BioC 3.3: CHECK report for OrganismDbi on morelia

Package: OrganismDbi

Version: 1.13.8

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings OrganismDbi_1.13.8.tar.gz

StartedAt: 2016-04-21 05:45:46 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 06:01:13 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 928.0 seconds

RetCode: 0

Status:  OK

CheckDir: OrganismDbi.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings OrganismDbi_1.13.8.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/OrganismDbi.Rcheck’
* using R version 3.3.0 beta (2016-04-06 r70435)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OrganismDbi/DESCRIPTION’ ... OK
* this is package ‘OrganismDbi’ version ‘1.13.8’
* 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 ‘OrganismDbi’ can be installed ... [15s/15s] 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
Unexported objects imported by ':::' calls:
  ‘AnnotationDbi:::.chooseCentralOrgPkgSymbol’
  ‘AnnotationDbi:::.mapIds’ ‘AnnotationDbi:::.resort’
  ‘AnnotationDbi:::.testForValidKeytype’
  ‘AnnotationDbi:::.testSelectArgs’ ‘BiocGenerics:::testPackage’
  ‘GenomicFeatures:::.makePackageName’
  ‘GenomicFeatures:::.set_group_names’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.biocAnnPackages’ ‘.extractPkgsAndCols’ ‘.gentlyExtractDbFiles’
  ‘.lookupDbNameFromKeytype’ ‘.mungeGraphData’ ‘.taxIdToOrgDb’
  ‘.taxIdToOrgDbName’ ‘.testGraphData’ ‘.testKeys’ ‘OrganismDb’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.taxIdToOrgDb: no visible global function definition for
  ‘AnnotationHub’
.taxIdToOrgDbName: no visible global function definition for
  ‘AnnotationHub’
available.GTFsForTxDbs: no visible global function definition for
  ‘AnnotationHub’
Undefined global functions or variables:
  AnnotationHub
* 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 ... [57s/529s] OK
Examples with CPU or elapsed time > 5s
                            user system elapsed
makeOrganismDbFromBiomart 14.501  0.504 342.147
rangeBasedAccessors        9.739  0.349  10.099
makeOrganismDbFromUCSC     8.657  0.310  80.507
makeOrganismDbFromTxDb     7.703  0.356  79.140
OrganismDb                 7.512  0.398   9.744
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘OrganismDbi_unit_tests.R’ [245s/272s]
 [245s/272s] 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/OrganismDbi.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
OrganismDb	7.512	0.398	9.744
coordinate-mapping-method	0.939	0.040	0.979
makeOrganismDbFromBiomart	14.501	0.504	342.147
makeOrganismDbFromTxDb	7.703	0.356	79.140
makeOrganismDbFromUCSC	8.657	0.310	80.507
makeOrganismPackage	0.003	0.000	0.003
rangeBasedAccessors	9.739	0.349	10.099