Package: RGalaxy

Version: 1.28.0

Command: C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RGalaxy.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings RGalaxy_1.28.0.tar.gz

StartedAt: 2019-10-16 06:28:24 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 06:29:47 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 82.9 seconds

RetCode: 0

Status:  OK

CheckDir: RGalaxy.Rcheck

Warnings: 0

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### Running command:
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###   C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RGalaxy.install-out.txt --library=C:\Users\biocbuild\bbs-3.9-bioc\R\library --no-vignettes --timings RGalaxy_1.28.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.9-bioc/meat/RGalaxy.Rcheck'
* using R version 3.6.1 (2019-07-05)
* 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 '1.28.0'
* 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 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
* 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 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 ...
** 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'
 OK
** running tests for arch 'x64' ...
  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
  'C:/Users/biocbuild/bbs-3.9-bioc/meat/RGalaxy.Rcheck/00check.log'
for details.

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/RGalaxy_1.28.0.tar.gz && rm -rf RGalaxy.buildbin-libdir && mkdir RGalaxy.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RGalaxy.buildbin-libdir RGalaxy_1.28.0.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL RGalaxy_1.28.0.zip && rm RGalaxy_1.28.0.tar.gz RGalaxy_1.28.0.zip
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  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  118k  100  118k    0     0  1840k      0 --:--:-- --:--:-- --:--:-- 2071k

install for i386

* installing *source* package 'RGalaxy' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RGalaxy'
    finding HTML links ... done
    GalaxyClasses                           html  
    GalaxyConfig-class                      html  
    GalaxyInputFile-class                   html  
    GalaxyOutput-class                      html  
    RserveConnection-class                  html  
    addTwoNumbers                           html  
    addTwoNumbersWithTest                   html  
    anotherTestFunction                     html  
    foo                                     html  
    functionToGalaxify                      html  
    galaxy                                  html  
    getFriendlyName                         html  
    probeLookup                             html  
    runFunctionalTest                       html  
    testFunctionWithGalaxySelectParam       html  
    testFunctionWithSelect                  html  
    utilities                               html  
** 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

install for x64

* installing *source* package 'RGalaxy' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RGalaxy' as RGalaxy_1.28.0.zip
* DONE (RGalaxy)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'RGalaxy' successfully unpacked and MD5 sums checked

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 
Note: Did not find section 'Details' in man page.


RUNIT TEST PROTOCOL -- Wed Oct 16 06:29:31 2019 
*********************************************** 
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 
   3.35    0.14    7.62 

R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 
Note: Did not find section 'Details' in man page.


RUNIT TEST PROTOCOL -- Wed Oct 16 06:29:40 2019 
*********************************************** 
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 
   3.71    0.14    8.82