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### Running command:
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###   /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_1.14.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.20-bioc/meat/wppi.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-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 Monterey 12.7.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘wppi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wppi’ version ‘1.14.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
  cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
 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
[2024-11-20 03:57:01] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 03:57:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 03:57:01] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-20 03:57:01] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-20 03:57:01] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-20 03:57:01] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-20 03:57:01] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-20 03:57:01] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 03:57:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 03:57:01] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-20 03:57:01] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-11-20 03:57:01] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-20 03:57:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 03:57:01] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-20 03:57:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 03:57:01] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-20 03:57:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 03:57:01] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-20 03:57:01] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 03:57:01] [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
[2024-11-20 03:57:16] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 03:57:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 03:57:16] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-20 03:57:16] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-11-20 03:57:16] [TRACE]   [OmnipathR] Cache is at `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-20 03:57:16] [TRACE]   [OmnipathR] Contains 1 files.
[2024-11-20 03:57:16] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-11-20 03:57:16] [TRACE]   [OmnipathR] Reading JSON from `/Users/biocbuild/Library/Caches/OmnipathR/cache.json` (encoding: UTF-8).
[2024-11-20 03:57:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 03:57:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2024-11-20 03:57:16] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-11-20 03:57:16] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-11-20 03:57:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 03:57:16] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-11-20 03:57:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 03:57:16] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-11-20 03:57:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 03:57:16] [TRACE]   [OmnipathR] Reading JSON from `/Library/Frameworks/R.framework/Versions/4.4-x86_64/Resources/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-11-20 03:57:16] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-11-20 03:57:16] [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                           25.361  0.501  25.957
score_candidate_genes_from_PPI 12.872  0.250  13.151
prioritization_genes           12.280  0.347  12.647
random_walk                    11.941  0.236  12.200
weighted_adj                    9.768  0.183   9.976
count_genes                     8.123  0.873   8.080
wppi_data                       6.159  0.138   6.324
filter_annot_with_network       5.434  0.155   5.594
common_neighbors                4.974  0.258  16.578
* 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-3.20-bioc/meat/wppi.Rcheck/00check.log’
for details.