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BioC 3.5: CHECK report for RGalaxy on toluca2

This page was generated on 2017-04-23 14:36:34 -0400 (Sun, 23 Apr 2017).

Package 1101/1377HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RGalaxy 1.19.0
Bioconductor Package Maintainer
Snapshot Date: 2017-04-22 17:18:01 -0400 (Sat, 22 Apr 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RGalaxy
Last Changed Rev: 122712 / Revision: 129046
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RGalaxy
Version: 1.19.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RGalaxy_1.19.0.tar.gz
StartedAt: 2017-04-23 09:00:16 -0400 (Sun, 23 Apr 2017)
EndedAt: 2017-04-23 09:01:12 -0400 (Sun, 23 Apr 2017)
EllapsedTime: 56.1 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_1.19.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck’
* using R Under development (unstable) (2017-02-15 r72187)
* 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 ‘1.19.0’
* 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 ... 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
GalaxyCharacterParam: no visible global function definition for ‘new’
GalaxyConfig: no visible global function definition for ‘new’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/AllClasses.R:40-41)
GalaxyInputFile: no visible global function definition for ‘new’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/AllClasses.R:217-218)
GalaxyIntegerParam: no visible global function definition for ‘new’
GalaxyLogicalParam: no visible global function definition for ‘new’
GalaxyNumericParam: no visible global function definition for ‘new’
GalaxyOutput: no visible global function definition for ‘new’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/AllClasses.R:206)
GalaxyParam: no visible global function definition for ‘new’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/AllClasses.R:152-155)
GalaxySelectParam: no visible global function definition for ‘new’
RserveConnection: no visible global function definition for ‘new’
anotherTestFunction: no visible global function definition for
  ‘read.delim’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/test_functions.R:84)
anotherTestFunction: no visible global function definition for
  ‘read.delim’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/test_functions.R:90)
anotherTestFunction: no visible global function definition for
  ‘write.csv’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/test_functions.R:97)
anotherTestFunction: no visible global function definition for ‘pdf’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/test_functions.R:99)
anotherTestFunction: no visible global function definition for ‘plot’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/test_functions.R:101)
anotherTestFunction: no visible global function definition for
  ‘dev.off’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/test_functions.R:102)
displayFunction: no visible global function definition for
  ‘capture.output’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:390)
editToolConfXML: no visible global function definition for
  ‘xmlInternalTreeParse’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:15)
editToolConfXML: no visible global function definition for
  ‘xpathSApply’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:16)
editToolConfXML: no visible global function definition for
  ‘xpathSApply’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:17-18)
editToolConfXML: no visible global function definition for ‘newXMLNode’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:21)
editToolConfXML: no visible global function definition for
  ‘xmlChildren’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:24)
editToolConfXML: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:32-35)
editToolConfXML: no visible global function definition for
  ‘removeNodes’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:37)
editToolConfXML: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:41)
editToolConfXML: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:41)
editToolConfXML: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:42)
editToolConfXML: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:42)
editToolConfXML: no visible global function definition for ‘newXMLNode’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:43)
editToolConfXML: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:44)
editToolConfXML: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:44)
editToolConfXML: no visible global function definition for ‘saveXML’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:45)
foo: no visible global function definition for ‘pdf’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/test_functions.R:118)
foo: no visible global function definition for ‘plot’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/test_functions.R:119)
foo: no visible binding for global variable ‘cars’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/test_functions.R:119)
foo: no visible global function definition for ‘dev.off’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/test_functions.R:120)
functionToGalaxify: no visible global function definition for
  ‘read.delim’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/test_functions.R:11)
functionToGalaxify: no visible global function definition for
  ‘read.delim’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/test_functions.R:17)
functionToGalaxify: no visible global function definition for
  ‘write.csv’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/test_functions.R:24)
functionToGalaxify: no visible global function definition for ‘png’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/test_functions.R:26)
functionToGalaxify: no visible global function definition for ‘plot’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/test_functions.R:28)
functionToGalaxify: no visible global function definition for ‘dev.off’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/test_functions.R:29)
galaxy: no visible global function definition for ‘newXMLNode’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:179)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:180)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:180)
galaxy: no visible global function definition for ‘packageDescription’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:181-182)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:183)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:183)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:184)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:184)
galaxy: no visible global function definition for ‘newXMLNode’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:186-187)
galaxy: no visible global function definition for ‘newXMLTextNode’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:186-187)
galaxy: no visible global function definition for ‘newXMLNode’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:202-203)
galaxy: no visible global function definition for ‘newXMLTextNode’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:202-203)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:208)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:208)
galaxy: no visible global function definition for ‘newXMLNode’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:209)
galaxy: no visible global function definition for ‘newXMLNode’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:210)
