BioC 3.5: CHECK report for ArrayExpress on veracruz2

Package: ArrayExpress

Version: 1.36.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ArrayExpress_1.36.1.tar.gz

StartedAt: 2017-10-18 00:30:36 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 00:34:15 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 219.0 seconds

RetCode: 0

Status:  OK

CheckDir: ArrayExpress.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ArrayExpress_1.36.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ArrayExpress.Rcheck’
* using R version 3.4.2 (2017-09-28)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ArrayExpress/DESCRIPTION’ ... OK
* this is package ‘ArrayExpress’ version ‘1.36.1’
* 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 ‘ArrayExpress’ 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.
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ae2bioc: no visible global function definition for ‘new’
extract.zip : <anonymous>: no visible global function definition for
  ‘unzip’
getAE : <anonymous>: no visible global function definition for
  ‘download.file’
getAE: no visible global function definition for ‘download.file’
getDataColsForAE1: no visible global function definition for
  ‘read.table’
preparePhenoDataFor2channel: no visible global function definition for
  ‘new’
queryAE: no visible global function definition for ‘download.file’
readDerivedDataFiles: no visible global function definition for
  ‘read.table’
readDerivedDataFiles: no visible global function definition for ‘new’
readDerivedDataMatrixFile: no visible global function definition for
  ‘read.table’
readDerivedDataMatrixFile: no visible global function definition for
  ‘new’
readExperimentData: no visible global function definition for ‘new’
readFeatures: no visible global function definition for ‘read.table’
readFeatures: no visible global function definition for ‘new’
readPhenoData: no visible global function definition for ‘new’
Undefined global functions or variables:
  download.file new read.table unzip
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "download.file", "read.table", "unzip")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
getAE        19.812  1.103  33.388
ArrayExpress  5.524  0.887  16.122
queryAE       2.646  0.111   6.218
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-bioc/meat/ArrayExpress.Rcheck/00check.log’
for details.

* installing *source* package ‘ArrayExpress’ ...
** R
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* DONE (ArrayExpress)

name	user	system	elapsed
ArrayExpress	5.524	0.887	16.122
ae2bioc	0.001	0.000	0.000
getAE	19.812	1.103	33.388
procset	0.000	0.000	0.001
queryAE	2.646	0.111	6.218