[ Started: 2023-04-12 00:38:19 CEST ]
[ OmnipathR v3.7.15 for BioC-3.17 from https://github.com/saezlab/OmnipathR@master ]
* using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-04-12_0032/OmnipathR/OmnipathR.Rcheck’
* using R version 4.3.0 beta (2023-04-08 r84203)
* 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 executable files ... 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 ... NOTE
installed size is 6.4Mb
sub-directories of 1Mb or more:
doc 5.4Mb
* 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
[2023-04-12 00:38:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-12 00:38:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-12 00:38:36] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-04-12 00:38:36] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-04-12 00:38:36] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-04-12 00:38:36] [TRACE] [OmnipathR] Contains 1 files.
[2023-04-12 00:38:36] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-04-12 00:38:36] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-12 00:38:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-12 00:38:36] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-04-12 00:38:36] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-04-12 00:38:36] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-04-12_0032/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-04-12 00:38:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-12 00:38:36] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-04-12_0032/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-04-12 00:38:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-12 00:38:36] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-04-12_0032/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-04-12 00:38:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-12 00:38:36] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-04-12_0032/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-04-12 00:38:36] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-12 00:38:36] [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
[2023-04-12 00:38:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-12 00:38:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-12 00:38:42] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2023-04-12 00:38:42] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2023-04-12 00:38:42] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2023-04-12 00:38:42] [TRACE] [OmnipathR] Contains 1 files.
[2023-04-12 00:38:42] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2023-04-12 00:38:42] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2023-04-12 00:38:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-12 00:38:42] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2023-04-12 00:38:42] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`.
[2023-04-12 00:38:42] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-04-12_0032/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2023-04-12 00:38:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-12 00:38:42] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-04-12_0032/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2023-04-12 00:38:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-12 00:38:42] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-04-12_0032/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2023-04-12 00:38:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-12 00:38:42] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-04-12_0032/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2023-04-12 00:38:42] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2023-04-12 00:38:42] [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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 3 NOTEs
See
‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2023-04-12_0032/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.
[ Finished: 2023-04-12 00:49:52 CEST ]