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CHECK report for TBX20BamSubset on riesling1

This page was generated on 2021-01-21 16:01:40 -0500 (Thu, 21 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE TBX20BamSubset PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 355/386HostnameOS / ArchINSTALLBUILDCHECK
TBX20BamSubset 1.27.0
D. Bindreither
Snapshot Date: 2021-01-21 09:00:14 -0500 (Thu, 21 Jan 2021)
URL: https://git.bioconductor.org/packages/TBX20BamSubset
Branch: master
Last Commit: 33bf3b9
Last Changed Date: 2020-10-27 09:56:21 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ OK ]

Summary

Package: TBX20BamSubset
Version: 1.27.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TBX20BamSubset.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings TBX20BamSubset_1.27.0.tar.gz
StartedAt: 2021-01-21 11:49:56 -0500 (Thu, 21 Jan 2021)
EndedAt: 2021-01-21 11:51:07 -0500 (Thu, 21 Jan 2021)
EllapsedTime: 71.1 seconds
RetCode: 0
Status:  OK  
CheckDir: TBX20BamSubset.Rcheck
Warnings: 0

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:TBX20BamSubset.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings TBX20BamSubset_1.27.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/TBX20BamSubset.Rcheck'
* using R Under development (unstable) (2020-12-30 r79736)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'TBX20BamSubset/DESCRIPTION' ... OK
* this is package 'TBX20BamSubset' version '1.27.0'
* 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 'TBX20BamSubset' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 98.2Mb
  sub-directories of 1Mb or more:
    extdata  98.1Mb
* 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 ... NOTE
Namespace in Imports field not imported from: 'xtable'
  All declared Imports should be used.
Package in Depends field not imported from: 'Rsamtools'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* 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 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: 2 NOTEs
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/TBX20BamSubset.Rcheck/00check.log'
for details.



Installation output

TBX20BamSubset.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/TBX20BamSubset_1.27.0.tar.gz && rm -rf TBX20BamSubset.buildbin-libdir && mkdir TBX20BamSubset.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=TBX20BamSubset.buildbin-libdir TBX20BamSubset_1.27.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL TBX20BamSubset_1.27.0.zip && rm TBX20BamSubset_1.27.0.tar.gz TBX20BamSubset_1.27.0.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
 37 94.5M   37 35.7M    0     0   105M      0 --:--:-- --:--:-- --:--:--  104M
100 94.5M  100 94.5M    0     0  70.8M      0  0:00:01  0:00:01 --:--:-- 70.8M

install for i386

* installing *source* package 'TBX20BamSubset' ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'TBX20BamSubset'
    finding HTML links ... done
    TBX20BamSubset-package                  html  
REDIRECT:topic	 TBX20BamSubset-package -> TBX20BamSubset-package.html [ SUCCESS ]
REDIRECT:topic	 TBX20BamSubset -> TBX20BamSubset-package.html [ SUCCESS ]
    getBamFileList                          html  
REDIRECT:topic	 getBamFileList -> getBamFileList.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 'TBX20BamSubset' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'TBX20BamSubset' as TBX20BamSubset_1.27.0.zip
* DONE (TBX20BamSubset)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'TBX20BamSubset' successfully unpacked and MD5 sums checked

Tests output


Example timings

TBX20BamSubset.Rcheck/examples_i386/TBX20BamSubset-Ex.timings

nameusersystemelapsed
TBX20BamSubset-package0.010.000.01
getBamFileList000

TBX20BamSubset.Rcheck/examples_x64/TBX20BamSubset-Ex.timings

nameusersystemelapsed
TBX20BamSubset-package000
getBamFileList000