##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:wppi.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings wppi_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/wppi.Rcheck’
* using R version 4.4.0 (2024-04-24)
* using platform: aarch64-apple-darwin20
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* 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 whether startup messages can be suppressed ... NOTE
[2024-06-28 13:35:53] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-28 13:35:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-28 13:35:53] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-06-28 13:35:53] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-06-28 13:35:53] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-06-28 13:35:53] [TRACE]   [OmnipathR] Contains 1 files.
[2024-06-28 13:35:53] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-06-28 13:35:53] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-28 13:35:53] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-28 13:35:53] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-06-28 13:35:54] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2024-06-28 13:35:54] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-06-28 13:35:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-28 13:35:54] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-06-28 13:35:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-28 13:35:54] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-06-28 13:35:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-28 13:35:54] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-06-28 13:35:54] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-28 13:35:54] [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
[2024-06-28 13:36:12] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-28 13:36:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-28 13:36:12] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-06-28 13:36:12] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-06-28 13:36:12] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-06-28 13:36:12] [TRACE]   [OmnipathR] Contains 1 files.
[2024-06-28 13:36:12] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-06-28 13:36:12] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-06-28 13:36:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-28 13:36:12] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-06-28 13:36:12] [TRACE]   [OmnipathR] Pandoc version: `3.1.2`.
[2024-06-28 13:36:12] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-06-28 13:36:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-28 13:36:12] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-06-28 13:36:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-28 13:36:12] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-06-28 13:36:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-28 13:36:12] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-06-28 13:36:12] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-06-28 13:36:12] [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                           33.100  0.462  33.717
score_candidate_genes_from_PPI 17.462  0.310  17.834
prioritization_genes           16.817  0.266  17.276
random_walk                    16.011  0.318  16.452
weighted_adj                   13.383  0.219  13.701
count_genes                    11.366  0.488  12.165
wppi_data                       8.979  0.125   9.126
filter_annot_with_network       8.120  0.139   8.330
common_neighbors                6.854  0.252  10.659
* 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
  ‘/Users/biocbuild/bbs-3.19-bioc/meat/wppi.Rcheck/00check.log’
for details.