BioC 3.5: CHECK report for RGalaxy on malbec2

Package: RGalaxy

Version: 1.20.1

Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings RGalaxy_1.20.1.tar.gz

StartedAt: 2017-08-16 01:48:36 -0400 (Wed, 16 Aug 2017)

EndedAt: 2017-08-16 01:49:22 -0400 (Wed, 16 Aug 2017)

EllapsedTime: 46.1 seconds

RetCode: 0

Status:  OK

CheckDir: RGalaxy.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD check --no-vignettes --timings RGalaxy_1.20.1.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck’
* using R version 3.4.1 (2017-06-30)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RGalaxy/DESCRIPTION’ ... OK
* this is package ‘RGalaxy’ version ‘1.20.1’
* 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' call to ‘RSclient’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘digest’ ‘optparse’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00check.log’
for details.

* 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)

name	user	system	elapsed
GalaxyClasses	0.040	0.004	0.042
GalaxyConfig-class	0.004	0.000	0.002
GalaxyInputFile-class	0.000	0.000	0.002
GalaxyOutput-class	0.004	0.000	0.004
RserveConnection-class	0.000	0.000	0.001
addTwoNumbers	0.000	0.000	0.001
addTwoNumbersWithTest	0.056	0.000	0.059
anotherTestFunction	0.008	0.004	0.008
functionToGalaxify	0.052	0.008	0.060
galaxy	0.004	0.000	0.002
getFriendlyName	0	0	0
probeLookup	2.200	0.020	2.267
utilities	0.004	0.000	0.001