OTUbase 1.26.0
Daniel Beck
| Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/OTUbase | | Last Changed Rev: 129126 / Revision: 131943 | | Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
##############################################################################
##############################################################################
###
### 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 3.4.1 (2017-06-30)
* 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.
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)