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CHECK report for BiocIO on tokay2

This page was generated on 2021-01-24 12:32:19 -0500 (Sun, 24 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE BiocIO PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 160/1932HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
BiocIO 1.1.2
Bioconductor Package Maintainer
Snapshot Date: 2021-01-23 14:40:18 -0500 (Sat, 23 Jan 2021)
URL: https://git.bioconductor.org/packages/BiocIO
Branch: master
Last Commit: e456aae
Last Changed Date: 2020-12-05 05:05:53 -0500 (Sat, 05 Dec 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK 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
riesling1 Windows Server 2019 Standard / x64  OK  OK  WARNINGS  OK 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: BiocIO
Version: 1.1.2
Command: C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocIO.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BiocIO_1.1.2.tar.gz
StartedAt: 2021-01-24 02:24:24 -0500 (Sun, 24 Jan 2021)
EndedAt: 2021-01-24 02:26:06 -0500 (Sun, 24 Jan 2021)
EllapsedTime: 102.7 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: BiocIO.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:BiocIO.install-out.txt --library=C:\Users\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings BiocIO_1.1.2.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BiocIO.Rcheck'
* using R Under development (unstable) (2021-01-05 r79797)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'BiocIO/DESCRIPTION' ... OK
* this is package 'BiocIO' version '1.1.2'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'BiocIO' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: cannot open file 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BiocIO.buildbin-libdir/00LOCK-BiocIO/00new/BiocIO/help/resource<-.html': Invalid argument
See 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BiocIO.Rcheck/00install.out' for details.
* 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 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 '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
See
  'C:/Users/biocbuild/bbs-3.13-bioc/meat/BiocIO.Rcheck/00check.log'
for details.



Installation output

BiocIO.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.13/bioc/src/contrib/BiocIO_1.1.2.tar.gz && rm -rf BiocIO.buildbin-libdir && mkdir BiocIO.buildbin-libdir && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=BiocIO.buildbin-libdir BiocIO_1.1.2.tar.gz && C:\Users\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL BiocIO_1.1.2.zip && rm BiocIO_1.1.2.tar.gz BiocIO_1.1.2.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  8755  100  8755    0     0   172k      0 --:--:-- --:--:-- --:--:--  194k

