BioC 2.13: CHECK report for ddCt on perceval

Package: ddCt

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ddCt_1.16.0.tar.gz

StartedAt: 2014-04-05 00:41:21 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 00:42:27 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 65.8 seconds

RetCode: 0

Status:  OK

CheckDir: ddCt.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/ddCt.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ddCt/DESCRIPTION’ ... OK
* this is package ‘ddCt’ version ‘1.16.0’
* 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 ... [5s/5s] 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:
  ‘lattice’ ‘methods’ ‘RColorBrewer’ ‘xtable’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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'
* 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘RT-PCR-Script-ddCt.Rnw’, ‘rtPCR-usage.Rnw’, ‘rtPCR.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [3s/3s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘unit.R’ [2s/2s]
 [3s/3s] 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-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	0.008	0.001	0.008
SDMFrame-class	0.084	0.005	0.090
SDMFrame	0.057	0.003	0.062
barploterrbar	0.013	0.001	0.014
ddCtExpression-class	0.158	0.006	0.165
ddCtExpression-methods	0.195	0.008	0.204
elistWrite-methods	0.080	0.002	0.082
errBarchartParameter-class	0.010	0.001	0.012
getDir	0.013	0.001	0.013
replaceVectorByEquality	0.011	0.001	0.012