BioC 3.5: CHECK report for OrganismDbi on malbec2

Package: OrganismDbi

Version: 1.18.0

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings OrganismDbi_1.18.0.tar.gz

StartedAt: 2017-08-16 01:06:10 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:16:38 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 627.9 seconds

RetCode: 0

Status:  OK

CheckDir: OrganismDbi.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 OrganismDbi_1.18.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/OrganismDbi.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 ‘OrganismDbi/DESCRIPTION’ ... OK
* this is package ‘OrganismDbi’ version ‘1.18.0’
* 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 ‘OrganismDbi’ 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 object imported by a ':::' call: ‘BiocGenerics:::testPackage’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.biocAnnPackages’ ‘.extractPkgsAndCols’ ‘.gentlyExtractDbFiles’
  ‘.lookupDbNameFromKeytype’ ‘.mungeGraphData’ ‘.taxIdToOrgDb’
  ‘.taxIdToOrgDbName’ ‘.testGraphData’ ‘.testKeys’ ‘OrganismDb’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.getMetaDataValue: no visible global function definition for
  ‘dbGetQuery’
Undefined global functions or variables:
  dbGetQuery
* 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
makeOrganismDbFromBiomart 15.816  0.232  46.932
OrganismDb                10.580  0.136  14.796
rangeBasedAccessors        7.128  0.024   7.154
makeOrganismDbFromTxDb     5.416  0.068  79.746
makeOrganismDbFromUCSC     4.892  0.052  80.705
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘OrganismDbi_unit_tests.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
  ‘/home/biocbuild/bbs-3.5-bioc/meat/OrganismDbi.Rcheck/00check.log’
for details.

* installing *source* package ‘OrganismDbi’ ...
** R
** inst
** preparing package for lazy loading
No methods found in "RSQLite" for requests: dbGetQuery
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "RSQLite" for requests: dbGetQuery
* DONE (OrganismDbi)

name	user	system	elapsed
OrganismDb	10.580	0.136	14.796
coordinate-mapping-method	1.288	0.004	1.290
makeOrganismDbFromBiomart	15.816	0.232	46.932
makeOrganismDbFromTxDb	5.416	0.068	79.746
makeOrganismDbFromUCSC	4.892	0.052	80.705
makeOrganismPackage	0.000	0.000	0.001
rangeBasedAccessors	7.128	0.024	7.154