BioC 3.5: CHECK report for ensembldb on oaxaca

Package: ensembldb

Version: 1.99.12

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ensembldb_1.99.12.tar.gz

StartedAt: 2017-03-04 02:22:26 -0800 (Sat, 04 Mar 2017)

EndedAt: 2017-03-04 02:33:30 -0800 (Sat, 04 Mar 2017)

EllapsedTime: 663.8 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_1.99.12.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/ensembldb.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* 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 ‘1.99.12’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘RMySQL’
* 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 ... NOTE
  installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   3.6Mb
* 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 ... OK
* 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-AnnotationDbi 5.606  0.738  21.812
ProteinFilters      2.938  1.889  50.666
EnsDb-exonsBy       2.612  0.652  47.494
GeneidFilter-class  0.742  0.220  11.148
* 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: 2 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-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	5.606	0.738	21.812
EnsDb-class	3.483	0.175	3.742
EnsDb-exonsBy	2.612	0.652	47.494
EnsDb-lengths	0.747	0.072	0.819
EnsDb-seqlevels	1.700	0.030	2.251
EnsDb-sequences	0.016	0.001	0.017
EnsDb-utils	0.467	0.007	0.474
EnsDb	2.267	0.133	2.400
GeneidFilter-class	0.742	0.220	11.148
ProteinFilters	2.938	1.889	50.666
ProteinFunctionality	0.411	0.194	0.796
SeqendFilter	0.046	0.000	0.046
hasProteinData-EnsDb-method	0.010	0.000	0.011
listEnsDbs	0.001	0.000	0.000
makeEnsemblDbPackage	0.956	0.050	1.013
useMySQL-EnsDb-method	0.013	0.000	0.013