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### Running command:
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###   E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:wppi.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings wppi_1.15.0.tar.gz
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* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/wppi.Rcheck'
* using R Under development (unstable) (2024-10-26 r87273 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
    gcc.exe (GCC) 13.2.0
    GNU Fortran (GCC) 13.2.0
* running under: Windows Server 2022 x64 (build 20348)
* 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 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
[2024-12-13 06:30:04] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-13 06:30:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-13 06:30:04] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-12-13 06:30:04] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-12-13 06:30:04] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-12-13 06:30:04] [TRACE]   [OmnipathR] Contains 1 files.
[2024-12-13 06:30:04] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-12-13 06:30:04] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-13 06:30:04] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-13 06:30:04] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-12-13 06:30:05] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-12-13 06:30:05] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-12-13 06:30:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-13 06:30:05] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-12-13 06:30:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-13 06:30:05] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-12-13 06:30:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-13 06:30:05] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-12-13 06:30:05] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-13 06:30:05] [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
[2024-12-13 06:30:26] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-13 06:30:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-13 06:30:26] [INFO]    [OmnipathR] Initialized cache: `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-12-13 06:30:26] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2024-12-13 06:30:26] [TRACE]   [OmnipathR] Cache is at `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-12-13 06:30:26] [TRACE]   [OmnipathR] Contains 1 files.
[2024-12-13 06:30:26] [TRACE]   [OmnipathR] Cache is locked: FALSE.
[2024-12-13 06:30:26] [TRACE]   [OmnipathR] Reading JSON from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR/cache.json` (encoding: UTF-8).
[2024-12-13 06:30:26] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-13 06:30:26] [SUCCESS] [OmnipathR] Removing all cache contents from `C:\Users\biocbuild\AppData\Local\Cache\OmnipathR`.
[2024-12-13 06:30:27] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2024-12-13 06:30:27] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/db/db_def.json` (encoding: UTF-8).
[2024-12-13 06:30:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-13 06:30:27] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/magic_bytes.json` (encoding: UTF-8).
[2024-12-13 06:30:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-13 06:30:27] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/urls.json` (encoding: UTF-8).
[2024-12-13 06:30:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-13 06:30:27] [TRACE]   [OmnipathR] Reading JSON from `E:/biocbuild/bbs-3.21-bioc/R/library/OmnipathR/internal/id_types.json` (encoding: UTF-8).
[2024-12-13 06:30:27] [TRACE]   [OmnipathR] JSON validation successful: TRUE
[2024-12-13 06:30:27] [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                           54.12   1.07   55.22
score_candidate_genes_from_PPI 28.34   0.36   28.75
prioritization_genes           27.68   0.53   28.22
random_walk                    26.71   0.52   27.41
weighted_adj                   21.80   0.45   22.25
common_neighbors               15.76   0.39   21.64
count_genes                    13.71   0.89   13.16
wppi_data                       9.03   0.07    9.11
filter_annot_with_network       8.78   0.20    9.00
* 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
  'E:/biocbuild/bbs-3.21-bioc/meat/wppi.Rcheck/00check.log'
for details.