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Package 452/658HostnameOS / ArchBUILDCHECKBUILD BIN
OTUbase 1.9.1
Daniel Beck
Snapshot Date: 2013-03-24 17:01:43 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OTUbase
Last Changed Rev: 72298 / Revision: 74774
Last Changed Date: 2013-01-04 13:18:09 -0800 (Fri, 04 Jan 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: OTUbase
Version: 1.9.1
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings OTUbase_1.9.1.tar.gz
StartedAt: 2013-03-25 03:31:30 -0700 (Mon, 25 Mar 2013)
EndedAt: 2013-03-25 03:36:42 -0700 (Mon, 25 Mar 2013)
EllapsedTime: 312.2 seconds
RetCode: 0
Status:  OK 
CheckDir: OTUbase.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.12-bioc/meat/OTUbase.Rcheck’
* using R version 3.0.0 beta (2013-03-19 r62328)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘OTUbase/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘OTUbase’ version ‘1.9.1’
* 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 ‘OTUbase’ can be installed ... [29s/31s] OK
* checking installed package size ... OK
* checking package 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
.onAttach: warning in packageDescription("OTUbase", field = "Version"):
  partial argument match of 'field' to 'fields'
.readADF: warning in read.table(file.path(dirPath, ADF), sep = "\t",
  head = T): partial argument match of 'head' to 'header'
.readRDP: warning in read.table(file.path(dirPath, ADF), head = F, sep
  = "\t", stringsAsFactors = F): partial argument match of 'head' to
  'header'
.readrdpfix: warning in read.table(file.path(dirPath, rdpfile), head =
  F, stringsAsFactors = F, sep = "\t"): partial argument match of
  'head' to 'header'
readTAXset: warning in read.table(file.path(dirPath, namefile), head =
  F, stringsAsFactors = F, sep = "\t"): partial argument match of
  'head' to 'header'
* 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 installed files from ‘inst/doc’ ... OK
* checking examples ... [20s/22s] 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  ‘/home/biocbuild/bbs-2.12-bioc/meat/OTUbase.Rcheck/00check.log’
for details.

OTUbase.Rcheck/00install.out:

* installing *source* package ‘OTUbase’ ...
** R
** inst
** preparing package for lazy loading
Warning in .simpleDuplicateClass(def, prev) :
  the specification for class “.ShortReadBase” in package ‘OTUbase’ seems equivalent to one from package ‘ShortRead’ and is not turning on duplicate class definitions for this class
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘Introduction_to_OTUbase.Rnw’ 
** testing if installed package can be loaded
Warning in .simpleDuplicateClass(def, prev) :
  the specification for class “.ShortReadBase” in package ‘OTUbase’ seems equivalent to one from package ‘ShortRead’ and is not turning on duplicate class definitions for this class
* DONE (OTUbase)

OTUbase.Rcheck/OTUbase-Ex.timings:

nameusersystemelapsed
OTUset-class0.7720.0120.930
TAXset-class0.7890.0040.968
abundance0.2400.0160.279
accessors0.1920.0160.232
assignmentData0.1720.0000.183
clusterSamples0.1720.0080.184
other_functions0.1720.0040.175
other_generics0.1680.0000.199
readOTUset0.1600.0040.169
readTAXset0.1400.0120.167
sampleData0.1680.0040.457
subOTUset0.2000.0120.260
subTAXset0.1760.0000.237