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BioC 2.13: CHECK report for ctc on perceval

This page was generated on 2014-04-05 09:51:35 -0700 (Sat, 05 Apr 2014).

Package 180/750HostnameOS / ArchBUILDCHECKBUILD BIN
ctc 1.36.0
Antoine Lucas
Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/ctc
Last Changed Rev: 81642 / Revision: 88450
Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: ctc
Version: 1.36.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch ctc_1.36.0.tar.gz
StartedAt: 2014-04-05 00:38:20 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 00:38:46 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 26.0 seconds
RetCode: 0
Status:  OK 
CheckDir: ctc.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/ctc.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 ‘ctc/DESCRIPTION’ ... OK
* this is package ‘ctc’ version ‘1.36.0’
* 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 ‘ctc’ 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 dependencies in R code ... NOTE
‘library’ or ‘require’ call to ‘amap’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘amap’
  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
.First.lib: warning in .packages(all = TRUE): partial argument match of
  'all' to 'all.available'
.onLoad: warning in .packages(all = TRUE): partial argument match of
  'all' to 'all.available'
hclust2treeview: warning in .packages(all = TRUE): partial argument
  match of 'all' to 'all.available'
r2atr: warning in write.table(data, file = file, row.name = FALSE,
  col.names = FALSE, quote = FALSE, sep = "\t"): partial argument match
  of 'row.name' to 'row.names'
r2gtr: warning in write.table(data, file = file, row.name = FALSE,
  col.names = FALSE, quote = FALSE, sep = "\t", dec = dec): partial
  argument match of 'row.name' to 'row.names'
* 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’:
  ‘ctc.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.13-bioc/meat/ctc.Rcheck/00check.log’
for details.

ctc.Rcheck/00install.out:

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

ctc.Rcheck/ctc-Ex.timings:

nameusersystemelapsed
hc2Newick0.0460.0050.051
hclust2treeview0.0500.0160.067
r2cluster0.0210.0010.023
r2gtr0.0330.0020.036
r2xcluster0.0730.0020.075
xcluster0.0130.0010.014
xcluster2r0.0180.0010.020