Package: a4

Version: 1.35.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:a4.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings a4_1.35.0.tar.gz

StartedAt: 2020-01-16 01:31:58 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 01:34:23 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 145.2 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: a4.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:a4.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings a4_1.35.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/a4.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘a4/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘a4’ version ‘1.35.0’
* 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 ‘a4’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'KEGG.db' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.11-bioc/meat/a4.Rcheck/00install.out’ for details.
* 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.
* 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:
  ‘a4Base’ ‘a4Classif’ ‘a4Core’ ‘a4Preproc’ ‘a4Reporting’
  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
.onAttach: no visible global function definition for
  ‘packageDescription’
Undefined global functions or variables:
  packageDescription
Consider adding
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
* checking for missing documentation entries ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.11-bioc/meat/a4.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 a4
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
* installing *source* package ‘a4’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Warning message:
Package 'KEGG.db' is deprecated and will be removed from Bioconductor
  version 3.12 
** help
No man pages found in package  ‘a4’ 
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'KEGG.db' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package can be loaded from final location
Warning: Package 'KEGG.db' is deprecated and will be removed from Bioconductor
  version 3.12
** testing if installed package keeps a record of temporary installation path
* DONE (a4)