BioC 3.5: CHECK report for ensembldb on malbec2

Package: ensembldb

Version: 2.0.4

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings ensembldb_2.0.4.tar.gz

StartedAt: 2017-08-15 22:48:48 -0400 (Tue, 15 Aug 2017)

EndedAt: 2017-08-15 22:55:10 -0400 (Tue, 15 Aug 2017)

EllapsedTime: 382.6 seconds

RetCode: 0

Status:  OK

CheckDir: ensembldb.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings ensembldb_2.0.4.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/ensembldb.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (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 ‘2.0.4’
* 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 ... NOTE
  installed size is  5.4Mb
  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 3.884  0.348  26.485
Filter-classes      2.648  0.708  15.207
EnsDb-exonsBy       2.076  0.204   6.399
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘testthat.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
  ‘/home/biocbuild/bbs-3.5-bioc/meat/ensembldb.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
EnsDb-AnnotationDbi	3.884	0.348	26.485
EnsDb-class	1.588	0.044	1.947
EnsDb-exonsBy	2.076	0.204	6.399
EnsDb-lengths	0.852	0.024	0.875
EnsDb-seqlevels	1.680	0.008	3.402
EnsDb-sequences	0.012	0.000	0.010
EnsDb-utils	0.540	0.004	0.546
EnsDb	1.484	0.048	1.536
Filter-classes	2.648	0.708	15.207
ProteinFunctionality	0.492	0.136	0.628
hasProteinData-EnsDb-method	0.012	0.000	0.010
listEnsDbs	0	0	0
makeEnsemblDbPackage	0.808	0.012	0.819
useMySQL-EnsDb-method	0.012	0.000	0.010