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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_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.15-bioc/meat/wppi.Rcheck’
* using R version 4.2.1 (2022-06-23)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘wppi/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wppi’ version ‘1.4.0’
* 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 ... 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 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
[2022-10-19 09:33:28] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2022-10-19 09:33:28] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2022-10-19 09:33:28] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2022-10-19 09:33:28] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2022-10-19 09:33:28] [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                           56.393  0.331  57.867
score_candidate_genes_from_PPI 31.602  0.233  34.031
prioritization_genes           30.029  0.274  33.338
random_walk                    29.375  0.259  32.273
count_genes                    21.975  1.703  23.882
weighted_adj                   21.827  0.135  23.167
functional_annot               10.432  0.719  13.124
wppi_data                       9.852  0.097   9.958
filter_annot_with_network       8.161  0.148   8.694
common_neighbors                7.461  0.409  10.197
wppi_go_data                    5.038  0.077   5.120
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.15-bioc/meat/wppi.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL wppi
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library’
* installing *source* package ‘wppi’ ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
[2022-10-18 15:59:09] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2022-10-18 15:59:09] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2022-10-18 15:59:09] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2022-10-18 15:59:09] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2022-10-18 15:59:09] [TRACE]   [OmnipathR] Cache locked: FALSE
Note: wrong number of arguments to '/' 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
[2022-10-18 15:59:16] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2022-10-18 15:59:16] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2022-10-18 15:59:16] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2022-10-18 15:59:16] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2022-10-18 15:59:16] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package can be loaded from final location
[2022-10-18 15:59:21] [INFO]    [OmnipathR] Initialized cache: `/Users/biocbuild/Library/Caches/OmnipathR`.
[2022-10-18 15:59:21] [TRACE]   [OmnipathR] Running on a build server, wiping cache.
[2022-10-18 15:59:21] [SUCCESS] [OmnipathR] Removing all cache contents from `/Users/biocbuild/Library/Caches/OmnipathR`.
[2022-10-18 15:59:21] [TRACE]   [OmnipathR] Pandoc version: `2.7.3`.
[2022-10-18 15:59:21] [TRACE]   [OmnipathR] Cache locked: FALSE
** testing if installed package keeps a record of temporary installation path
* DONE (wppi)