BioC 3.0: CHECK report for AnnotationHub on moscato1

Package: AnnotationHub

Version: 1.6.0

Command: D:\biocbld\bbs-3.0-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --no-vignettes --timings AnnotationHub_1.6.0.tar.gz

StartedAt: 2015-04-09 22:35:12 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 22:40:57 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 344.4 seconds

RetCode: 0

Status:  OK

CheckDir: AnnotationHub.Rcheck

Warnings: 0

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### Running command:
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###   D:\biocbld\bbs-3.0-bioc\R\bin\R.exe --arch i386 CMD check --no-multiarch --no-vignettes --timings AnnotationHub_1.6.0.tar.gz
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* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/AnnotationHub.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'AnnotationHub/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'AnnotationHub' version '1.6.0'
* 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 ... NOTE
Found the following hidden files and directories:
  .BBSoptions
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'AnnotationHub' can be installed ... [23s] 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 ... NOTE
'library' or 'require' call to 'Rsamtools' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'IRanges'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: 'BiocGenerics:::testPackage'
  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
.getRda: no visible global function definition for 'metadata<-'
.toDataFrame : .makeVecs: no visible global function definition for
  'splitAsList'
display,AnnotationHub: no visible global function definition for
  'unstrsplit'
* 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 ... [28s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
AnnotationHub-class 4.06   0.03   16.38
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'AnnotationHub_unit_tests.R' [89s]
 [90s] OK
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: 'AnnotationForge'
* 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

NOTE: There were 4 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/AnnotationHub.Rcheck/00check.log'
for details.

* installing *source* package 'AnnotationHub' ...
** R
** inst
** preparing package for lazy loading
Note: the specification for S3 class "AsIs" in package 'RJSONIO' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class "AsIs" in package 'RJSONIO' seems equivalent to one from package 'BiocGenerics': not turning on duplicate class definitions for this class.
* DONE (AnnotationHub)

name	user	system	elapsed
AnnotationHub-class	4.06	0.03	16.38