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CHECK report for tximeta on tokay2

This page was generated on 2020-10-17 11:57:58 -0400 (Sat, 17 Oct 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE tximeta PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 1851/1905HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
tximeta 1.6.3
Michael Love
Snapshot Date: 2020-10-16 14:40:19 -0400 (Fri, 16 Oct 2020)
URL: https://git.bioconductor.org/packages/tximeta
Branch: RELEASE_3_11
Last Commit: 65c2753
Last Changed Date: 2020-08-20 08:14:52 -0400 (Thu, 20 Aug 2020)
malbec2 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] NA 
machv2 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: tximeta
Version: 1.6.3
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:tximeta.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings tximeta_1.6.3.tar.gz
StartedAt: 2020-10-17 09:06:22 -0400 (Sat, 17 Oct 2020)
EndedAt: 2020-10-17 09:17:07 -0400 (Sat, 17 Oct 2020)
EllapsedTime: 644.8 seconds
RetCode: 0
Status:  OK  
CheckDir: tximeta.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:tximeta.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings tximeta_1.6.3.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/tximeta.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 'tximeta/DESCRIPTION' ... OK
* this is package 'tximeta' version '1.6.3'
* 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 'tximeta' 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 files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
addIds 15.73   1.61   46.78
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
        user system elapsed
addIds 14.47   0.86   15.82
* 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: OK


Installation output

tximeta.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/tximeta_1.6.3.tar.gz && rm -rf tximeta.buildbin-libdir && mkdir tximeta.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=tximeta.buildbin-libdir tximeta_1.6.3.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL tximeta_1.6.3.zip && rm tximeta_1.6.3.tar.gz tximeta_1.6.3.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  373k  100  373k    0     0  2668k      0 --:--:-- --:--:-- --:--:-- 2786k

install for i386

* installing *source* package 'tximeta' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'tximeta'
    finding HTML links ... done
    addExons                                html  
    addIds                                  html  
    getTximetaBFC                           html  
    linkedTxome                             html  
    makeDGEList                             html  
    retrieveDb                              html  
    splitSE                                 html  
    summarizeToGene                         html  
    tximeta-package                         html  
    finding level-2 HTML links ... done

    tximeta                                 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 'tximeta' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'tximeta' as tximeta_1.6.3.zip
* DONE (tximeta)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'tximeta' successfully unpacked and MD5 sums checked

Tests output

tximeta.Rcheck/tests_i386/testthat.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.

> library("testthat")
> library("tximeta")
> test_check("tximeta")
== testthat results  ===========================================================
[ OK: 37 | SKIPPED: 4 | WARNINGS: 0 | FAILED: 0 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
  54.51    7.46   65.75 

tximeta.Rcheck/tests_x64/testthat.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.

> library("testthat")
> library("tximeta")
> test_check("tximeta")
== testthat results  ===========================================================
[ OK: 37 | SKIPPED: 4 | WARNINGS: 0 | FAILED: 0 ]
Warning message:
call dbDisconnect() when finished working with a connection 
> 
> proc.time()
   user  system elapsed 
  64.04    4.85   72.73 

Example timings

tximeta.Rcheck/examples_i386/tximeta-Ex.timings

nameusersystemelapsed
addIds15.73 1.6146.78
getTximetaBFC000
linkedTxome0.480.040.56
retrieveDb2.420.112.53
splitSE0.100.000.09
summarizeToGene3.420.063.49
tximeta1.530.071.59

tximeta.Rcheck/examples_x64/tximeta-Ex.timings

nameusersystemelapsed
addIds14.47 0.8615.82
getTximetaBFC000
linkedTxome0.310.020.33
retrieveDb2.370.092.48
splitSE0.090.000.10
summarizeToGene3.660.143.79
tximeta1.970.062.03