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BioC 3.5: CHECK report for OTUbase on tokay2

This page was generated on 2017-10-18 14:20:53 -0400 (Wed, 18 Oct 2017).

Package 935/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
OTUbase 1.26.0
Daniel Beck
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/OTUbase
Branch: RELEASE_3_5
Last Commit: af3d881
Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: OTUbase
Version: 1.26.0
Command: rm -rf OTUbase.buildbin-libdir OTUbase.Rcheck && mkdir OTUbase.buildbin-libdir OTUbase.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OTUbase.buildbin-libdir OTUbase_1.26.0.tar.gz >OTUbase.Rcheck\00install.out 2>&1 && cp OTUbase.Rcheck\00install.out OTUbase-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=OTUbase.buildbin-libdir --install="check:OTUbase-install.out" --force-multiarch --no-vignettes --timings OTUbase_1.26.0.tar.gz
StartedAt: 2017-10-18 01:50:43 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 01:54:54 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 251.2 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 && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=OTUbase.buildbin-libdir OTUbase_1.26.0.tar.gz >OTUbase.Rcheck\00install.out 2>&1 && cp OTUbase.Rcheck\00install.out OTUbase-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=OTUbase.buildbin-libdir --install="check:OTUbase-install.out" --force-multiarch --no-vignettes --timings OTUbase_1.26.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/OTUbase.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* 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 '1.26.0'
* 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
  'C:/Users/biocbuild/bbs-3.5-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_1.26.0.zip
* DONE (OTUbase)

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

nameusersystemelapsed
OTUset-class0.430.000.44
TAXset-class0.460.000.45
abundance0.300.020.31
accessors0.620.000.64
assignmentData0.100.000.09
clusterSamples0.140.000.14
other_functions0.30.00.3
other_generics0.090.000.09
readOTUset0.110.000.11
readTAXset0.140.000.14
sampleData0.120.000.13
subOTUset0.110.000.11
subTAXset0.210.000.20

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

nameusersystemelapsed
OTUset-class0.570.000.58
TAXset-class0.550.000.54
abundance0.360.020.37
accessors0.740.000.73
assignmentData0.110.000.11
clusterSamples0.150.000.16
other_functions0.380.000.37
other_generics0.110.000.11
readOTUset0.120.000.13
readTAXset0.140.000.14
sampleData0.160.000.16
subOTUset0.140.000.14
subTAXset0.240.000.24