##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:RITAN.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings RITAN_1.31.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.21-bioc/meat/RITAN.Rcheck’
* using R Under development (unstable) (2024-11-20 r87352)
* 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 ‘RITAN/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘RITAN’ version ‘1.31.0’
* 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'
 INFO
Imports includes 22 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable.  Move as many as possible to Suggests and
use conditionally.
* 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 ‘RITAN’ can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import 'ensembldb::keys' by 'hash::keys' when loading 'RITAN'
  Warning: replacing previous import 'ensembldb::filter' by 'stats::filter' when loading 'RITAN'
See ‘/Users/biocbuild/bbs-3.21-bioc/meat/RITAN.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘BgeeDB’
A package should be listed in only one of these fields.
* 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 dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
  'BgeeDB' 'knitr'
  All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
enrichment_symbols: no visible binding for global variable
  'active_genesets'
icon_dual_between: no visible binding for global variable 'all_symbols'
icon_single_within: no visible binding for global variable
  'all_symbols'
load_geneset_symbols: no visible binding for global variable
  'geneset_list'
load_geneset_symbols: no visible binding for global variable
  'active_genesets'
plot.term_enrichment_by_subset: no visible binding for global variable
  'Var2'
plot.term_enrichment_by_subset: no visible binding for global variable
  'Var1'
show_active_genesets_hist: no visible binding for global variable
  'active_genesets'
term_enrichment : process_source: no visible binding for global
  variable 'active_genesets'
Undefined global functions or variables:
  Var1 Var2 active_genesets all_symbols geneset_list
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.21-bioc/meat/RITAN.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL RITAN
###
##############################################################################
##############################################################################


* installing to library ‘/Library/Frameworks/R.framework/Versions/4.5-x86_64/Resources/library’
* installing *source* package ‘RITAN’ ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Warning: replacing previous import 'ensembldb::keys' by 'hash::keys' when loading 'RITAN'
Warning: replacing previous import 'ensembldb::filter' by 'stats::filter' when loading 'RITAN'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: replacing previous import 'ensembldb::keys' by 'hash::keys' when loading 'RITAN'
Warning: replacing previous import 'ensembldb::filter' by 'stats::filter' when loading 'RITAN'
** testing if installed package can be loaded from final location
Warning: replacing previous import 'ensembldb::keys' by 'hash::keys' when loading 'RITAN'
Warning: replacing previous import 'ensembldb::filter' by 'stats::filter' when loading 'RITAN'
** testing if installed package keeps a record of temporary installation path
* DONE (RITAN)