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BioC 2.13: CHECK report for clstutils on zin1

This page was generated on 2014-04-05 09:48:01 -0700 (Sat, 05 Apr 2014).

Package 147/750HostnameOS / ArchBUILDCHECKBUILD BIN
clstutils 1.10.0
Noah Hoffman
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/clstutils
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: clstutils
Version: 1.10.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings clstutils_1.10.0.tar.gz
StartedAt: 2014-04-05 00:24:02 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 00:25:02 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 59.6 seconds
RetCode: 0
Status:  OK 
CheckDir: clstutils.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/clstutils.Rcheck’
* using R version 3.0.3 (2014-03-06)
* using platform: x86_64-unknown-linux-gnu (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 ... [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 ‘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 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 ... [13s/14s] OK
Examples with CPU or elapsed time > 5s
                   user system elapsed
classifyPlacements 7.42  0.216    7.71
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘runalltests.R’ [26s/26s]
 [26s/26s] 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
  ‘/home/biocbuild/bbs-2.13-bioc/meat/clstutils.Rcheck/00check.log’
for details.

clstutils.Rcheck/00install.out:

* 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)

clstutils.Rcheck/clstutils-Ex.timings:

nameusersystemelapsed
classifyPlacements7.4200.2167.710
clstutils-package0.0120.0000.011
findOutliers0.0560.0000.063
maxDists0.0840.0040.087
prettyTree0.0680.0000.070
refpkgContents0.1120.0160.125
seqdat0.0000.0040.004
seqs0.0120.0000.009
taxonomyFromRefpkg0.1280.0320.156
treeDists4.3640.1604.532