BioC 2.14: CHECK report for PSICQUIC on petty

Package: PSICQUIC

Version: 1.2.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch PSICQUIC_1.2.1.tar.gz

StartedAt: 2014-10-07 23:35:22 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:39:19 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 236.4 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: PSICQUIC.Rcheck

Warnings: 2

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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 PSICQUIC_1.2.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/PSICQUIC.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PSICQUIC/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘PSICQUIC’ version ‘1.2.1’
* 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 ‘PSICQUIC’ can be installed ... [17s/18s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.translate.geneSymbol: no visible binding for global variable
  ‘tbl.refseq’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  ‘addStandardNames’
Undocumented S4 methods:
  generic 'addStandardNames' and siglist 'IDMapper'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'IDMapper-class':
\S4method{addGeneInfo}{IDMapper}
  Code: function(object, tbl)
  Docs: function(object, tbl.interactions)
  Argument names in code not in docs:
    tbl
  Argument names in docs not in code:
    tbl.interactions
  Mismatches in argument names:
    Position: 2 Code: tbl Docs: tbl.interactions

* 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 ... [12s/62s] OK
Examples with CPU or elapsed time > 5s
                user system elapsed
PSICQUIC-class 2.138  0.088  34.502
interactions   0.811  0.049  11.450
IDMapper-class 0.323  0.022   5.386
* 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

WARNING: There were 2 warnings.
NOTE: There was 1 note.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/PSICQUIC.Rcheck/00check.log’
for details.

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

name	user	system	elapsed
IDMapper-class	0.323	0.022	5.386
PSICQUIC-class	2.138	0.088	34.502
interactions	0.811	0.049	11.450
providers	0.025	0.001	0.680
rawQuery	0.052	0.003	1.262
webBrowser-functions	0.001	0.000	0.001