galaxy: no visible global function definition for ‘newXMLNode’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:211-212)
galaxy: no visible global function definition for ‘newXMLNode’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:220)
galaxy: no visible global function definition for ‘newXMLNode’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:223)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:224)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:224)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:225)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:225)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:226)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:226)
galaxy: no visible global function definition for ‘newXMLNode’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:228)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:229)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:229)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:231-232)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:231-232)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:233)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:233)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:237-239)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:237-239)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:242)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:242)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:247-248)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:247-248)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:255)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:255)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:257-261)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:257-261)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:263)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:263)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:275-277)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:275-277)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:282-283)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:282-283)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:288-289)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:288-289)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:290-291)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:290-291)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:295)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:295)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:300-301)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:300-301)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:302-304)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:302-304)
galaxy: no visible global function definition for ‘newXMLNode’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:315-316)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:317)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:317)
galaxy: no visible global function definition for ‘newXMLNode’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:328)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:332)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:332)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:333)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:333)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:334)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:334)
galaxy: no visible global function definition for ‘newXMLNode’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:345)
galaxy: no visible global function definition for ‘newXMLNode’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:348)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:349)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:349)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:357-358)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:357-358)
galaxy: no visible global function definition for ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:363)
galaxy: no visible global function definition for ‘xmlAttrs<-’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:363)
galaxy: no visible global function definition for ‘newXMLNode’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:371)
galaxy: no visible global function definition for ‘newXMLTextNode’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:371)
galaxy: no visible global function definition for ‘saveXML’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:372)
getFuncInfo: no visible global function definition for ‘extends’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:537-538)
getFuncInfo: no visible global function definition for ‘extends’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:558-561)
getManPage: no visible global function definition for ‘parse_Rd’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/man.R:6)
getManSection: no visible global function definition for ‘parse_Rd’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/man.R:27)
getSupportedExtensions: no visible global function definition for
  ‘xmlInternalTreeParse’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:488)
getSupportedExtensions: no visible global function definition for
  ‘xpathSApply’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:489)
getSupportedExtensions: no visible binding for global variable
  ‘xmlAttrs’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/galaxy.R:490)
getVersion: no visible global function definition for
  ‘packageDescription’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/utils.R:79-80)
parseSectionFromText: no visible global function definition for
  ‘capture.output’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/man.R:62)
parseSectionFromText: no visible global function definition for
  ‘Rd2txt’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/man.R:62)
probeLookup: no visible global function definition for ‘select’
  (/Users/biocbuild/bbs-3.5-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-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/test_functions.R:149-150)
probeLookup: no visible global function definition for ‘write.csv’
  (/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00_pkg_src/RGalaxy/R/test_functions.R:151)
Undefined global functions or variables:
  Rd2txt capture.output cars dev.off extends hgu95av2.db new newXMLNode
  newXMLTextNode packageDescription parse_Rd pdf plot png read.delim
  removeNodes saveXML select write.csv xmlAttrs xmlAttrs<- xmlChildren
  xmlInternalTreeParse xpathSApply
Consider adding
  importFrom("datasets", "cars")
  importFrom("grDevices", "dev.off", "pdf", "png")
  importFrom("graphics", "plot")
  importFrom("methods", "extends", "new")
  importFrom("utils", "capture.output", "packageDescription",
             "read.delim", "write.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘runTests.R’
 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-3.5-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
GalaxyClasses0.0690.0020.073
GalaxyConfig-class0.0030.0000.003
GalaxyInputFile-class0.0040.0010.004
GalaxyOutput-class0.0070.0000.007
RserveConnection-class0.0020.0000.003
addTwoNumbers0.0010.0010.001
addTwoNumbersWithTest0.0760.0010.082
anotherTestFunction0.0110.0020.013
functionToGalaxify0.0600.0050.071
galaxy0.0030.0010.003
getFriendlyName0.0010.0000.001
probeLookup2.9440.0693.026
utilities0.0020.0000.001