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CHECK report for RTCGA.rnaseq on riesling1

This page was generated on 2021-01-21 16:01:38 -0500 (Thu, 21 Jan 2021).

TO THE DEVELOPERS/MAINTAINERS OF THE RTCGA.rnaseq PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 317/386HostnameOS / ArchINSTALLBUILDCHECK
RTCGA.rnaseq 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.rnaseq
Branch: master
Last Commit: 9d5127b
Last Changed Date: 2020-10-27 10:13:53 -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.rnaseq
Version: 20151101.21.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTCGA.rnaseq.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings RTCGA.rnaseq_20151101.21.0.tar.gz
StartedAt: 2021-01-21 11:45:36 -0500 (Thu, 21 Jan 2021)
EndedAt: 2021-01-21 11:48:42 -0500 (Thu, 21 Jan 2021)
EllapsedTime: 186.0 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: RTCGA.rnaseq.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.rnaseq.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings RTCGA.rnaseq_20151101.21.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/RTCGA.rnaseq.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.rnaseq/DESCRIPTION' ... OK
* this is package 'RTCGA.rnaseq' 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.rnaseq' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: cannot open file 'D:/biocbuild/bbs-3.13-data-experiment/meat/RTCGA.rnaseq.buildbin-libdir/00LOCK-RTCGA.rnaseq/00new/RTCGA.rnaseq/help/ACC.rnaseq,BLCA.rnaseq,BRCA.rnaseq,CESC.rnaseq,CHOL.rnaseq,COAD.rnaseq,COADREAD.rnaseq,DLBC.rnaseq,ESCA.rnaseq,GBMLGG.rnaseq,GBM.rnaseq,HNSC.rnaseq,KICH.rnaseq,KIPAN.rnaseq,KIRC.rnaseq,KIRP.rnaseq,LAML.rnaseq,LGG.rnaseq,LIHC.rnaseq,LUAD.rnaseq,LUSC.rnaseq,OV.rnaseq,PAAD.rnaseq,PCPG.rnaseq,PRAD.rnaseq,READ.rnaseq,SARC.rnaseq,SKCM.rnaseq,STAD.rnaseq,STES.rnaseq,TGCT.rnaseq,THCA.rnaseq,THYM.rnaseq,UCEC.rnaseq,UCS.rnaseq,UVM.rnaseq.html': No such file or directory
See 'D:/biocbuild/bbs-3.13-data-experiment/meat/RTCGA.rnaseq.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 920.2Mb
  sub-directories of 1Mb or more:
    data  920.0Mb
* 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 ... 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.rnaseq.Rcheck/00check.log'
for details.

Installation output

RTCGA.rnaseq.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.rnaseq_20151101.21.0.tar.gz && rm -rf RTCGA.rnaseq.buildbin-libdir && mkdir RTCGA.rnaseq.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RTCGA.rnaseq.buildbin-libdir RTCGA.rnaseq_20151101.21.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL RTCGA.rnaseq_20151101.21.0.zip && rm RTCGA.rnaseq_20151101.21.0.tar.gz RTCGA.rnaseq_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
  1  612M    1 6391k    0     0  16.6M      0  0:00:36 --:--:--  0:00:36 16.6M
 11  612M   11 68.1M    0     0  51.3M      0  0:00:11  0:00:01  0:00:10 51.3M
 19  612M   19  117M    0     0  49.6M      0  0:00:12  0:00:02  0:00:10 49.6M
 26  612M   26  163M    0     0  49.0M      0  0:00:12  0:00:03  0:00:09 49.0M
 41  612M   41  255M    0     0  58.9M      0  0:00:10  0:00:04  0:00:06 58.9M
 50  612M   50  311M    0     0  58.5M      0  0:00:10  0:00:05  0:00:05 61.6M
 60  612M   60  368M    0     0  58.2M      0  0:00:10  0:00:06  0:00:04 60.1M
 74  612M   74  454M    0     0  62.0M      0  0:00:09  0:00:07  0:00:02 67.9M
 85  612M   85  522M    0     0  62.7M      0  0:00:09  0:00:08  0:00:01 71.8M
 98  612M   98  603M    0     0  64.6M      0  0:00:09  0:00:09 --:--:-- 69.5M
100  612M  100  612M    0     0  65.0M      0  0:00:09  0:00:09 --:--:-- 73.6M

install for i386

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

Rd warning: cannot open file 'D:/biocbuild/bbs-3.13-data-experiment/meat/RTCGA.rnaseq.buildbin-libdir/00LOCK-RTCGA.rnaseq/00new/RTCGA.rnaseq/help/ACC.rnaseq,BLCA.rnaseq,BRCA.rnaseq,CESC.rnaseq,CHOL.rnaseq,COAD.rnaseq,COADREAD.rnaseq,DLBC.rnaseq,ESCA.rnaseq,GBMLGG.rnaseq,GBM.rnaseq,HNSC.rnaseq,KICH.rnaseq,KIPAN.rnaseq,KIRC.rnaseq,KIRP.rnaseq,LAML.rnaseq,LGG.rnaseq,LIHC.rnaseq,LUAD.rnaseq,LUSC.rnaseq,OV.rnaseq,PAAD.rnaseq,PCPG.rnaseq,PRAD.rnaseq,READ.rnaseq,SARC.rnaseq,SKCM.rnaseq,STAD.rnaseq,STES.rnaseq,TGCT.rnaseq,THCA.rnaseq,THYM.rnaseq,UCEC.rnaseq,UCS.rnaseq,UVM.rnaseq.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.rnaseq' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RTCGA.rnaseq' as RTCGA.rnaseq_20151101.21.0.zip
* DONE (RTCGA.rnaseq)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'RTCGA.rnaseq' successfully unpacked and MD5 sums checked

Tests output

Example timings