wppi_1.12.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.19-bioc/meat/wppi.Rcheck’ * using R version 4.4.0 beta (2024-04-15 r86425) * using platform: aarch64-unknown-linux-gnu * R was compiled by gcc (GCC) 10.3.1 GNU Fortran (GCC) 10.3.1 * running under: openEuler 22.03 (LTS-SP1) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘wppi/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘wppi’ version ‘1.12.0’ * 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 for sufficient/correct file permissions ... OK * checking whether package ‘wppi’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ 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 [2024-05-08 13:09:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-08 13:09:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-08 13:09:37] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-05-08 13:09:37] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-08 13:09:37] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-05-08 13:09:37] [TRACE] [OmnipathR] Contains 1 files. [2024-05-08 13:09:37] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-08 13:09:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-08 13:09:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-08 13:09:37] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-05-08 13:09:37] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2024-05-08 13:09:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-08 13:09:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-08 13:09:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-08 13:09:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-08 13:09:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-08 13:09:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-08 13:09:37] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-08 13:09:37] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-08 13:09:37] [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 [2024-05-08 13:09:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-08 13:09:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-08 13:09:55] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-05-08 13:09:55] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-05-08 13:09:55] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-05-08 13:09:55] [TRACE] [OmnipathR] Contains 1 files. [2024-05-08 13:09:55] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-05-08 13:09:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-05-08 13:09:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-08 13:09:55] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-05-08 13:09:55] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2024-05-08 13:09:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-05-08 13:09:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-08 13:09:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-05-08 13:09:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-08 13:09:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-05-08 13:09:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-08 13:09:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-beta-2024-04-15_r86425/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-05-08 13:09:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-05-08 13:09:55] [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 files in ‘vignettes’ ... OK * checking examples ... OK Examples with CPU (user + system) or elapsed time > 5s user system elapsed wppi 39.257 0.095 39.424 score_candidate_genes_from_PPI 20.651 0.056 20.767 prioritization_genes 19.980 0.119 20.178 random_walk 19.359 0.059 19.490 weighted_adj 14.498 0.048 14.574 count_genes 10.732 0.350 17.509 common_neighbors 8.463 0.472 15.310 filter_annot_with_network 8.159 0.075 8.269 wppi_data 8.092 0.060 8.166 in_omnipath 4.976 0.004 5.002 functional_annot 2.409 0.198 16.371 * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking running R code from vignettes ... SKIPPED * checking re-building of vignette outputs ... SKIPPED * checking PDF version of manual ... OK * DONE Status: 3 NOTEs See ‘/home/biocbuild/bbs-3.19-bioc/meat/wppi.Rcheck/00check.log’ for details.