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BioC 3.4: CHECK report for OTUbase on moscato1

This page was generated on 2016-09-21 03:43:10 -0700 (Wed, 21 Sep 2016).

Package 855/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OTUbase 1.23.0
Daniel Beck
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/OTUbase
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: OTUbase
Version: 1.23.0
Command: rm -rf OTUbase.buildbin-libdir OTUbase.Rcheck && mkdir OTUbase.buildbin-libdir OTUbase.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OTUbase.buildbin-libdir OTUbase_1.23.0.tar.gz >OTUbase.Rcheck\00install.out 2>&1 && cp OTUbase.Rcheck\00install.out OTUbase-install.out && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=OTUbase.buildbin-libdir --install="check:OTUbase-install.out" --force-multiarch --no-vignettes --timings OTUbase_1.23.0.tar.gz
StartedAt: 2016-09-20 13:28:37 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 13:32:43 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 245.7 seconds
RetCode: 0
Status:  OK  
CheckDir: OTUbase.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf OTUbase.buildbin-libdir OTUbase.Rcheck && mkdir OTUbase.buildbin-libdir OTUbase.Rcheck && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OTUbase.buildbin-libdir OTUbase_1.23.0.tar.gz >OTUbase.Rcheck\00install.out 2>&1 && cp OTUbase.Rcheck\00install.out OTUbase-install.out  && D:\biocbld\bbs-3.4-bioc\R\bin\R.exe CMD check --library=OTUbase.buildbin-libdir --install="check:OTUbase-install.out" --force-multiarch --no-vignettes --timings OTUbase_1.23.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.4-bioc/meat/OTUbase.Rcheck'
* using R version 3.3.1 (2016-06-21)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'OTUbase/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'OTUbase' version '1.23.0'
* 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 whether package 'OTUbase' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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: no visible global function definition for
  'vegdist'
clusterSamples,.TAXset: no visible global function definition for
  'vegdist'
Undefined global functions or variables:
  diversity estimateR 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... 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
  'D:/biocbld/bbs-3.4-bioc/meat/OTUbase.Rcheck/00check.log'
for details.


OTUbase.Rcheck/00install.out:


install for i386

* installing *source* package 'OTUbase' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded

install for x64

* installing *source* package 'OTUbase' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'OTUbase' as OTUbase_1.23.0.zip
* DONE (OTUbase)

OTUbase.Rcheck/examples_i386/OTUbase-Ex.timings:

nameusersystemelapsed
OTUset-class0.510.020.53
TAXset-class0.390.000.39
abundance0.160.010.17
accessors0.070.000.08
assignmentData0.080.000.07
clusterSamples0.090.000.37
other_functions0.080.000.08
other_generics0.080.000.08
readOTUset0.080.000.08
readTAXset0.070.000.08
sampleData0.100.000.09
subOTUset0.090.000.09
subTAXset0.090.000.10

OTUbase.Rcheck/examples_x64/OTUbase-Ex.timings:

nameusersystemelapsed
OTUset-class0.570.000.58
TAXset-class0.50.00.5
abundance0.170.000.17
accessors0.080.000.08
assignmentData0.090.000.09
clusterSamples0.100.020.16
other_functions0.070.000.08
other_generics0.080.000.08
readOTUset0.080.000.08
readTAXset0.090.000.09
sampleData0.080.000.08
subOTUset0.090.000.09
subTAXset0.080.000.08