Back to Multiple platform build/check report for BioC 3.13 experimental data
A[B]CDEFGHIJKLMNOPQRSTUVWXYZ

CHECK report for brgedata on riesling1

This page was generated on 2021-01-11 15:59:28 -0500 (Mon, 11 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE brgedata PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 41/385HostnameOS / ArchINSTALLBUILDCHECK
brgedata 1.13.0
Carlos Ruiz-Arenas
Snapshot Date: 2021-01-11 09:00:09 -0500 (Mon, 11 Jan 2021)
URL: https://git.bioconductor.org/packages/brgedata
Branch: master
Last Commit: c9c7e98
Last Changed Date: 2020-10-27 10:23:31 -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: brgedata
Version: 1.13.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:brgedata.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings brgedata_1.13.0.tar.gz
StartedAt: 2021-01-11 11:14:07 -0500 (Mon, 11 Jan 2021)
EndedAt: 2021-01-11 11:17:53 -0500 (Mon, 11 Jan 2021)
EllapsedTime: 225.9 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: brgedata.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:brgedata.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings brgedata_1.13.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/brgedata.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 'brgedata/DESCRIPTION' ... OK
* this is package 'brgedata' version '1.13.0'
* 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 'brgedata' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 638.3Mb
  sub-directories of 1Mb or more:
    data     184.2Mb
    extdata  454.1Mb
* 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 ... 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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... WARNING
  Warning: found non-ASCII strings
  'Average Brominated THM uptake (<b5>g/day)' in object 'brge_expo'
  'Average Chloroform uptake (<b5>g/day)' in object 'brge_expo'
  'Average total THM uptake (<b5>g/day)' in object 'brge_expo'
  'Benzene levels (<b5>g/m3)' in object 'brge_expo'
  'BPA (<b5>g/g creatine)' in object 'brge_expo'
  'Mercury (<b5>g/l)' in object 'brge_expo'
  'NO2 levels (<b5>g/m3)' in object 'brge_expo'
  'PFBS (<b5>g/l)' in object 'brge_expo'
  'PFHxS (<b5>g/l)' in object 'brge_expo'
  'PFOA (<b5>g/l)' in object 'brge_expo'
  '<b5>g/l' in object 'brge_expo'
* checking data for ASCII and uncompressed saves ... 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
brge_methy 8.86   0.65   11.44
** running examples for arch 'x64' ... OK
Examples with CPU (user + system) or elapsed time > 5s
           user system elapsed
brge_methy 9.13   0.59   11.65
* 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 WARNING, 1 NOTE
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/brgedata.Rcheck/00check.log'
for details.



Installation output

brgedata.Rcheck/00install.out

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://172.29.0.4/BBS/3.13/data-experiment/src/contrib/brgedata_1.13.0.tar.gz && rm -rf brgedata.buildbin-libdir && mkdir brgedata.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=brgedata.buildbin-libdir brgedata_1.13.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL brgedata_1.13.0.zip && rm brgedata_1.13.0.tar.gz brgedata_1.13.0.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
 11  284M   11 32.8M    0     0  92.9M      0  0:00:03 --:--:--  0:00:03 92.7M
 25  284M   25 73.8M    0     0  54.5M      0  0:00:05  0:00:01  0:00:04 54.5M
 41  284M   41  117M    0     0  47.2M      0  0:00:06  0:00:02  0:00:04 47.2M
 59  284M   59  170M    0     0  50.7M      0  0:00:05  0:00:03  0:00:02 50.7M
 87  284M   87  250M    0     0  57.4M      0  0:00:04  0:00:04 --:--:-- 57.4M
100  284M  100  284M    0     0  60.6M      0  0:00:04  0:00:04 --:--:-- 57.9M

install for i386

* installing *source* package 'brgedata' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'brgedata'
    finding HTML links ... done
    BRGEdata                                html  
REDIRECT:topic	 brgedata -> BRGEdata.html [ SUCCESS ]
REDIRECT:topic	 brgedata-package -> BRGEdata.html [ SUCCESS ]
    brge_expo                               html  
REDIRECT:topic	 brge_expo -> brge_expo.html [ SUCCESS ]
    brge_gexp                               html  
REDIRECT:topic	 brge_gexp -> brge_gexp.html [ SUCCESS ]
    brge_methy                              html  
REDIRECT:topic	 brge_methy -> brge_methy.html [ SUCCESS ]
    brge_prot                               html  
REDIRECT:topic	 brge_prot -> brge_prot.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 'brgedata' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'brgedata' as brgedata_1.13.0.zip
* DONE (brgedata)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'brgedata' successfully unpacked and MD5 sums checked

Tests output


Example timings

brgedata.Rcheck/examples_i386/brgedata-Ex.timings

nameusersystemelapsed
brge_gexp1.460.031.50
brge_methy 8.86 0.6511.44
brge_prot000

brgedata.Rcheck/examples_x64/brgedata-Ex.timings

nameusersystemelapsed
brge_gexp1.370.021.39
brge_methy 9.13 0.5911.65
brge_prot000