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BioC 3.0: CHECK report for ddCt on perceval

This page was generated on 2015-04-10 09:54:36 -0700 (Fri, 10 Apr 2015).

Package 224/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
ddCt 1.20.0
Jitao David Zhang
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/ddCt
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ WARNINGS ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK 

Summary

Package: ddCt
Version: 1.20.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ddCt_1.20.0.tar.gz
StartedAt: 2015-04-10 00:37:33 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 00:38:39 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 65.5 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: ddCt.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ddCt_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/ddCt.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.20.0’
* 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/8s] 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:
  ‘lattice’ ‘methods’ ‘RColorBrewer’ ‘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 ... WARNING
Found the following file(s) containing GNU extensions:
  Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
* 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’ [2s/2s]
 [2s/2s] 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

WARNING: There was 1 warning.
NOTE: There were 2 notes.
See
  ‘/Users/biocbuild/bbs-3.0-bioc/meat/ddCt.Rcheck/00check.log’
for details.

ddCt.Rcheck/00install.out:

* 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)

ddCt.Rcheck/ddCt-Ex.timings:

nameusersystemelapsed
InputReader-class0.0880.0010.089
SDMFrame-class0.0380.0040.041
SDMFrame0.0130.0040.016
barploterrbar0.0070.0020.009
ddCtExpression-class0.1260.0020.127
ddCtExpression-methods0.0650.0010.067
elistWrite-methods0.0640.0010.065
errBarchartParameter-class0.0000.0000.001
getDir0.0000.0000.001
replaceVectorByEquality0.0010.0010.001