BioC 3.4: CHECK report for ensembldb on morelia

Package: ensembldb

Version: 1.6.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ensembldb_1.6.2.tar.gz

StartedAt: 2017-04-15 01:41:24 -0700 (Sat, 15 Apr 2017)

EndedAt: 2017-04-15 01:59:40 -0700 (Sat, 15 Apr 2017)

EllapsedTime: 1095.8 seconds

RetCode: 0

Status:  OK

CheckDir: ensembldb.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ensembldb_1.6.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.4-bioc/meat/ensembldb.Rcheck’
* using R version 3.3.3 (2017-03-06)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ensembldb/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ensembldb’ version ‘1.6.2’
* 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 ‘ensembldb’ can be installed ... 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:
  'GenomicFeatures:::fetchChromLengthsFromEnsembl'
  'GenomicFeatures:::fetchChromLengthsFromEnsemblPlants'
  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 ... OK
* 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 ... OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
EnsDb-exonsBy       2.252  0.825 303.190
EnsDb-AnnotationDbi 0.950  0.321 150.907
GeneidFilter-class  0.712  0.329 131.799
EnsDb-seqlevels     0.844  0.034   5.980
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.4-bioc/meat/ensembldb.Rcheck/00check.log’
for details.

* installing *source* package ‘ensembldb’ ...
** R
** inst
** preparing package for lazy loading
Creating a new generic function for ‘transcriptLengths’ in package ‘ensembldb’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ensembldb)

name	user	system	elapsed
EnsDb-AnnotationDbi	0.950	0.321	150.907
EnsDb-class	1.448	0.103	4.354
EnsDb-exonsBy	2.252	0.825	303.190
EnsDb-lengths	0.439	0.053	0.492
EnsDb-seqlevels	0.844	0.034	5.980
EnsDb-sequences	0.012	0.001	0.018
EnsDb-utils	0.213	0.005	0.218
EnsDb	1.415	0.067	2.011
GeneidFilter-class	0.712	0.329	131.799
SeqendFilter	0.052	0.001	0.053
listEnsDbs	0.001	0.000	0.001
makeEnsemblDbPackage	0.675	0.046	2.064
useMySQL-EnsDb-method	0.011	0.001	0.011