BioC 3.3: CHECK report for ensembldb on morelia

Package: ensembldb

Version: 1.3.19

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ensembldb_1.3.19.tar.gz

StartedAt: 2016-04-21 02:02:55 -0700 (Thu, 21 Apr 2016)

EndedAt: 2016-04-21 02:12:13 -0700 (Thu, 21 Apr 2016)

EllapsedTime: 558.1 seconds

RetCode: 0

Status:  OK

CheckDir: ensembldb.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 ensembldb_1.3.19.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/ensembldb.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 ‘ensembldb/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ensembldb’ version ‘1.3.19’
* 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 ... [21s/24s] 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 ... [48s/108s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
EnsDb-exonsBy       12.877  3.392  48.438
EnsDb-lengths        6.556  0.744   7.393
EnsDb-AnnotationDbi  3.335  0.768  21.757
GeneidFilter-class   3.256  0.714  11.973
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [200s/220s]
 [200s/221s] 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-3.3-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	3.335	0.768	21.757
EnsDb-class	2.319	0.163	2.872
EnsDb-exonsBy	12.877	3.392	48.438
EnsDb-lengths	6.556	0.744	7.393
EnsDb-seqlevels	2.335	0.167	3.050
EnsDb-sequences	0.014	0.001	0.015
EnsDb-utils	1.098	0.474	1.574
GeneidFilter-class	3.256	0.714	11.973
SeqendFilter	0.082	0.001	0.085
makeEnsemblDbPackage	0.621	0.029	0.657