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CHECK report for dorothea on riesling1

This page was generated on 2021-01-18 15:58:47 -0500 (Mon, 18 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE dorothea PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 99/385HostnameOS / ArchINSTALLBUILDCHECK
dorothea 1.3.0
Christian H. Holland
Snapshot Date: 2021-01-18 09:00:15 -0500 (Mon, 18 Jan 2021)
URL: https://git.bioconductor.org/packages/dorothea
Branch: master
Last Commit: 6e2b837
Last Changed Date: 2020-10-27 10:31:26 -0500 (Tue, 27 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 [ WARNINGS ]

Summary

Package: dorothea
Version: 1.3.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dorothea.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings dorothea_1.3.0.tar.gz
StartedAt: 2021-01-18 11:19:41 -0500 (Mon, 18 Jan 2021)
EndedAt: 2021-01-18 11:21:19 -0500 (Mon, 18 Jan 2021)
EllapsedTime: 97.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: dorothea.Rcheck
Warnings: 1

Command output

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##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:dorothea.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings dorothea_1.3.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/dorothea.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 'dorothea/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'dorothea' version '1.3.0'
* package encoding: UTF-8
* 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:
  .travis.yml
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 'dorothea' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: cannot open file 'D:/biocbuild/bbs-3.13-data-experiment/meat/dorothea.buildbin-libdir/00LOCK-dorothea/00new/dorothea/help/%>%.html': Invalid argument
See 'D:/biocbuild/bbs-3.13-data-experiment/meat/dorothea.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 35.2Mb
  sub-directories of 1Mb or more:
    data       7.9Mb
    extdata   17.2Mb
    help       1.3Mb
    testdata   8.5Mb
* 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
run_viper 6.38    0.2    6.58
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
          user system elapsed
run_viper 6.58   0.35    6.92
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'testthat.R'
 OK
** running tests for arch 'x64' ...
  Running 'testthat.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
  'D:/biocbuild/bbs-3.13-data-experiment/meat/dorothea.Rcheck/00check.log'
for details.



Installation output

dorothea.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/dorothea_1.3.0.tar.gz && rm -rf dorothea.buildbin-libdir && mkdir dorothea.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=dorothea.buildbin-libdir dorothea_1.3.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL dorothea_1.3.0.zip && rm dorothea_1.3.0.tar.gz dorothea_1.3.0.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
100 29.8M  100 29.8M    0     0  37.1M      0 --:--:-- --:--:-- --:--:-- 37.1M

install for i386

* installing *source* package 'dorothea' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'dorothea'
    finding HTML links ... done
    df2regulon                              html  
REDIRECT:topic	 df2regulon -> df2regulon.html [ SUCCESS ]
    dorothea-package                        html  
REDIRECT:topic	 dorothea -> dorothea-package.html [ SUCCESS ]
REDIRECT:topic	 dorothea-package -> dorothea-package.html [ SUCCESS ]
    dorothea_hs                             html  
REDIRECT:topic	 dorothea_hs -> dorothea_hs.html [ SUCCESS ]
    dorothea_mm                             html  
REDIRECT:topic	 dorothea_mm -> dorothea_mm.html [ SUCCESS ]
    entire_database                         html  
REDIRECT:topic	 entire_database -> entire_database.html [ SUCCESS ]
    pipe                                    html  
REDIRECT:topic	 %>% -> pipe.html [ FAIL ]
REDIRECT:file	 pipe.html -> pipe.html [ SUCCESS ]
Rd warning: cannot open file 'D:/biocbuild/bbs-3.13-data-experiment/meat/dorothea.buildbin-libdir/00LOCK-dorothea/00new/dorothea/help/%>%.html': Invalid argument
    run_viper                               html  
REDIRECT:topic	 run_viper -> run_viper.html [ SUCCESS ]
*** copying figures
** 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 'dorothea' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'dorothea' as dorothea_1.3.0.zip
* DONE (dorothea)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'dorothea' successfully unpacked and MD5 sums checked

Tests output

dorothea.Rcheck/tests_i386/testthat.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.

> library(testthat)
> library(dorothea)
> 
> test_check("dorothea")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ]
> 
> proc.time()
   user  system elapsed 
  15.03    1.12   16.14 

dorothea.Rcheck/tests_x64/testthat.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.

> library(testthat)
> library(dorothea)
> 
> test_check("dorothea")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 16 ]
> 
> proc.time()
   user  system elapsed 
  15.70    0.84   16.53 

Example timings

dorothea.Rcheck/examples_i386/dorothea-Ex.timings

nameusersystemelapsed
df2regulon0.310.020.33
pipe000
run_viper6.380.206.58

dorothea.Rcheck/examples_x64/dorothea-Ex.timings

nameusersystemelapsed
df2regulon0.360.000.36
pipe000
run_viper6.580.356.92