Package: RGalaxy

Version: 1.28.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RGalaxy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RGalaxy_1.28.0.tar.gz

StartedAt: 2019-10-16 06:13:01 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 06:14:31 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 89.6 seconds

RetCode: 0

Status:  OK

CheckDir: RGalaxy.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RGalaxy.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RGalaxy_1.28.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/RGalaxy.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RGalaxy/DESCRIPTION’ ... OK
* this is package ‘RGalaxy’ version ‘1.28.0’
* 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 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.
Package in Depends field not imported from: ‘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 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/RGalaxy.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RGalaxy
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘RGalaxy’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RGalaxy)

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> BiocGenerics:::testPackage("RGalaxy")

Attaching package: 'tools'

The following object is masked from 'package:XML':

    toHTML

null device 
          1 
Note: Did not find section 'Details' in man page.


RUNIT TEST PROTOCOL -- Wed Oct 16 06:14:20 2019 
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Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
RGalaxy RUnit Tests - 9 test functions, 0 errors, 0 failures
Number of test functions: 9 
Number of errors: 0 
Number of failures: 0 
Warning messages:
1: Not enough information to create a functional test. 
2: Not enough information to create a functional test. 
3: Not enough information to create a functional test. 
4: Not enough information to create a functional test. 
5: Not enough information to create a functional test. 
6: Not enough information to create a functional test. 
> 
> proc.time()
   user  system elapsed 
 10.190   1.497  13.309 

name	user	system	elapsed
GalaxyClasses	0.080	0.004	0.083
GalaxyConfig-class	0.004	0.000	0.004
GalaxyInputFile-class	0.004	0.000	0.004
GalaxyOutput-class	0.01	0.00	0.01
RserveConnection-class	0.003	0.000	0.003
addTwoNumbers	0.001	0.001	0.002
addTwoNumbersWithTest	0.026	0.002	0.029
anotherTestFunction	0.015	0.004	0.021
functionToGalaxify	0.072	0.020	0.098
galaxy	0.002	0.001	0.005
getFriendlyName	0.001	0.001	0.002
probeLookup	4.056	0.285	4.398
utilities	0.002	0.001	0.003