Package: AGDEX

Version: 1.28.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AGDEX.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AGDEX_1.28.0.tar.gz

StartedAt: 2018-10-16 19:48:46 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 19:50:19 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 93.1 seconds

RetCode: 0

Status:  OK

CheckDir: AGDEX.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:AGDEX.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings AGDEX_1.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/AGDEX.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AGDEX/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AGDEX’ version ‘1.28.0’
* 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 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 ... 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 ‘plot’
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
  plot pnorm points prcomp qnorm read.table sampleNames write.table
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "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 sizes of PDF files under ‘inst/doc’ ... 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 ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.7-bioc/meat/AGDEX.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL AGDEX
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘AGDEX’ ...
** 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
* DONE (AGDEX)

name	user	system	elapsed
agdex	0.623	0.015	0.641
agdex.scatterplot	0.015	0.003	0.019
get.gset.result.details	0.034	0.003	0.037
gset.data	0.002	0.000	0.003
human.data	0.012	0.002	0.015
make.dex.set.object	0.038	0.008	0.046
map.data	0.002	0.000	0.003
mouse.data	0.019	0.002	0.021
read.agdex.gset.details	0.001	0.000	0.001
read.agdex.result	0.001	0.000	0.001
write.agdex.gset.details	0.033	0.003	0.036
write.agdex.result	0.009	0.003	0.013