############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/R/R/bin/R CMD check --install=check:wppi.install-out.txt --library=/home/biocbuild/R/R/site-library --no-vignettes --timings wppi_1.15.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/wppi.Rcheck’ * using R Under development (unstable) (2024-11-24 r87369) * using platform: aarch64-unknown-linux-gnu * R was compiled by aarch64-unknown-linux-gnu-gcc (GCC) 14.2.0 GNU Fortran (GCC) 14.2.0 * running under: openEuler 24.03 (LTS) * using session charset: UTF-8 * using option ‘--no-vignettes’ * checking for file ‘wppi/DESCRIPTION’ ... OK * checking extension type ... Package * this is package ‘wppi’ version ‘1.15.0’ * 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 ... WARNING Found the following significant warnings: Warning: program compiled against libxml 212 using older 211 See ‘/home/biocbuild/bbs-3.21-bioc/meat/wppi.Rcheck/00install.out’ for details. * 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 ...Warning: program compiled against libxml 212 using older 211 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 ... NOTE Warning: program compiled against libxml 212 using older 211 [2024-12-25 12:29:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-25 12:29:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-25 12:29:35] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-12-25 12:29:35] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-12-25 12:29:35] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-12-25 12:29:35] [TRACE] [OmnipathR] Contains 1 files. [2024-12-25 12:29:35] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-12-25 12:29:35] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-25 12:29:35] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-25 12:29:35] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-12-25 12:29:36] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2024-12-25 12:29:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-12-25 12:29:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-25 12:29:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-12-25 12:29:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-25 12:29:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-12-25 12:29:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-25 12:29:36] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-12-25 12:29:36] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-25 12:29:36] [TRACE] [OmnipathR] Cache locked: FALSE A namespace must be able to be loaded with just the base namespace loaded: otherwise if the namespace gets loaded by a saved object, the session will be unable to start. Probably some imports need to be declared in the NAMESPACE file. * 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 Warning: program compiled against libxml 212 using older 211 [2024-12-25 12:29:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-25 12:29:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-25 12:29:55] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-12-25 12:29:55] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-12-25 12:29:55] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-12-25 12:29:55] [TRACE] [OmnipathR] Contains 1 files. [2024-12-25 12:29:55] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-12-25 12:29:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-25 12:29:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-25 12:29:55] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-12-25 12:29:55] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2024-12-25 12:29:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-12-25 12:29:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-25 12:29:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-12-25 12:29:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-25 12:29:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-12-25 12:29:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-25 12:29:55] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-12-25 12:29:55] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-25 12:29:55] [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 ... NOTE Warning: program compiled against libxml 212 using older 211 * checking S3 generic/method consistency ... WARNING Warning: program compiled against libxml 212 using older 211 See section ‘Generic functions and methods’ in the ‘Writing R Extensions’ manual. * checking replacement functions ... WARNING Warning: program compiled against libxml 212 using older 211 The argument of a replacement function which corresponds to the right hand side must be named ‘value’. * checking foreign function calls ... NOTE Warning: program compiled against libxml 212 using older 211 See chapter ‘System and foreign language interfaces’ in the ‘Writing R Extensions’ manual. * checking R code for possible problems ... NOTE Warning: program compiled against libxml 212 using older 211 [2024-12-25 12:30:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-25 12:30:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-25 12:30:19] [INFO] [OmnipathR] Initialized cache: `/home/biocbuild/.cache/OmnipathR`. [2024-12-25 12:30:19] [TRACE] [OmnipathR] Running on a build server, wiping cache. [2024-12-25 12:30:19] [TRACE] [OmnipathR] Cache is at `/home/biocbuild/.cache/OmnipathR`. [2024-12-25 12:30:19] [TRACE] [OmnipathR] Contains 1 files. [2024-12-25 12:30:19] [TRACE] [OmnipathR] Cache is locked: FALSE. [2024-12-25 12:30:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/.cache/OmnipathR/cache.json` (encoding: UTF-8). [2024-12-25 12:30:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-25 12:30:19] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/biocbuild/.cache/OmnipathR`. [2024-12-25 12:30:19] [TRACE] [OmnipathR] Pandoc version: `2.12`. [2024-12-25 12:30:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/db/db_def.json` (encoding: UTF-8). [2024-12-25 12:30:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-25 12:30:19] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8). [2024-12-25 12:30:19] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-25 12:30:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/urls.json` (encoding: UTF-8). [2024-12-25 12:30:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-25 12:30:20] [TRACE] [OmnipathR] Reading JSON from `/home/biocbuild/R/R-4.5.0-devel_2024-11-24/site-library/OmnipathR/internal/id_types.json` (encoding: UTF-8). [2024-12-25 12:30:20] [TRACE] [OmnipathR] JSON validation successful: TRUE [2024-12-25 12:30:20] [TRACE] [OmnipathR] Cache locked: FALSE * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... OK * checking for missing documentation entries ... WARNING Warning: program compiled against libxml 212 using older 211 All user-level objects in a package should have documentation entries. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * checking for code/documentation mismatches ... WARNING Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 Warning: program compiled against libxml 212 using older 211 * checking Rd \usage sections ... NOTE Warning: program compiled against libxml 212 using older 211 The \usage entries for S3 methods should use the \method markup and not their full name. See chapter ‘Writing R documentation files’ in the ‘Writing R Extensions’ manual. * 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 59.604 0.144 61.197 score_candidate_genes_from_PPI 30.950 0.114 33.814 prioritization_genes 30.732 0.124 35.494 random_walk 29.094 0.197 33.477 weighted_adj 24.389 0.020 26.365 common_neighbors 16.558 0.421 24.240 count_genes 13.191 0.266 24.626 filter_annot_with_network 8.571 0.102 11.754 wppi_data 8.592 0.044 9.189 in_omnipath 4.669 0.036 5.386 subgraph_op 4.600 0.015 5.348 graph_from_op 4.487 0.065 5.462 functional_annot 2.308 0.161 30.145 * 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: 5 WARNINGs, 7 NOTEs See ‘/home/biocbuild/bbs-3.21-bioc/meat/wppi.Rcheck/00check.log’ for details.