BioC 3.1: CHECK report for ddCt on morelia

Package: ddCt

Version: 1.22.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings ddCt_1.22.0.tar.gz

StartedAt: 2015-10-09 01:07:47 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 01:08:24 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 37.0 seconds

RetCode: 0

Status:  OK

CheckDir: ddCt.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 ddCt_1.22.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/ddCt.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ddCt/DESCRIPTION’ ... OK
* this is package ‘ddCt’ version ‘1.22.0’
* 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 ‘ddCt’ can be installed ... [2s/2s] 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘RColorBrewer’ ‘lattice’ ‘methods’ ‘xtable’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ddCtReport: warning in write.htmltable(cbind(rownames(lv), lv), title =
  "Level", file = file.path(html.path, "level")): partial argument
  match of 'file' to 'filename'
ddCtReport: warning in write.htmltable(cbind(rownames(Ct), Ct), title =
  "Ct", file = file.path(html.path, "Ct")): partial argument match of
  'file' to 'filename'
ddCtReport: warning in write.htmltable(cbind(rownames(dCtValues),
  dCtValues), title = "dCt", file = file.path(html.path, "dCt")):
  partial argument match of 'file' to 'filename'
ddCtReport: warning in write.htmltable(cbind(rownames(ddCtValues),
  ddCtValues), title = "ddCt", file = file.path(html.path, "ddCt")):
  partial argument match of 'file' to 'filename'
ddCtErrBarchart: no visible global function definition for ‘brewer.pal’
ddCtErrBarchart: no visible global function definition for ‘barchart’
panel.barchart.errbar: no visible global function definition for
  ‘panel.barchart’
panel.barchart.errbar: no visible global function definition for
  ‘panel.segments’
panel.ddCtErrBarchart: no visible global function definition for
  ‘panel.grid’
panel.ddCtErrBarchart: no visible global function definition for
  ‘panel.abline’
panel.ddCtErrBarchart: no visible global function definition for
  ‘panel.text’
xtable.ddCt: no visible global function definition for ‘xtable’
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [2s/2s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘unit.R’ [1s/1s]
 [1s/1s] 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
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/ddCt.Rcheck/00check.log’
for details.

* installing *source* package ‘ddCt’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘summary’ from package ‘base’ in package ‘ddCt’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ddCt)

name	user	system	elapsed
InputReader-class	0.001	0.000	0.002
SDMFrame-class	0.089	0.002	0.091
SDMFrame	0.012	0.001	0.013
barploterrbar	0.006	0.000	0.006
ddCtExpression-class	0.094	0.004	0.098
ddCtExpression-methods	0.052	0.010	0.062
elistWrite-methods	0.071	0.005	0.077
errBarchartParameter-class	0.000	0.000	0.001
getDir	0.000	0.001	0.017
replaceVectorByEquality	0.001	0.001	0.002