[ Started: 2024-01-11 13:53:50 CET ]
[ OmnipathR v3.8.2 for BioC-3.17 from https://github.com/saezlab/OmnipathR@RELEASE_3_17 ]
* using log directory ‘/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2024-01-11_1347/OmnipathR/OmnipathR.Rcheck’
* using R version 4.3.1 (2023-06-16)
* 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 22.04.3 LTS
* using session charset: UTF-8
* checking for file ‘OmnipathR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OmnipathR’ version ‘3.8.2’
* 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 6.3Mb
sub-directories of 1Mb or more:
doc 5.3Mb
* 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
[2024-01-11 13:54:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-01-11 13:54:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-01-11 13:54:08] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-01-11 13:54:08] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-01-11 13:54:08] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-01-11 13:54:08] [TRACE] [OmnipathR] Contains 1 files.
[2024-01-11 13:54:08] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-01-11 13:54:08] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-01-11 13:54:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-01-11 13:54:08] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-01-11 13:54:08] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-01-11 13:54:08] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2024-01-11_1347/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-01-11 13:54:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-01-11 13:54:08] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2024-01-11_1347/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-01-11 13:54:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-01-11 13:54:08] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2024-01-11_1347/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-01-11 13:54:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-01-11 13:54:08] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2024-01-11_1347/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-01-11 13:54:08] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-01-11 13:54:08] [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
[2024-01-11 13:54:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-01-11 13:54:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-01-11 13:54:14] [INFO] [OmnipathR] Initialized cache: `/home/omnipath/.cache/OmnipathR`.
[2024-01-11 13:54:14] [TRACE] [OmnipathR] Running on a build server, wiping cache.
[2024-01-11 13:54:14] [TRACE] [OmnipathR] Cache is at `/home/omnipath/.cache/OmnipathR`.
[2024-01-11 13:54:14] [TRACE] [OmnipathR] Contains 1 files.
[2024-01-11 13:54:14] [TRACE] [OmnipathR] Cache is locked: FALSE.
[2024-01-11 13:54:14] [TRACE] [OmnipathR] Reading JSON from `/home/omnipath/.cache/OmnipathR/cache.json` (encoding: UTF-8).
[2024-01-11 13:54:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-01-11 13:54:14] [SUCCESS] [OmnipathR] Removing all cache contents from `/home/omnipath/.cache/OmnipathR`.
[2024-01-11 13:54:14] [TRACE] [OmnipathR] Pandoc version: `2.9.2.1`.
[2024-01-11 13:54:14] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2024-01-11_1347/OmnipathR/OmnipathR.Rcheck/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-01-11 13:54:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-01-11 13:54:14] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2024-01-11_1347/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-01-11 13:54:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-01-11 13:54:14] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2024-01-11_1347/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-01-11 13:54:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-01-11 13:54:14] [TRACE] [OmnipathR] Reading JSON from `/mnt/disk0/build/bioc-check/omnipathr/bioc-3.17/2024-01-11_1347/OmnipathR/OmnipathR.Rcheck/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-01-11 13:54:14] [TRACE] [OmnipathR] JSON validation successful: TRUE
[2024-01-11 13:54:14] [TRACE] [OmnipathR] Cache locked: FALSE
uniprot_idmapping_id_types: no visible binding for global variable
‘groups’
uniprot_idmapping_id_types: no visible binding for global variable
‘items’
Undefined global functions or variables:
groups items
* 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-3.17/2024-01-11_1347/OmnipathR/OmnipathR.Rcheck/00check.log’
for details.
[ Finished: 2024-01-11 14:05:47 CET ]