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: 2017-10-18 02:01:01 -0400 (Wed, 18 Oct 2017)

EndedAt: 2017-10-18 02:01:49 -0400 (Wed, 18 Oct 2017)

EllapsedTime: 48.1 seconds

RetCode: 1

Status:  ERROR

CheckDir: RGalaxy.Rcheck

Warnings: NA

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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 3.4.2 (2017-09-28)
* 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’
 ERROR
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  FAILURE in test_missing_param: Error in checkEquals(expected, output) : 1 string mismatch
  
  
  Test files with failing tests
  
     test_galaxy.R 
       test_missing_param 
  
  
  Error in BiocGenerics:::testPackage("RGalaxy") : 
    unit tests failed for package RGalaxy
  In addition: Warning messages:
  1: Not enough information to create a functional test. 
  2: Not enough information to create a functional test. 
  Execution halted
* 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 ERROR, 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00check.log’
for details.

R version 3.4.2 (2017-09-28) -- "Short Summer"
Copyright (C) 2017 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

null device 
          1 
Timing stopped at: 1.216 0.04 1.266
Error in checkEquals(expected, output) : 1 string mismatch

In addition: 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. 
Note: Did not find section 'Details' in man page.


RUNIT TEST PROTOCOL -- Wed Oct 18 02:01:46 2017 
*********************************************** 
Number of test functions: 9 
Number of errors: 0 
Number of failures: 1 

 
1 Test Suite : 
RGalaxy RUnit Tests - 9 test functions, 0 errors, 1 failure
FAILURE in test_missing_param: Error in checkEquals(expected, output) : 1 string mismatch


Test files with failing tests

   test_galaxy.R 
     test_missing_param 


Error in BiocGenerics:::testPackage("RGalaxy") : 
  unit tests failed for package RGalaxy
In addition: Warning messages:
1: Not enough information to create a functional test. 
2: Not enough information to create a functional test. 
Execution halted

* 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	0.044	0.000	0.045
GalaxyConfig-class	0.000	0.000	0.002
GalaxyInputFile-class	0.004	0.000	0.003
GalaxyOutput-class	0.024	0.000	0.023
RserveConnection-class	0.000	0.000	0.002
addTwoNumbers	0.004	0.000	0.000
addTwoNumbersWithTest	0.044	0.008	0.054
anotherTestFunction	0.004	0.004	0.008
functionToGalaxify	0.060	0.000	0.062
galaxy	0.004	0.000	0.001
getFriendlyName	0.000	0.000	0.001
probeLookup	2.296	0.032	2.369
utilities	0.000	0.000	0.002