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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD check --install=check:AGDEX.install-out.txt --library=/home/biocbuild/bbs-3.22-bioc/R/site-library --timings AGDEX_1.57.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.22-bioc/meat/AGDEX.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
    gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
    GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.3 LTS
* using session charset: UTF-8
* checking for file ‘AGDEX/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AGDEX’ version ‘1.57.0’
* 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 ‘AGDEX’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Non-standard license specification:
  GPL Version 2 or later
Standardizable: TRUE
Standardized license specification:
  GPL (>= 2)
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘Biobase’ ‘GSEABase’
  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 ... NOTE
agdex: no visible global function definition for ‘exprs’
agdex: no visible global function definition for ‘qnorm’
agdex: no visible global function definition for ‘pnorm’
agdex: no visible global function definition for ‘sampleNames’
agdex: no visible global function definition for ‘pData’
agdex.scatterplot: no visible global function definition for ‘points’
agdex.scatterplot: no visible global function definition for ‘lines’
agdex.scatterplot: no visible global function definition for ‘prcomp’
agdex.scatterplot: no visible global function definition for ‘abline’
gsc.to.index.list: no visible global function definition for ‘geneIds’
prep.dex.set: no visible global function definition for ‘exprs’
prep.dex.set: no visible global function definition for ‘pData’
read.agdex.gset.details: no visible global function definition for
  ‘read.table’
read.agdex.gset.list: no visible global function definition for
  ‘read.table’
read.agdex.result: no visible global function definition for
  ‘read.table’
read.enrich.gset.list: no visible global function definition for
  ‘read.table’
read.gset.collection: no visible global function definition for
  ‘read.table’
read.gset.collection: no visible global function definition for
  ‘GeneSet’
read.gset.collection: no visible global function definition for
  ‘geneIds<-’
read.gset.collection: no visible global function definition for
  ‘GeneSetCollection’
write.agdex.gset.details: no visible global function definition for
  ‘write.table’
write.agdex.result: no visible global function definition for
  ‘write.table’
write.gset.list.result: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  GeneSet GeneSetCollection abline exprs geneIds geneIds<- lines pData
  pnorm points prcomp qnorm read.table sampleNames write.table
Consider adding
  importFrom("graphics", "abline", "lines", "points")
  importFrom("stats", "pnorm", "prcomp", "qnorm")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.22-bioc/meat/AGDEX.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD INSTALL AGDEX
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* installing to library ‘/home/biocbuild/bbs-3.22-bioc/R/site-library’
* installing *source* package ‘AGDEX’ ...
** this is package ‘AGDEX’ version ‘1.57.0’
** using staged installation
** R
** data
** 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
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (AGDEX)