install for i386

* installing *source* package 'BiocIO' ...
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'BiocIO'
    finding HTML links ... done
    BiocFile-class                          html  
REDIRECT:topic	 class:BiocFile -> BiocFile-class.html [ FAIL ]
REDIRECT:topic	 BiocFile-class -> BiocFile-class.html [ SUCCESS ]
REDIRECT:topic	 class:CompressedFile -> BiocFile-class.html [ FAIL ]
REDIRECT:topic	 CompressedFile-class -> BiocFile-class.html [ SUCCESS ]
REDIRECT:topic	 BiocFileList-class -> BiocFile-class.html [ SUCCESS ]
REDIRECT:topic	 path -> BiocFile-class.html [ SUCCESS ]
REDIRECT:topic	 path,BiocFile-method -> BiocFile-class.html [ SUCCESS ]
REDIRECT:topic	 resource -> BiocFile-class.html [ SUCCESS ]
REDIRECT:topic	 resource<- -> BiocFile-class.html [ FAIL ]
REDIRECT:topic	 fileFormat -> BiocFile-class.html [ SUCCESS ]
REDIRECT:topic	 fileFormat,BiocFile-method -> BiocFile-class.html [ SUCCESS ]
REDIRECT:topic	 fileFormat,CompressedFile-method -> BiocFile-class.html [ SUCCESS ]
REDIRECT:topic	 fileFormat,character-method -> BiocFile-class.html [ SUCCESS ]
REDIRECT:topic	 BiocFileList -> BiocFile-class.html [ SUCCESS ]
REDIRECT:topic	 show,BiocFile-method -> BiocFile-class.html [ SUCCESS ]
REDIRECT:topic	 FileForFormat -> BiocFile-class.html [ SUCCESS ]
REDIRECT:topic	 bestFileFormat -> BiocFile-class.html [ SUCCESS ]
REDIRECT:topic	 bestFileFormat,GRangesList-method -> BiocFile-class.html [ SUCCESS ]
REDIRECT:topic	 bestFileFormat,GenomicRanges-method -> BiocFile-class.html [ SUCCESS ]
REDIRECT:topic	 bestFileFormat,IntegerRangesList-method -> BiocFile-class.html [ SUCCESS ]
REDIRECT:topic	 bestFileFormat,RleList-method -> BiocFile-class.html [ SUCCESS ]
REDIRECT:topic	 decompress -> BiocFile-class.html [ SUCCESS ]
REDIRECT:topic	 decompress,ANY-method -> BiocFile-class.html [ SUCCESS ]
REDIRECT:topic	 decompress,CompressedFile-method -> BiocFile-class.html [ SUCCESS ]
REDIRECT:topic	 decompress,GZFile-method -> BiocFile-class.html [ SUCCESS ]
REDIRECT:topic	 decompress,character-method -> BiocFile-class.html [ SUCCESS ]
REDIRECT:topic	 as.character,BiocFile-method -> BiocFile-class.html [ SUCCESS ]
Rd warning: cannot open file 'C:/Users/biocbuild/bbs-3.13-bioc/meat/BiocIO.buildbin-libdir/00LOCK-BiocIO/00new/BiocIO/help/resource<-.html': Invalid argument
    export                                  html  
REDIRECT:topic	 export -> export.html [ SUCCESS ]
REDIRECT:topic	 export,ANY,connection,character-method -> export.html [ SUCCESS ]
REDIRECT:topic	 export,ANY,connection,missing-method -> export.html [ SUCCESS ]
REDIRECT:topic	 export,ANY,CompressedFile,missing-method -> export.html [ SUCCESS ]
REDIRECT:topic	 export,ANY,missing,character-method -> export.html [ SUCCESS ]
REDIRECT:topic	 export,ANY,character,missing-method -> export.html [ SUCCESS ]
REDIRECT:topic	 export,ANY,character,character-method -> export.html [ SUCCESS ]
REDIRECT:topic	 import -> export.html [ SUCCESS ]
REDIRECT:topic	 import,connection,character,ANY-method -> export.html [ SUCCESS ]
REDIRECT:topic	 import,connection,missing,ANY-method -> export.html [ SUCCESS ]
REDIRECT:topic	 import,CompressedFile,missing,ANY-method -> export.html [ SUCCESS ]
REDIRECT:topic	 import,character,missing,ANY-method -> export.html [ SUCCESS ]
REDIRECT:topic	 import,character,character,ANY-method -> export.html [ SUCCESS ]
REDIRECT:topic	 import,missing,ANY,character-method -> export.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 'BiocIO' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'BiocIO' as BiocIO_1.1.2.zip
* DONE (BiocIO)
* installing to library 'C:/Users/biocbuild/bbs-3.13-bioc/R/library'
package 'BiocIO' successfully unpacked and MD5 sums checked

Tests output

BiocIO.Rcheck/tests_i386/testthat.Rout


R Under development (unstable) (2021-01-05 r79797) -- "Unsuffered Consequences"
Copyright (C) 2021 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(BiocIO)
> 
> test_check("BiocIO")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
   1.85    0.12    1.98 

BiocIO.Rcheck/tests_x64/testthat.Rout


R Under development (unstable) (2021-01-05 r79797) -- "Unsuffered Consequences"
Copyright (C) 2021 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(BiocIO)
> 
> test_check("BiocIO")
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 8 ]
> 
> proc.time()
   user  system elapsed 
   1.50    0.14    1.62 

Example timings

BiocIO.Rcheck/examples_i386/BiocIO-Ex.timings

nameusersystemelapsed
BiocFile-class0.030.000.04
export0.010.000.01

BiocIO.Rcheck/examples_x64/BiocIO-Ex.timings

nameusersystemelapsed
BiocFile-class0.050.000.04
export0.010.000.02