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 ] | |  |
| windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings OTUbase_1.20.0.tar.gz
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* 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.
* 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)