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CHECK report for systemPipeRdata on riesling1

This page was generated on 2021-01-14 15:59:12 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE systemPipeRdata PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 349/385HostnameOS / ArchINSTALLBUILDCHECK
systemPipeRdata 1.19.1
Thomas Girke
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/systemPipeRdata
Branch: master
Last Commit: c0cc246
Last Changed Date: 2020-10-29 21:10:57 -0500 (Thu, 29 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ]

Summary

Package: systemPipeRdata
Version: 1.19.1
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:systemPipeRdata.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings systemPipeRdata_1.19.1.tar.gz
StartedAt: 2021-01-14 11:43:46 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 11:44:27 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 41.2 seconds
RetCode: 0
Status:  OK  
CheckDir: systemPipeRdata.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:systemPipeRdata.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings systemPipeRdata_1.19.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/systemPipeRdata.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'systemPipeRdata/DESCRIPTION' ... OK
* this is package 'systemPipeRdata' version '1.19.1'
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
  inst/extdata/param/.batchtools.conf.R
  inst/extdata/param/.batchtools.conf.R.sge
  inst/extdata/param/.batchtools.conf.R.torque
  inst/extdata/workflows/new/.batchtools.conf.R
  inst/rmarkdown/templates/systemPipeR_new/skeleton/.batchtools.conf.R
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
* checking for portable file names ... OK
* checking whether package 'systemPipeRdata' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 294.7Mb
  sub-directories of 1Mb or more:
    extdata  294.5Mb
* 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 ... OK
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... 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
  'D:/biocbuild/bbs-3.13-data-experiment/meat/systemPipeRdata.Rcheck/00check.log'
for details.



Installation output

systemPipeRdata.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/systemPipeRdata_1.19.1.tar.gz && rm -rf systemPipeRdata.buildbin-libdir && mkdir systemPipeRdata.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=systemPipeRdata.buildbin-libdir systemPipeRdata_1.19.1.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL systemPipeRdata_1.19.1.zip && rm systemPipeRdata_1.19.1.tar.gz systemPipeRdata_1.19.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
 10  258M   10 26.9M    0     0   104M      0  0:00:02 --:--:--  0:00:02  103M
 51  258M   51  133M    0     0   105M      0  0:00:02  0:00:01  0:00:01  105M
 88  258M   88  228M    0     0   101M      0  0:00:02  0:00:02 --:--:--  101M
100  258M  100  258M    0     0   102M      0  0:00:02  0:00:02 --:--:--  102M

install for i386

* installing *source* package 'systemPipeRdata' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'systemPipeRdata'
    finding HTML links ... done
    availableWF                             html  
REDIRECT:topic	 availableWF -> availableWF.html [ SUCCESS ]
    genWorkenvir                            html  
REDIRECT:topic	 genWorkenvir -> genWorkenvir.html [ SUCCESS ]
    pathList                                html  
REDIRECT:topic	 pathList -> pathList.html [ SUCCESS ]
** 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 'systemPipeRdata' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'systemPipeRdata' as systemPipeRdata_1.19.1.zip
* DONE (systemPipeRdata)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'systemPipeRdata' successfully unpacked and MD5 sums checked

Tests output

systemPipeRdata.Rcheck/tests_i386/runTests.Rout


R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
Copyright (C) 2020 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("systemPipeRdata")


RUNIT TEST PROTOCOL -- Thu Jan 14 11:44:16 2021 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
systemPipeRdata RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   0.29    0.04    0.32 

systemPipeRdata.Rcheck/tests_x64/runTests.Rout


R Under development (unstable) (2020-12-30 r79736) -- "Unsuffered Consequences"
Copyright (C) 2020 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("systemPipeRdata")


RUNIT TEST PROTOCOL -- Thu Jan 14 11:44:16 2021 
*********************************************** 
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
systemPipeRdata RUnit Tests - 1 test function, 0 errors, 0 failures
Number of test functions: 1 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   0.29    0.04    0.32 

Example timings

systemPipeRdata.Rcheck/examples_i386/systemPipeRdata-Ex.timings

nameusersystemelapsed
availableWF000
genWorkenvir000
pathList000

systemPipeRdata.Rcheck/examples_x64/systemPipeRdata-Ex.timings

nameusersystemelapsed
availableWF000
genWorkenvir000
pathList000