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CHECK report for biobtreeR on tokay1

This page was generated on 2020-08-07 12:19:21 -0400 (Fri, 07 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE biobtreeR PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 146/1882HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
biobtreeR 1.1.0
Tamer Gur
Snapshot Date: 2020-08-06 14:50:46 -0400 (Thu, 06 Aug 2020)
URL: https://git.bioconductor.org/packages/biobtreeR
Branch: master
Last Commit: aa78b02
Last Changed Date: 2020-05-19 07:05:00 -0400 (Tue, 19 May 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: biobtreeR
Version: 1.1.0
Command: C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biobtreeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings biobtreeR_1.1.0.tar.gz
StartedAt: 2020-08-07 05:59:48 -0400 (Fri, 07 Aug 2020)
EndedAt: 2020-08-07 06:00:53 -0400 (Fri, 07 Aug 2020)
EllapsedTime: 64.7 seconds
RetCode: 0
Status:  OK  
CheckDir: biobtreeR.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:biobtreeR.install-out.txt --library=C:\Users\biocbuild\bbs-3.12-bioc\R\library --no-vignettes --timings biobtreeR_1.1.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.12-bioc/meat/biobtreeR.Rcheck'
* using R version 4.0.2 (2020-06-22)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'biobtreeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'biobtreeR' version '1.1.0'
* 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 ... OK
* checking for portable file names ... OK
* checking whether package 'biobtreeR' 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
bbBuiltInDB 0.74    0.3    6.94
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
            user system elapsed
bbBuiltInDB  0.7   0.18    5.58
* 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

biobtreeR.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/biobtreeR_1.1.0.tar.gz && rm -rf biobtreeR.buildbin-libdir && mkdir biobtreeR.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=biobtreeR.buildbin-libdir biobtreeR_1.1.0.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL biobtreeR_1.1.0.zip && rm biobtreeR_1.1.0.tar.gz biobtreeR_1.1.0.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  641k  100  641k    0     0  4798k      0 --:--:-- --:--:-- --:--:-- 4933k

install for i386

* installing *source* package 'biobtreeR' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'biobtreeR'
    finding HTML links ... done
    bbBuildCustomDB                         html  
    bbBuiltInDB                             html  
    bbConfig-class                          html  
    bbEntry                                 html  
    bbEntryFilter                           html  
    bbEntryPage                             html  
    bbListAttrs                             html  
    bbListDatasets                          html  
    bbMapping                               html  
    bbSearch                                html  
    bbStart                                 html  
    bbStop                                  html  
    bbUseOutDir                             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 'biobtreeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'biobtreeR' as biobtreeR_1.1.0.zip
* DONE (biobtreeR)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'biobtreeR' successfully unpacked and MD5 sums checked

Tests output


Example timings

biobtreeR.Rcheck/examples_i386/biobtreeR-Ex.timings

nameusersystemelapsed
bbBuildCustomDB000
bbBuiltInDB0.740.306.94
bbEntry0.140.023.39
bbEntryFilter0.000.000.01
bbEntryPage0.000.000.02
bbListAttrs000
bbListDatasets0.520.230.75
bbMapping0.010.000.03
bbSearch0.020.000.02
bbStart0.000.000.76
bbStop0.000.000.13
bbUseOutDir000

biobtreeR.Rcheck/examples_x64/biobtreeR-Ex.timings

nameusersystemelapsed
bbBuildCustomDB000
bbBuiltInDB0.700.185.58
bbEntry0.250.002.48
bbEntryFilter0.000.020.02
bbEntryPage000
bbListAttrs000
bbListDatasets0.560.220.78
bbMapping0.000.010.03
bbSearch0.000.020.03
bbStart0.000.000.28
bbStop0.000.000.14
bbUseOutDir000