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BioC 3.2: CHECK report for OTUbase on linux1.bioconductor.org

This page was generated on 2015-10-27 17:24:42 -0400 (Tue, 27 Oct 2015).

Package 738/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OTUbase 1.20.0
Daniel Beck
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/OTUbase
Last Changed Rev: 109589 / Revision: 109947
Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 Oct 2015)
linux1.bioconductor.org Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: OTUbase
Version: 1.20.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings OTUbase_1.20.0.tar.gz
StartedAt: 2015-10-27 06:29:31 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 06:32:33 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 182.0 seconds
RetCode: 0
Status:  OK 
CheckDir: OTUbase.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings OTUbase_1.20.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/OTUbase.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-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 ‘1.20.0’
* 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 ‘OTUbase’ can be installed ... [18s/18s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
* 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
Package in Depends field not imported from: ‘vegan’
  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
.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'
o_diversity: no visible global function definition for ‘diversity’
o_estimateR : <anonymous>: no visible global function definition for
  ‘estimateR’
clusterSamples,.OTUset : .local: no visible global function definition
  for ‘vegdist’
clusterSamples,.TAXset : .local: no visible global function definition
  for ‘vegdist’
* 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 files in ‘vignettes’ ... OK
* checking examples ... [13s/15s] 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

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/OTUbase.Rcheck/00check.log’
for details.


OTUbase.Rcheck/00install.out:

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

OTUbase.Rcheck/OTUbase-Ex.timings:

nameusersystemelapsed
OTUset-class0.6260.0200.645
TAXset-class0.6000.0000.599
abundance0.2550.0120.267
accessors0.1470.0120.160
assignmentData0.1610.0000.193
clusterSamples0.1550.0000.252
other_functions0.5520.0000.665
other_generics0.1460.0000.240
readOTUset0.1470.0040.183
readTAXset0.1130.0080.138
sampleData0.1540.0080.286
subOTUset0.1870.0000.367
subTAXset0.1310.0000.149