BioC 3.4: CHECK report for ensembldb on zin1

Package: ensembldb

Version: 1.5.11

Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings ensembldb_1.5.11.tar.gz

StartedAt: 2016-09-15 05:47:59 -0700 (Thu, 15 Sep 2016)

EndedAt: 2016-09-15 05:53:19 -0700 (Thu, 15 Sep 2016)

EllapsedTime: 320.8 seconds

RetCode: 0

Status:  OK

CheckDir: ensembldb.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings ensembldb_1.5.11.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/ensembldb.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘1.5.11’
* 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       7.020  0.956  12.136
EnsDb-AnnotationDbi 2.184  0.196   5.120
* 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
  ‘/home/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’
Creating a generic function for ‘print’ from package ‘base’ 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	2.184	0.196	5.120
EnsDb-class	1.452	0.072	1.522
EnsDb-exonsBy	7.020	0.956	12.136
EnsDb-lengths	1.828	0.140	1.970
EnsDb-seqlevels	1.328	0.048	1.378
EnsDb-sequences	0.008	0.000	0.009
EnsDb-utils	0.748	0.124	0.871
GeneidFilter-class	2.448	0.264	3.782
SeqendFilter	0.056	0.000	0.059
makeEnsemblDbPackage	0.416	0.008	0.425