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### Running command:
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###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD check --install=check:GCSscore.install-out.txt --library=/home/biocbuild/bbs-3.18-bioc/R/site-library --timings GCSscore_1.16.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.18-bioc/meat/GCSscore.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 ‘GCSscore/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘GCSscore’ version ‘1.16.0’
* 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 ‘GCSscore’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'GCSscore' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.18-bioc/meat/GCSscore.Rcheck/00install.out’ for details.
* checking installed package size ... NOTE
  installed size is 12.0Mb
  sub-directories of 1Mb or more:
    extdata  11.6Mb
* 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 loading without being on the library search path ... OK
* checking startup messages can be suppressed ... 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 ... 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
  ‘GCSscore.Rnw’ using ‘UTF-8’... failed
 ERROR
Errors in running code in vignettes:
when running code in ‘GCSscore.Rnw’
  ...
*This package will only be generated once for each chip-type*
*Or if probeFile version for the chip-type needs to be updated*
writing intermediary .probe_tab file to temporary directory
Importing the data.
Warning in packageDescription(thispkg) :
  no package 'AnnotationForge' was found

  When sourcing ‘GCSscore.R’:
Error: $ operator is invalid for atomic vectors
Execution halted

* checking re-building of vignette outputs ... NOTE
Error(s) in re-building vignettes:
--- re-building ‘GCSscore.Rnw’ using Sweave
Warning: Package 'GCSscore' is deprecated and will be removed from Bioconductor
  version 3.19
GCSscore supports the selected chip-type: Clariom_S_Mouse
Bioconductor platform design (.pd) package already installed for: Clariom_S_Mouse
GCS-score analysis initiated for chip-type: Clariom_S_Mouse
GCS-score 'probeFile' package needs to be installed for chip-type: Clariom_S_Mouse
typeFilter set to (0) by default for best .CEL file scaling and normalization statistics 
 all probe_id types (including control probe_ids and bgp probe_ids) will be for GCS-score calculation.
it is generally recommended to leave the typeFilter option set to (0)
** Checking if Bioconductor annotation (.db) packages are installed chip-type: Clariom_S_Mouse **  


Annotation package (clariomsmousetranscriptcluster.db) already installed for chip-type: Clariom_S_Mouse

 ** Generating probeFile package for chip-type: Clariom_S_Mouse **
*This package will only be generated once for each chip-type*
*Or if probeFile version for the chip-type needs to be updated*
writing intermediary .probe_tab file to temporary directory
Warning in packageDescription(thispkg) :
  no package 'AnnotationForge' was found

Error: processing vignette 'GCSscore.Rnw' failed with diagnostics:
 chunk 2 
Error in desc$Package : $ operator is invalid for atomic vectors

--- failed re-building ‘GCSscore.Rnw’

SUMMARY: processing the following file failed:
  ‘GCSscore.Rnw’

Error: Vignette re-building failed.
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.18-bioc/meat/GCSscore.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /home/biocbuild/bbs-3.18-bioc/R/bin/R CMD INSTALL GCSscore
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* installing to library ‘/home/biocbuild/bbs-3.18-bioc/R/site-library’
* installing *source* package ‘GCSscore’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'GCSscore' is deprecated and will be removed from Bioconductor
  version 3.19
** testing if installed package can be loaded from final location
Warning: Package 'GCSscore' is deprecated and will be removed from Bioconductor
  version 3.19
** testing if installed package keeps a record of temporary installation path
* DONE (GCSscore)