BioC 3.2: CHECK report for AnnotationHubData on oaxaca

Package: AnnotationHubData

Version: 1.0.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AnnotationHubData_1.0.2.tar.gz

StartedAt: 2016-04-22 21:50:36 -0700 (Fri, 22 Apr 2016)

EndedAt: 2016-04-22 22:02:46 -0700 (Fri, 22 Apr 2016)

EllapsedTime: 729.8 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: AnnotationHubData.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings AnnotationHubData_1.0.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/AnnotationHubData.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘AnnotationHubData/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘AnnotationHubData’ version ‘1.0.2’
* 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 ‘AnnotationHubData’ can be installed ... [22s/22s] OK
* checking installed package size ... OK
* 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 dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘curl’
Missing objects imported by ':::' calls:
  ‘AnnotationHub:::.db_connection’ ‘AnnotationHub:::.metadata’
Unexported object imported by a ':::' call: ‘OrganismDbi:::.packageTaxIds’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.NCBIMetadataFromUrl: no visible binding for global variable ‘results’
.NCBIMetadataFromUrl: no visible binding for global variable ‘specData’
.runRecipes: no visible binding for global variable ‘ahroot’
getAHTrackDates: no visible global function definition for
  ‘snapshotUrl’
trackWithAuxiliaryTablesToGRanges: no visible global function
  definition for ‘outputfile’
updateResources: no visible binding for global variable
  ‘listOfExistingResources’
* 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [11s/11s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [88s/516s]
 [88s/516s] 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: 1 WARNING, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/AnnotationHubData.Rcheck/00check.log’
for details.

* installing *source* package ‘AnnotationHubData’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (AnnotationHubData)

name	user	system	elapsed
AnnotationHubMetadata-class	0.004	0.001	0.004
ImportPreparer-class	0.002	0.001	0.002
upload_to_S3	0.000	0.000	0.001