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CHECK report for RnBeads.hg19 on riesling1

This page was generated on 2021-01-21 16:01:37 -0500 (Thu, 21 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE RnBeads.hg19 PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 303/386HostnameOS / ArchINSTALLBUILDCHECK
RnBeads.hg19 1.23.0
RnBeadsAnnotationCreator
Snapshot Date: 2021-01-21 09:00:14 -0500 (Thu, 21 Jan 2021)
URL: https://git.bioconductor.org/packages/RnBeads.hg19
Branch: master
Last Commit: d816cbe
Last Changed Date: 2020-10-27 10:12:54 -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: RnBeads.hg19
Version: 1.23.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RnBeads.hg19.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings RnBeads.hg19_1.23.0.tar.gz
StartedAt: 2021-01-21 11:43:43 -0500 (Thu, 21 Jan 2021)
EndedAt: 2021-01-21 11:45:33 -0500 (Thu, 21 Jan 2021)
EllapsedTime: 110.8 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: RnBeads.hg19.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:RnBeads.hg19.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings RnBeads.hg19_1.23.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/RnBeads.hg19.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 'RnBeads.hg19/DESCRIPTION' ... OK
* this is package 'RnBeads.hg19' 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 'RnBeads.hg19' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 100.3Mb
  sub-directories of 1Mb or more:
    data     89.2Mb
    extdata  11.1Mb
* checking package 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
Package in Depends field not imported from: 'GenomicRanges'
  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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... WARNING
  Failed with error:  'package 'TxDb.Hsapiens.UCSC.hg19.knownGene' could not be loaded'
  Error loading dataset 'rnb.set.example':
   Error in .requirePackage(package) : 
    unable to find required package 'RnBeads'
  
  The dataset(s) may use package(s) not declared in the DESCRIPTION file.
* checking data for ASCII and uncompressed saves ... OK
* checking examples ... NONE
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 2 NOTEs
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/RnBeads.hg19.Rcheck/00check.log'
for details.



Installation output

RnBeads.hg19.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/RnBeads.hg19_1.23.0.tar.gz && rm -rf RnBeads.hg19.buildbin-libdir && mkdir RnBeads.hg19.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RnBeads.hg19.buildbin-libdir RnBeads.hg19_1.23.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL RnBeads.hg19_1.23.0.zip && rm RnBeads.hg19_1.23.0.tar.gz RnBeads.hg19_1.23.0.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
 76  100M   76 76.8M    0     0  98.4M      0  0:00:01 --:--:--  0:00:01 98.2M
100  100M  100  100M    0     0   101M      0 --:--:-- --:--:-- --:--:--  101M

install for i386

* installing *source* package 'RnBeads.hg19' ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RnBeads.hg19'
    finding HTML links ... done
    hg19                                    html  
REDIRECT:topic	 hg19 -> hg19.html [ SUCCESS ]
    regions                                 html  
REDIRECT:topic	 regions -> regions.html [ SUCCESS ]
    rnb.set.example                         html  
REDIRECT:topic	 rnb.set.example -> rnb.set.example.html [ SUCCESS ]
    sites                                   html  
REDIRECT:topic	 sites -> sites.html [ SUCCESS ]
** building package indices
** 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 'RnBeads.hg19' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RnBeads.hg19' as RnBeads.hg19_1.23.0.zip
* DONE (RnBeads.hg19)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'RnBeads.hg19' successfully unpacked and MD5 sums checked

Tests output


Example timings