BioC 3.0: CHECK report for UniProt.ws on oaxaca

Package: UniProt.ws

Version: 2.6.2

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch UniProt.ws_2.6.2.tar.gz

StartedAt: 2015-04-10 04:02:20 -0700 (Fri, 10 Apr 2015)

EndedAt: 2015-04-10 04:14:12 -0700 (Fri, 10 Apr 2015)

EllapsedTime: 712.1 seconds

RetCode: 0

Status:  OK

CheckDir: UniProt.ws.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 --no-multiarch UniProt.ws_2.6.2.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/UniProt.ws.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘UniProt.ws/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘UniProt.ws’ version ‘2.6.2’
* 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 ‘UniProt.ws’ can be installed ... [11s/37s] 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
Packages in Depends field not imported from:
  ‘RCurl’ ‘RSQLite’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
  ‘AnnotationDbi:::.colsArgumentWarning’ ‘AnnotationDbi:::.resort’
  ‘BiocGenerics:::testPackage’
  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 ... NOTE
.createTables: no visible global function definition for
  ‘sqliteQuickSQL’
.onLoad: no visible global function definition for ‘UniProt.ws’
.tryGetResult: no visible global function definition for ‘getForm’
* 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 ... [8s/73s] OK
Examples with CPU or elapsed time > 5s
                 user system elapsed
UniProtWS-class 2.216   0.03  43.899
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘UniProt.ws_unit_tests.R’ [9s/128s]
 [9s/129s] 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

NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/UniProt.ws.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
UniProtWS-class	2.216	0.030	43.899
colsAndKeytypes	0.090	0.004	2.062