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CHECK report for RTCGA.methylation on riesling1

This page was generated on 2021-01-14 15:59:11 -0500 (Thu, 14 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE RTCGA.methylation PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 312/385HostnameOS / ArchINSTALLBUILDCHECK
RTCGA.methylation 1.19.0
Marcin Kosinski
Snapshot Date: 2021-01-14 09:00:13 -0500 (Thu, 14 Jan 2021)
URL: https://git.bioconductor.org/packages/RTCGA.methylation
Branch: master
Last Commit: 7e0854d
Last Changed Date: 2020-10-27 10:16:33 -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 [ WARNINGS ]

Summary

Package: RTCGA.methylation
Version: 1.19.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTCGA.methylation.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings RTCGA.methylation_1.19.0.tar.gz
StartedAt: 2021-01-14 11:39:47 -0500 (Thu, 14 Jan 2021)
EndedAt: 2021-01-14 11:42:17 -0500 (Thu, 14 Jan 2021)
EllapsedTime: 150.3 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: RTCGA.methylation.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:RTCGA.methylation.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings RTCGA.methylation_1.19.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/RTCGA.methylation.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 'RTCGA.methylation/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RTCGA.methylation' version '1.19.0'
* 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 'RTCGA.methylation' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: cannot open file 'D:/biocbuild/bbs-3.13-data-experiment/meat/RTCGA.methylation.buildbin-libdir/00LOCK-RTCGA.methylation/00new/RTCGA.methylation/help/BRCA.methylation,COAD.methylation,COADREAD.methylation,GBM.methylation,GBMLGG.methylation,KIPAN.methylation,KIRC.methylation,KIRP.methylation,LAML.methylation,LUAD.methylation,LUSC.methylation,OV.methylation,OV.methylation1,OV.methylation2,READ.methylation,STAD.methylation,STES.methylation,UCEC.methylation.html': No such file or directory
See 'D:/biocbuild/bbs-3.13-data-experiment/meat/RTCGA.methylation.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 672.1Mb
  sub-directories of 1Mb or more:
    data  672.0Mb
* 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 ... OK
* checking data for ASCII and uncompressed saves ... 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: 1 WARNING, 1 NOTE
See
  'D:/biocbuild/bbs-3.13-data-experiment/meat/RTCGA.methylation.Rcheck/00check.log'
for details.



Installation output

RTCGA.methylation.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/RTCGA.methylation_1.19.0.tar.gz && rm -rf RTCGA.methylation.buildbin-libdir && mkdir RTCGA.methylation.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RTCGA.methylation.buildbin-libdir RTCGA.methylation_1.19.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL RTCGA.methylation_1.19.0.zip && rm RTCGA.methylation_1.19.0.tar.gz RTCGA.methylation_1.19.0.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
  4  622M    4 25.5M    0     0  55.4M      0  0:00:11 --:--:--  0:00:11 55.4M
 20  622M   20  125M    0     0  86.1M      0  0:00:07  0:00:01  0:00:06 86.0M
 37  622M   37  231M    0     0  94.0M      0  0:00:06  0:00:02  0:00:04 94.0M
 50  622M   50  313M    0     0  90.6M      0  0:00:06  0:00:03  0:00:03 90.6M
 65  622M   65  405M    0     0  90.8M      0  0:00:06  0:00:04  0:00:02 90.8M
 74  622M   74  465M    0     0  84.3M      0  0:00:07  0:00:05  0:00:02 86.9M
 81  622M   81  509M    0     0  77.4M      0  0:00:08  0:00:06  0:00:02 74.9M
 90  622M   90  566M    0     0  75.2M      0  0:00:08  0:00:07  0:00:01 66.0M
100  622M  100  622M    0     0  76.7M      0  0:00:08  0:00:08 --:--:-- 66.4M

install for i386

* installing *source* package 'RTCGA.methylation' ...
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'RTCGA.methylation'
    finding HTML links ... done
    methylation                             html  
REDIRECT:topic	 BRCA.methylation -> methylation.html [ SUCCESS ]
REDIRECT:topic	 BRCA.methylation,COAD.methylation,COADREAD.methylation,GBM.methylation,GBMLGG.methylation,KIPAN.methylation,KIRC.methylation,KIRP.methylation,LAML.methylation,LUAD.methylation,LUSC.methylation,OV.methylation,OV.methylation1,OV.methylation2,READ.methylation,STAD.methylation,STES.methylation,UCEC.methylation -> methylation.html [ FAIL ]
REDIRECT:topic	 COAD.methylation -> methylation.html [ SUCCESS ]
REDIRECT:topic	 COADREAD.methylation -> methylation.html [ SUCCESS ]
REDIRECT:topic	 GBM.methylation -> methylation.html [ SUCCESS ]
REDIRECT:topic	 GBMLGG.methylation -> methylation.html [ SUCCESS ]
REDIRECT:topic	 KIPAN.methylation -> methylation.html [ SUCCESS ]
REDIRECT:topic	 KIRC.methylation -> methylation.html [ SUCCESS ]
REDIRECT:topic	 KIRP.methylation -> methylation.html [ SUCCESS ]
REDIRECT:topic	 LAML.methylation -> methylation.html [ SUCCESS ]
REDIRECT:topic	 LUAD.methylation -> methylation.html [ SUCCESS ]
REDIRECT:topic	 LUSC.methylation -> methylation.html [ SUCCESS ]
REDIRECT:topic	 OV.methylation1 -> methylation.html [ SUCCESS ]
REDIRECT:topic	 OV.methylation2 -> methylation.html [ SUCCESS ]
REDIRECT:topic	 READ.methylation -> methylation.html [ SUCCESS ]
REDIRECT:topic	 STAD.methylation -> methylation.html [ SUCCESS ]
REDIRECT:topic	 STES.methylation -> methylation.html [ SUCCESS ]
REDIRECT:topic	 UCEC.methylation -> methylation.html [ SUCCESS ]
REDIRECT:topic	 methylation -> methylation.html [ SUCCESS ]
    finding level-2 HTML links ... done

Rd warning: cannot open file 'D:/biocbuild/bbs-3.13-data-experiment/meat/RTCGA.methylation.buildbin-libdir/00LOCK-RTCGA.methylation/00new/RTCGA.methylation/help/BRCA.methylation,COAD.methylation,COADREAD.methylation,GBM.methylation,GBMLGG.methylation,KIPAN.methylation,KIRC.methylation,KIRP.methylation,LAML.methylation,LUAD.methylation,LUSC.methylation,OV.methylation,OV.methylation1,OV.methylation2,READ.methylation,STAD.methylation,STES.methylation,UCEC.methylation.html': No such file or directory
** 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 'RTCGA.methylation' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RTCGA.methylation' as RTCGA.methylation_1.19.0.zip
* DONE (RTCGA.methylation)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'RTCGA.methylation' successfully unpacked and MD5 sums checked

Tests output


Example timings

RTCGA.methylation.Rcheck/examples_i386/RTCGA.methylation-Ex.timings

nameusersystemelapsed
methylation000

RTCGA.methylation.Rcheck/examples_x64/RTCGA.methylation-Ex.timings

nameusersystemelapsed
methylation000