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CHECK report for RTCGA.clinical on riesling1

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

TO THE DEVELOPERS/MAINTAINERS OF THE RTCGA.clinical PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 310/386HostnameOS / ArchINSTALLBUILDCHECK
RTCGA.clinical 20151101.21.0
Marcin Kosinski
Snapshot Date: 2021-01-21 09:00:14 -0500 (Thu, 21 Jan 2021)
URL: https://git.bioconductor.org/packages/RTCGA.clinical
Branch: master
Last Commit: c14e85c
Last Changed Date: 2020-10-27 10:13:45 -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.clinical
Version: 20151101.21.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTCGA.clinical.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings RTCGA.clinical_20151101.21.0.tar.gz
StartedAt: 2021-01-21 11:44:35 -0500 (Thu, 21 Jan 2021)
EndedAt: 2021-01-21 11:46:08 -0500 (Thu, 21 Jan 2021)
EllapsedTime: 93.1 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: RTCGA.clinical.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.clinical.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings RTCGA.clinical_20151101.21.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/RTCGA.clinical.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.clinical/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RTCGA.clinical' version '20151101.21.0'
* 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.clinical' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: cannot open file 'D:/biocbuild/bbs-3.13-data-experiment/meat/RTCGA.clinical.buildbin-libdir/00LOCK-RTCGA.clinical/00new/RTCGA.clinical/help/ACC.clinical,BLCA.clinical,BRCA.clinical,CESC.clinical,CHOL.clinical,COAD.clinical,COADREAD.clinical,DLBC.clinical,ESCA.clinical,FPPP.clinical,GBM.clinical,GBMLGG.clinical,HNSC.clinical,KICH.clinical,KIPAN.clinical,KIRC.clinical,KIRP.clinical,LAML.clinical,LGG.clinical,LIHC.clinical,LUAD.clinical,LUSC.clinical,MESO.clinical,OV.clinical,PAAD.clinical,PCPG.clinical,PRAD.clinical,READ.clinical,SARC.clinical,SKCM.clinical,STAD.clinical,STES.clinical,TGCT.clinical,THCA.clinical,THYM.clinical,UCEC.clinical,UCS.clinical,UVM.clinical.html': No such file or directory
See 'D:/biocbuild/bbs-3.13-data-experiment/meat/RTCGA.clinical.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 20.8Mb
  sub-directories of 1Mb or more:
    data  20.7Mb
* 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 ... NONE
* 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.clinical.Rcheck/00check.log'
for details.



Installation output

RTCGA.clinical.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.clinical_20151101.21.0.tar.gz && rm -rf RTCGA.clinical.buildbin-libdir && mkdir RTCGA.clinical.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RTCGA.clinical.buildbin-libdir RTCGA.clinical_20151101.21.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL RTCGA.clinical_20151101.21.0.zip && rm RTCGA.clinical_20151101.21.0.tar.gz RTCGA.clinical_20151101.21.0.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
 16 13.9M   16 2405k    0     0  6643k      0  0:00:02 --:--:--  0:00:02 6643k
100 13.9M  100 13.9M    0     0  12.2M      0  0:00:01  0:00:01 --:--:-- 12.2M

install for i386

* installing *source* package 'RTCGA.clinical' ...
** 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.clinical'
    finding HTML links ... done
    clinical                                html  
REDIRECT:topic	 ACC.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 ACC.clinical,BLCA.clinical,BRCA.clinical,CESC.clinical,CHOL.clinical,COAD.clinical,COADREAD.clinical,DLBC.clinical,ESCA.clinical,FPPP.clinical,GBM.clinical,GBMLGG.clinical,HNSC.clinical,KICH.clinical,KIPAN.clinical,KIRC.clinical,KIRP.clinical,LAML.clinical,LGG.clinical,LIHC.clinical,LUAD.clinical,LUSC.clinical,MESO.clinical,OV.clinical,PAAD.clinical,PCPG.clinical,PRAD.clinical,READ.clinical,SARC.clinical,SKCM.clinical,STAD.clinical,STES.clinical,TGCT.clinical,THCA.clinical,THYM.clinical,UCEC.clinical,UCS.clinical,UVM.clinical -> clinical.html [ FAIL ]
REDIRECT:topic	 BLCA.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 BRCA.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 CESC.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 CHOL.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 COAD.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 COADREAD.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 DLBC.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 ESCA.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 FPPP.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 GBM.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 GBMLGG.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 HNSC.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 KICH.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 KIPAN.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 KIRC.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 KIRP.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 LAML.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 LGG.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 LIHC.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 LUAD.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 LUSC.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 MESO.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 OV.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 PAAD.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 PCPG.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 PRAD.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 READ.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 SARC.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 SKCM.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 STAD.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 STES.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 TGCT.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 THCA.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 THYM.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 UCEC.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 UCS.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 UVM.clinical -> clinical.html [ SUCCESS ]
REDIRECT:topic	 clinical -> clinical.html [ SUCCESS ]
    finding level-2 HTML links ... done

Rd warning: cannot open file 'D:/biocbuild/bbs-3.13-data-experiment/meat/RTCGA.clinical.buildbin-libdir/00LOCK-RTCGA.clinical/00new/RTCGA.clinical/help/ACC.clinical,BLCA.clinical,BRCA.clinical,CESC.clinical,CHOL.clinical,COAD.clinical,COADREAD.clinical,DLBC.clinical,ESCA.clinical,FPPP.clinical,GBM.clinical,GBMLGG.clinical,HNSC.clinical,KICH.clinical,KIPAN.clinical,KIRC.clinical,KIRP.clinical,LAML.clinical,LGG.clinical,LIHC.clinical,LUAD.clinical,LUSC.clinical,MESO.clinical,OV.clinical,PAAD.clinical,PCPG.clinical,PRAD.clinical,READ.clinical,SARC.clinical,SKCM.clinical,STAD.clinical,STES.clinical,TGCT.clinical,THCA.clinical,THYM.clinical,UCEC.clinical,UCS.clinical,UVM.clinical.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.clinical' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RTCGA.clinical' as RTCGA.clinical_20151101.21.0.zip
* DONE (RTCGA.clinical)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'RTCGA.clinical' successfully unpacked and MD5 sums checked

Tests output


Example timings