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BioC 3.2: CHECK report for RGalaxy on oaxaca

This page was generated on 2015-10-27 17:40:07 -0400 (Tue, 27 Oct 2015).

Package 875/1104HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RGalaxy 1.14.0
Bioconductor Package Maintainer
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/RGalaxy
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  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
windows1.bioconductor.org Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: RGalaxy
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RGalaxy_1.14.0.tar.gz
StartedAt: 2015-10-27 07:13:57 -0400 (Tue, 27 Oct 2015)
EndedAt: 2015-10-27 07:14:57 -0400 (Tue, 27 Oct 2015)
EllapsedTime: 60.1 seconds
RetCode: 0
Status:  OK 
CheckDir: RGalaxy.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RGalaxy_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RGalaxy/DESCRIPTION’ ... OK
* this is package ‘RGalaxy’ version ‘1.14.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Package which this enhances but not available for checking: ‘RSclient’
* 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 ‘RGalaxy’ can be installed ... [4s/4s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
  ‘RSclient’ ‘hgu95av2.db’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘XML’ ‘digest’ ‘methods’ ‘optparse’ ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': ‘tools:::md5sum’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘tools:::.Rd_get_argument_table’ ‘tools:::.Rd_get_metadata’
  ‘tools:::fetchRdDB’
  See the note in ?`:::` about the use of this operator.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘parseSectionFromText’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
editToolConfXML: no visible global function definition for
  ‘xmlInternalTreeParse’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:15)
editToolConfXML: no visible global function definition for
  ‘xpathSApply’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:16)
editToolConfXML: no visible global function definition for
  ‘xpathSApply’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:17-18)
editToolConfXML: no visible global function definition for ‘newXMLNode’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:21)
editToolConfXML: no visible global function definition for
  ‘xmlChildren’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:24)
editToolConfXML: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:32-35)
editToolConfXML: no visible global function definition for
  ‘removeNodes’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:37)
editToolConfXML: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:41)
editToolConfXML: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:41)
editToolConfXML: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:42)
editToolConfXML: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:42)
editToolConfXML: no visible global function definition for ‘newXMLNode’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:43)
editToolConfXML: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:44)
editToolConfXML: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:44)
editToolConfXML: no visible global function definition for ‘saveXML’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:45)
galaxy: no visible global function definition for ‘newXMLNode’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:179)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:180)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:180)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:183)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:183)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:184)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:184)
galaxy: no visible global function definition for ‘newXMLNode’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:186-187)
galaxy: no visible global function definition for ‘newXMLTextNode’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:186-187)
galaxy: no visible global function definition for ‘newXMLNode’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:202-203)
galaxy: no visible global function definition for ‘newXMLTextNode’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:202-203)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:208)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:208)
galaxy: no visible global function definition for ‘newXMLNode’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:209)
galaxy: no visible global function definition for ‘newXMLNode’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:210)
galaxy: no visible global function definition for ‘newXMLNode’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:211-212)
galaxy: no visible global function definition for ‘newXMLNode’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:220)
galaxy: no visible global function definition for ‘newXMLNode’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:223)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:224)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:224)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:225)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:225)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:226)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:226)
galaxy: no visible global function definition for ‘newXMLNode’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:228)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:229)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:229)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:231-232)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:231-232)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:233)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:233)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:237-239)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:237-239)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:242)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:242)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:247-248)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:247-248)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:255)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:255)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:257-261)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:257-261)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:263)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:263)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:275-277)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:275-277)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:282-283)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:282-283)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:288-289)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:288-289)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:290-291)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:290-291)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:295)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:295)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:300-301)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:300-301)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:302-304)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:302-304)
galaxy: no visible global function definition for ‘newXMLNode’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:315-316)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:317)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:317)
galaxy: no visible global function definition for ‘newXMLNode’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:328)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:332)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:332)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:333)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:333)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:334)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:334)
galaxy: no visible global function definition for ‘newXMLNode’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:345)
galaxy: no visible global function definition for ‘newXMLNode’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:348)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:349)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:349)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:357-358)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:357-358)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:363)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:363)
galaxy: no visible global function definition for ‘newXMLNode’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:371)
galaxy: no visible global function definition for ‘newXMLTextNode’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:371)
galaxy: no visible global function definition for ‘saveXML’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:372)
getManPage: no visible global function definition for ‘parse_Rd’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/man.R:6)
getManSection: no visible global function definition for ‘parse_Rd’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/man.R:27)
getSupportedExtensions: no visible global function definition for
  ‘xmlInternalTreeParse’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:488)
getSupportedExtensions: no visible global function definition for
  ‘xpathSApply’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:489)
getSupportedExtensions: no visible binding for global variable
  ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:490)
parseSectionFromText: no visible global function definition for
  ‘Rd2txt’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/man.R:62)
probeLookup: no visible global function definition for ‘select’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/test_functions.R:149-150)
probeLookup: no visible binding for global variable ‘hgu95av2.db’
  (/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/test_functions.R:149-150)
* 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 ... [5s/5s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’ [9s/9s]
 [9s/9s] 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
  ‘/Users/biocbuild/bbs-3.2-bioc/meat/RGalaxy.Rcheck/00check.log’
for details.

RGalaxy.Rcheck/00install.out:

* installing *source* package ‘RGalaxy’ ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RGalaxy)

RGalaxy.Rcheck/RGalaxy-Ex.timings:

nameusersystemelapsed
GalaxyClasses0.0320.0020.034
GalaxyConfig-class0.0030.0000.004
GalaxyInputFile-class0.0050.0010.005
GalaxyOutput-class0.0090.0000.009
RserveConnection-class0.0030.0000.002
addTwoNumbers0.0010.0000.002
addTwoNumbersWithTest0.0360.0020.037
anotherTestFunction0.0110.0020.013
functionToGalaxify0.0360.0060.047
galaxy0.0020.0000.003
getFriendlyName0.0010.0000.001
probeLookup3.2980.0643.385
utilities0.0020.0000.002