##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD check --install=check:RGalaxy.install-out.txt --library=/home/biocbuild/bbs-3.14-bioc/R/library --no-vignettes --timings RGalaxy_1.38.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.14-bioc/meat/RGalaxy.Rcheck’
* using R version 4.1.3 (2022-03-10)
* 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 ‘1.38.0’
* 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 ... WARNING
Found the following significant warnings:
  Warning: Package 'RGalaxy' is deprecated and will be removed from Bioconductor
See ‘/home/biocbuild/bbs-3.14-bioc/meat/RGalaxy.Rcheck/00install.out’ for details.
* 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: 1 WARNING, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.14-bioc/meat/RGalaxy.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.14-bioc/R/bin/R CMD INSTALL RGalaxy
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.14-bioc/R/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
Warning: Package 'RGalaxy' is deprecated and will be removed from Bioconductor
  version 3.15
** testing if installed package can be loaded from final location
Warning: Package 'RGalaxy' is deprecated and will be removed from Bioconductor
  version 3.15
** testing if installed package keeps a record of temporary installation path
* DONE (RGalaxy)

R version 4.1.3 (2022-03-10) -- "One Push-Up"
Copyright (C) 2022 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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

Warning: Package 'RGalaxy' is deprecated and will be removed from Bioconductor
  version 3.15 
Warning: Package 'RGalaxy' is deprecated and will be removed from Bioconductor
  version 3.15 
null device 
          1 
Warning: Package 'RGalaxy' is deprecated and will be removed from Bioconductor
  version 3.15 
Note: Did not find section 'Details' in man page.


RUNIT TEST PROTOCOL -- Tue Apr 12 09:01:58 2022 
*********************************************** 
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: Package 'RGalaxy' is deprecated and will be removed from Bioconductor
  version 3.15 
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. 
7: Not enough information to create a functional test. 
> 
> proc.time()
   user  system elapsed 
  4.883   0.343   5.203