BioC 2.13: CHECK report for clstutils on perceval

Package: clstutils

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch clstutils_1.10.0.tar.gz

StartedAt: 2014-04-05 00:26:21 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 00:28:12 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 111.5 seconds

RetCode: 0

Status:  OK

CheckDir: clstutils.Rcheck

Warnings: 0

* using log directory ‘/Users/biocbuild/bbs-2.13-bioc/meat/clstutils.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 ‘clstutils/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘clstutils’ version ‘1.10.0’
* 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 ‘clstutils’ can be installed ... [3s/3s] 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 ‘rjson’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘ape’ ‘rjson’
  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 ... NOTE
Foreign function call to a different package:
  .Call("seq_root2tip", ..., PACKAGE = "ape")
See the chapter ‘System and foreign language interfaces’ of the
‘Writing R Extensions’ manual.
* checking R code for possible problems ... OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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’:
  ‘pplacerDemo.Rnw’, ‘refSet.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [24s/25s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
classifyPlacements 13.924  0.651  14.963
treeDists           6.702  0.452   7.295
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runalltests.R’ [47s/49s]
 [47s/50s] 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/clstutils.Rcheck/00check.log’
for details.

* installing *source* package ‘clstutils’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (clstutils)

name	user	system	elapsed
classifyPlacements	13.924	0.651	14.963
clstutils-package	0.016	0.004	0.020
findOutliers	0.101	0.011	0.113
maxDists	0.136	0.022	0.162
prettyTree	0.127	0.009	0.136
refpkgContents	0.144	0.030	0.178
seqdat	0.005	0.004	0.009
seqs	0.015	0.009	0.024
taxonomyFromRefpkg	0.151	0.027	0.182
treeDists	6.702	0.452	7.295