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BioC 3.5: CHECK report for RGalaxy on tokay2

This page was generated on 2017-10-18 14:21:55 -0400 (Wed, 18 Oct 2017).

Package 1104/1381HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RGalaxy 1.20.1
Bioconductor Package Maintainer
Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017)
URL: https://git.bioconductor.org/packages/RGalaxy
Branch: RELEASE_3_5
Last Commit: 0ec2070
Last Changed Date: 2017-07-11 15:57:07 -0400 (Tue, 11 Jul 2017)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK  ERROR 
tokay2 Windows Server 2012 R2 Standard / x64  NotNeeded  OK [ ERROR ] OK 
veracruz2 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  ERROR  OK 

Summary

Package: RGalaxy
Version: 1.20.1
Command: rm -rf RGalaxy.buildbin-libdir RGalaxy.Rcheck && mkdir RGalaxy.buildbin-libdir RGalaxy.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RGalaxy.buildbin-libdir RGalaxy_1.20.1.tar.gz >RGalaxy.Rcheck\00install.out 2>&1 && cp RGalaxy.Rcheck\00install.out RGalaxy-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=RGalaxy.buildbin-libdir --install="check:RGalaxy-install.out" --force-multiarch --no-vignettes --timings RGalaxy_1.20.1.tar.gz
StartedAt: 2017-10-18 02:30:52 -0400 (Wed, 18 Oct 2017)
EndedAt: 2017-10-18 02:32:28 -0400 (Wed, 18 Oct 2017)
EllapsedTime: 95.6 seconds
RetCode: 1
Status:  ERROR  
CheckDir: RGalaxy.Rcheck
Warnings: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf RGalaxy.buildbin-libdir RGalaxy.Rcheck && mkdir RGalaxy.buildbin-libdir RGalaxy.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RGalaxy.buildbin-libdir RGalaxy_1.20.1.tar.gz >RGalaxy.Rcheck\00install.out 2>&1 && cp RGalaxy.Rcheck\00install.out RGalaxy-install.out  &&  C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=RGalaxy.buildbin-libdir --install="check:RGalaxy-install.out" --force-multiarch --no-vignettes --timings RGalaxy_1.20.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'runTests.R'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/i386/R" CMD BATCH --vanilla  "runTests.R" "runTests.Rout"' had status 1 
 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
** running tests for arch 'x64' ...
  Running 'runTests.R'
Warning message:
running command '"C:/Users/BIOCBU˜1/BBS-3˜1.5-B/R/bin/x64/R" CMD BATCH --vanilla  "runTests.R" "runTests.Rout"' had status 1 
 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: 2 ERRORs, 2 NOTEs
See
  'C:/Users/biocbuild/bbs-3.5-bioc/meat/RGalaxy.Rcheck/00check.log'
for details.

runTests.Rout.fail:


R version 3.4.2 Patched (2017-10-07 r73498) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-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: 0.16 0 1.57
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 02:32:12 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

runTests.Rout.fail:


R version 3.4.2 Patched (2017-10-07 r73498) -- "Short Summer"
Copyright (C) 2017 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (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: 0.14 0 1.59
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 02:32:23 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

RGalaxy.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'RGalaxy' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RGalaxy' as RGalaxy_1.20.1.zip
* DONE (RGalaxy)

RGalaxy.Rcheck/examples_i386/RGalaxy-Ex.timings:

nameusersystemelapsed
GalaxyClasses0.040.000.05
GalaxyConfig-class000
GalaxyInputFile-class0.020.000.01
GalaxyOutput-class0.020.000.02
RserveConnection-class000
addTwoNumbers000
addTwoNumbersWithTest0.040.020.06
anotherTestFunction0.060.000.06
functionToGalaxify0.040.020.05
galaxy000
getFriendlyName000
probeLookup2.790.143.05
utilities000

RGalaxy.Rcheck/examples_x64/RGalaxy-Ex.timings:

nameusersystemelapsed
GalaxyClasses0.080.000.08
GalaxyConfig-class0.020.000.01
GalaxyInputFile-class0.000.020.02
GalaxyOutput-class0.010.000.01
RserveConnection-class000
addTwoNumbers0.020.000.02
addTwoNumbersWithTest0.060.000.06
anotherTestFunction0.060.000.06
functionToGalaxify0.040.000.04
galaxy000
getFriendlyName000
probeLookup2.830.012.85
utilities000