BioC 3.3: CHECK report for OrganismDbi on oaxaca

Package: OrganismDbi

Version: 1.14.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings OrganismDbi_1.14.1.tar.gz

StartedAt: 2016-10-13 04:46:35 -0700 (Thu, 13 Oct 2016)

EndedAt: 2016-10-13 04:56:19 -0700 (Thu, 13 Oct 2016)

EllapsedTime: 584.1 seconds

RetCode: 1

Status:  ERROR

CheckDir: OrganismDbi.Rcheck

Warnings: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings OrganismDbi_1.14.1.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/OrganismDbi.Rcheck’
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OrganismDbi/DESCRIPTION’ ... OK
* this is package ‘OrganismDbi’ version ‘1.14.1’
* 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 ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
Running examples in ‘OrganismDbi-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: makeOrganismDbFromTxDb
> ### Title: Make an OrganismDb object from an existing TxDb object.
> ### Aliases: makeOrganismDbFromTxDb
> 
> ### ** Examples
> 
> ## lets start with a txdb object
> transcript_ids <- c(
+     "uc009uzf.1",
+     "uc009uzg.1",
+     "uc009uzh.1",
+     "uc009uzi.1",
+     "uc009uzj.1"
+ )
> txdbMouse <- makeTxDbFromUCSC(genome="mm9", tablename="knownGene",
+                           transcript_ids=transcript_ids)
Error in normArgTable(value, x) : unknown table name 'chromInfo'
Calls: makeTxDbFromUCSC ... tableName<- -> tableName<- -> .local -> normArgTable
Execution halted
* 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: 1 ERROR, 1 NOTE
See
  ‘/Users/biocbuild/bbs-3.3-bioc/meat/OrganismDbi.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
OrganismDb	8.773	0.526	15.098
coordinate-mapping-method	1.100	0.037	1.139
makeOrganismDbFromBiomart	18.028	0.720	88.246