Back to Multiple platform build/check report for BioC 3.11
ABC[D]EFGHIJKLMNOPQRSTUVWXYZ

CHECK report for DupChecker on tokay2

This page was generated on 2020-02-03 13:23:17 -0500 (Mon, 03 Feb 2020).

Package 492/1822HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DupChecker 1.25.0
"Quanhu SHENG"
Snapshot Date: 2020-02-02 16:45:09 -0500 (Sun, 02 Feb 2020)
URL: https://git.bioconductor.org/packages/DupChecker
Branch: master
Last Commit: f75d1dd
Last Changed Date: 2019-10-29 13:37:33 -0500 (Tue, 29 Oct 2019)
malbec2 Linux (Ubuntu 18.04.3 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: DupChecker
Version: 1.25.0
Command: C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DupChecker.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings DupChecker_1.25.0.tar.gz
StartedAt: 2020-02-03 05:46:45 -0500 (Mon, 03 Feb 2020)
EndedAt: 2020-02-03 05:47:28 -0500 (Mon, 03 Feb 2020)
EllapsedTime: 43.5 seconds
RetCode: 0
Status:  OK  
CheckDir: DupChecker.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:DupChecker.install-out.txt --library=C:\Users\biocbuild\bbs-3.11-bioc\R\library --no-vignettes --timings DupChecker_1.25.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'C:/Users/biocbuild/bbs-3.11-bioc/meat/DupChecker.Rcheck'
* using R Under development (unstable) (2020-01-27 r77730)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'DupChecker/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'DupChecker' version '1.25.0'
* 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 'DupChecker' 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 ... NOTE
arrayExpressDownload: no visible global function definition for
  'download.file'
geoDownload: no visible global function definition for 'download.file'
geoDownload: no visible global function definition for 'untar'
getFtpFilenames: no visible global function definition for 'read.table'
Undefined global functions or variables:
  download.file read.table untar
Consider adding
  importFrom("utils", "download.file", "read.table", "untar")
to your NAMESPACE file.
* 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 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 NOTE
See
  'C:/Users/biocbuild/bbs-3.11-bioc/meat/DupChecker.Rcheck/00check.log'
for details.



Installation output

DupChecker.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.11/bioc/src/contrib/DupChecker_1.25.0.tar.gz && rm -rf DupChecker.buildbin-libdir && mkdir DupChecker.buildbin-libdir && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=DupChecker.buildbin-libdir DupChecker_1.25.0.tar.gz && C:\Users\biocbuild\bbs-3.11-bioc\R\bin\R.exe CMD INSTALL DupChecker_1.25.0.zip && rm DupChecker_1.25.0.tar.gz DupChecker_1.25.0.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  8983  100  8983    0     0  95218      0 --:--:-- --:--:-- --:--:--   99k

install for i386

* installing *source* package 'DupChecker' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'DupChecker'
    finding HTML links ... done
    arrayExpressDownload                    html  
    buildFileTable                          html  
    geoDownload                             html  
    validateFile                            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 'DupChecker' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'DupChecker' as DupChecker_1.25.0.zip
* DONE (DupChecker)
* installing to library 'C:/Users/biocbuild/bbs-3.11-bioc/R/library'
package 'DupChecker' successfully unpacked and MD5 sums checked

Tests output


Example timings

DupChecker.Rcheck/examples_i386/DupChecker-Ex.timings

nameusersystemelapsed
arrayExpressDownload0.030.001.59
buildFileTable0.000.000.07
geoDownload0.140.001.19
validateFile0.030.060.86

DupChecker.Rcheck/examples_x64/DupChecker-Ex.timings

nameusersystemelapsed
arrayExpressDownload0.030.001.41
buildFileTable0.000.010.02
geoDownload0.200.000.71
validateFile0.020.000.02