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CHECK report for stjudem on riesling1

This page was generated on 2021-01-21 16:01:39 -0500 (Thu, 21 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE stjudem PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 347/386HostnameOS / ArchINSTALLBUILDCHECK
stjudem 1.31.0
Joern Toedling
Snapshot Date: 2021-01-21 09:00:14 -0500 (Thu, 21 Jan 2021)
URL: https://git.bioconductor.org/packages/stjudem
Branch: master
Last Commit: 0683f3a
Last Changed Date: 2020-10-27 09:47:09 -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: stjudem
Version: 1.31.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:stjudem.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings stjudem_1.31.0.tar.gz
StartedAt: 2021-01-21 11:48:49 -0500 (Thu, 21 Jan 2021)
EndedAt: 2021-01-21 11:49:37 -0500 (Thu, 21 Jan 2021)
EllapsedTime: 48.8 seconds
RetCode: 0
Status:  OK  
CheckDir: stjudem.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:stjudem.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings stjudem_1.31.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/stjudem.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 'stjudem/DESCRIPTION' ... OK
* this is package 'stjudem' version '1.31.0'
* 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 'stjudem' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 27.6Mb
  sub-directories of 1Mb or more:
    data  27.6Mb
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
File 'stjudem/R/zzz.R':
  .onLoad calls:
    packageStartupMessage("Type 'data(stjude)' to load the data set.")
    packageStartupMessage("Then type 'summary(stjude)' for an overview of the data structure.")
    packageStartupMessage("See package 'macat' for examplary analyses.")

See section 'Good practice' in '?.onAttach'.
* 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 examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking PDF version of manual ... OK
* DONE

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



Installation output

stjudem.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/stjudem_1.31.0.tar.gz && rm -rf stjudem.buildbin-libdir && mkdir stjudem.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=stjudem.buildbin-libdir stjudem_1.31.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL stjudem_1.31.0.zip && rm stjudem_1.31.0.tar.gz stjudem_1.31.0.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
  0 27.5M    0  1213    0     0  12252      0  0:39:21 --:--:--  0:39:21 12130
 10 27.5M   10 2867k    0     0  2662k      0  0:00:10  0:00:01  0:00:09 2659k
 15 27.5M   15 4431k    0     0  2091k      0  0:00:13  0:00:02  0:00:11 2090k
 86 27.5M   86 23.8M    0     0  8057k      0  0:00:03  0:00:03 --:--:-- 8054k
100 27.5M  100 27.5M    0     0  9216k      0  0:00:03  0:00:03 --:--:-- 9213k

install for i386

* installing *source* package 'stjudem' ...
** using staged installation
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'stjudem'
    finding HTML links ... done
    stjude                                  html  
REDIRECT:topic	 stjude -> stjude.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 'stjudem' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'stjudem' as stjudem_1.31.0.zip
* DONE (stjudem)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'stjudem' successfully unpacked and MD5 sums checked

Tests output


Example timings

stjudem.Rcheck/examples_i386/stjudem-Ex.timings

nameusersystemelapsed
stjude2.390.042.44

stjudem.Rcheck/examples_x64/stjudem-Ex.timings

nameusersystemelapsed
stjude1.870.031.90