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CHECK report for ListerEtAlBSseq on riesling1

This page was generated on 2021-01-18 15:58:48 -0500 (Mon, 18 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE ListerEtAlBSseq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 198/385HostnameOS / ArchINSTALLBUILDCHECK
ListerEtAlBSseq 1.23.0
Kamal Kishore
Snapshot Date: 2021-01-18 09:00:15 -0500 (Mon, 18 Jan 2021)
URL: https://git.bioconductor.org/packages/ListerEtAlBSseq
Branch: master
Last Commit: cd9fe96
Last Changed Date: 2020-10-27 10:10:02 -0500 (Tue, 27 Oct 2020)
malbec2 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
riesling1 Windows Server 2019 Standard / x64  OK  OK [ WARNINGS ]

Summary

Package: ListerEtAlBSseq
Version: 1.23.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ListerEtAlBSseq.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ListerEtAlBSseq_1.23.0.tar.gz
StartedAt: 2021-01-18 11:29:37 -0500 (Mon, 18 Jan 2021)
EndedAt: 2021-01-18 11:32:15 -0500 (Mon, 18 Jan 2021)
EllapsedTime: 158.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: ListerEtAlBSseq.Rcheck
Warnings: 1

Command output

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###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:ListerEtAlBSseq.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings ListerEtAlBSseq_1.23.0.tar.gz
###
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##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/ListerEtAlBSseq.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 'ListerEtAlBSseq/DESCRIPTION' ... OK
* this is package 'ListerEtAlBSseq' version '1.23.0'
* 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 'ListerEtAlBSseq' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 659.0Mb
  sub-directories of 1Mb or more:
    data       2.9Mb
    extdata  656.0Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Non-standard license specification:
  Artistic 2.0
Standardizable: TRUE
Standardized license specification:
  Artistic-2.0
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... 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 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in 'vignettes' ... WARNING
Files in the 'vignettes' directory but no files in 'inst/doc':
  'ListerEtAlBSseq.rnw'
Files named as vignettes but with no recognized vignette engine:
   'vignettes/ListerEtAlBSseq.rnw'
(Is a VignetteBuilder field missing?)
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/ListerEtAlBSseq.Rcheck/00check.log'
for details.



Installation output

ListerEtAlBSseq.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/ListerEtAlBSseq_1.23.0.tar.gz && rm -rf ListerEtAlBSseq.buildbin-libdir && mkdir ListerEtAlBSseq.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=ListerEtAlBSseq.buildbin-libdir ListerEtAlBSseq_1.23.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL ListerEtAlBSseq_1.23.0.zip && rm ListerEtAlBSseq_1.23.0.tar.gz ListerEtAlBSseq_1.23.0.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
 12  658M   12 81.6M    0     0   105M      0  0:00:06 --:--:--  0:00:06  105M
 13  658M   13 87.6M    0     0  48.3M      0  0:00:13  0:00:01  0:00:12 48.3M
 21  658M   21  142M    0     0  48.9M      0  0:00:13  0:00:02  0:00:11 48.9M
 26  658M   26  172M    0     0  44.6M      0  0:00:14  0:00:03  0:00:11 44.6M
 33  658M   33  220M    0     0  45.0M      0  0:00:14  0:00:04  0:00:10 45.0M
 40  658M   40  267M    0     0  46.3M      0  0:00:14  0:00:05  0:00:09 37.2M
 56  658M   56  372M    0     0  54.9M      0  0:00:11  0:00:06  0:00:05 57.3M
 72  658M   72  478M    0     0  61.5M      0  0:00:10  0:00:07  0:00:03 69.0M
 88  658M   88  582M    0     0  66.2M      0  0:00:09  0:00:08  0:00:01 83.1M
100  658M  100  658M    0     0  69.5M      0  0:00:09  0:00:09 --:--:-- 95.9M

install for i386

* installing *source* package 'ListerEtAlBSseq' ...
** using staged installation
** data
** inst
** help
*** installing help indices
  converting help for package 'ListerEtAlBSseq'
    finding HTML links ... done
    H1.WGBS                                 html  
REDIRECT:topic	 H1.WGBS -> H1.WGBS.html [ SUCCESS ]
    IMR90.WGBS                              html  
REDIRECT:topic	 IMR90.WGBS -> IMR90.WGBS.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 'ListerEtAlBSseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'ListerEtAlBSseq' as ListerEtAlBSseq_1.23.0.zip
* DONE (ListerEtAlBSseq)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'ListerEtAlBSseq' successfully unpacked and MD5 sums checked

Tests output


Example timings

ListerEtAlBSseq.Rcheck/examples_i386/ListerEtAlBSseq-Ex.timings

nameusersystemelapsed
H1.WGBS0.140.040.21
IMR90.WGBS0.160.000.16

ListerEtAlBSseq.Rcheck/examples_x64/ListerEtAlBSseq-Ex.timings

nameusersystemelapsed
H1.WGBS0.170.000.17
IMR90.WGBS0.130.010.14