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CHECK report for geneplast on tokay2

This page was generated on 2020-10-17 11:56:39 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE geneplast PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 686/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
geneplast 1.14.0
Mauro Castro
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/geneplast
Branch: RELEASE_3_11
Last Commit: ee325db
Last Changed Date: 2020-04-27 14:58:22 -0400 (Mon, 27 Apr 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: geneplast
Version: 1.14.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:geneplast.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings geneplast_1.14.0.tar.gz
StartedAt: 2020-10-17 04:20:19 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 04:21:34 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 75.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: geneplast.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:geneplast.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings geneplast_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/geneplast.Rcheck'
* using R version 4.0.3 (2020-10-10)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'geneplast/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'geneplast' version '1.14.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'geneplast' 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 ... 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 ... WARNING
File 'data/datalist' contains malformed line(s):
  ''
* 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
** 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: 1 WARNING
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/geneplast.Rcheck/00check.log'
for details.



Installation output

geneplast.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/geneplast_1.14.0.tar.gz && rm -rf geneplast.buildbin-libdir && mkdir geneplast.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=geneplast.buildbin-libdir geneplast_1.14.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL geneplast_1.14.0.zip && rm geneplast_1.14.0.tar.gz geneplast_1.14.0.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 3159k  100 3159k    0     0  32.7M      0 --:--:-- --:--:-- --:--:-- 35.4M

install for i386

* installing *source* package 'geneplast' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'geneplast'
    finding HTML links ... done
    OGP-class                               html  
    OGR-class                               html  
    geneplast-package                       html  
    gpdata                                  html  
    gplast                                  html  
    gplast.get                              html  
    gplast.preprocess                       html  
    groot                                   html  
    groot.get                               html  
    groot.plot                              html  
    groot.preprocess                        html  
    ogr2igraph                              html  
    ogr2tni                                 html  
    ppidata                                 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 'geneplast' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'geneplast' as geneplast_1.14.0.zip
* DONE (geneplast)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'geneplast' successfully unpacked and MD5 sums checked

Tests output

geneplast.Rcheck/tests_i386/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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("geneplast")
-Preprocessing for input data...

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-Preprocessing for input data...

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RUNIT TEST PROTOCOL -- Sat Oct 17 04:21:19 2020 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
geneplast RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   2.21    0.20    2.40 

geneplast.Rcheck/tests_x64/runTests.Rout


R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
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("geneplast")
-Preprocessing for input data...

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-Preprocessing for input data...

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RUNIT TEST PROTOCOL -- Sat Oct 17 04:21:22 2020 
*********************************************** 
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
geneplast RUnit Tests - 2 test functions, 0 errors, 0 failures
Number of test functions: 2 
Number of errors: 0 
Number of failures: 0 
> 
> proc.time()
   user  system elapsed 
   2.50    0.09    2.59 

Example timings

geneplast.Rcheck/examples_i386/geneplast-Ex.timings

nameusersystemelapsed
gpdata0.220.000.22
gplast0.170.010.19
gplast.get0.140.000.14
gplast.preprocess0.120.010.14
groot1.690.001.69
groot.get1.390.021.40
groot.plot1.470.001.50
groot.preprocess0.420.010.44
ogr2igraph000
ogr2tni000
ppidata0.000.020.02

geneplast.Rcheck/examples_x64/geneplast-Ex.timings

nameusersystemelapsed
gpdata0.100.000.11
gplast0.150.000.14
gplast.get0.100.020.13
gplast.preprocess0.110.000.11
groot1.600.011.61
groot.get1.360.021.37
groot.plot1.640.001.64
groot.preprocess0.310.000.31
ogr2igraph000
ogr2tni000
ppidata000