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### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:ccTutorial.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings ccTutorial_1.40.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.18-data-experiment/meat/ccTutorial.Rcheck’
* using R version 4.3.3 (2024-02-29)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
    gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
    GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* checking for file ‘ccTutorial/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ccTutorial’ version ‘1.40.0’
* 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 ‘ccTutorial’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'Ringo' is deprecated and will be removed from Bioconductor
  Warning: Package 'ccTutorial' is deprecated and will be removed from
See ‘/home/biocbuild/bbs-3.18-data-experiment/meat/ccTutorial.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 785.0Mb
  sub-directories of 1Mb or more:
    PairData       448.5Mb
    data            77.8Mb
    exonerateData  202.3Mb
    expression      49.9Mb
    vignettes        6.3Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘Biobase’
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 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... NOTE

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

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 ... NOTE
Packages in Depends field not imported from:
  ‘Ringo’ ‘affy’ ‘topGO’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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 data for ASCII and uncompressed saves ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
    user system elapsed
X 12.098    0.4  12.499
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘ccTutorial.Rnw’... OK
  ‘ccTutorialSupplement.Rnw’... OK
 NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-data-experiment/meat/ccTutorial.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL ccTutorial
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘ccTutorial’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
Warning message:
Package 'Ringo' is deprecated and will be removed from Bioconductor
  version 3.19 
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'Ringo' is deprecated and will be removed from Bioconductor
  version 3.19

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
Warning: Package 'ccTutorial' is deprecated and will be removed from
  Bioconductor version 3.19
** testing if installed package can be loaded from final location
Warning: Package 'Ringo' is deprecated and will be removed from Bioconductor
  version 3.19

groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.
Warning: Package 'ccTutorial' is deprecated and will be removed from
  Bioconductor version 3.19
** testing if installed package keeps a record of temporary installation path
* DONE (ccTutorial)