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CHECK report for RTCGA.mutations on riesling1

This page was generated on 2021-03-01 15:56:11 -0500 (Mon, 01 Mar 2021).

To the developers/maintainers of the RTCGA.mutations package:
Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 319/391HostnameOS / ArchINSTALLBUILDCHECK
RTCGA.mutations 20151101.21.0
Marcin Kosinski
Snapshot Date: 2021-03-01 09:00:05 -0500 (Mon, 01 Mar 2021)
URL: https://git.bioconductor.org/packages/RTCGA.mutations
Branch: master
Last Commit: 61c8ad9
Last Changed Date: 2020-10-27 10:13:48 -0500 (Tue, 27 Oct 2020)
rex3Linux (Ubuntu 20.04.2 LTS) / x86_64  OK    OK    OK  UNNEEDED, same version exists in internal repository
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS  

Summary

Package: RTCGA.mutations
Version: 20151101.21.0
Command: D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD check --force-multiarch --install=check:RTCGA.mutations.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings RTCGA.mutations_20151101.21.0.tar.gz
StartedAt: 2021-03-01 11:55:49 -0500 (Mon, 01 Mar 2021)
EndedAt: 2021-03-01 11:59:54 -0500 (Mon, 01 Mar 2021)
EllapsedTime: 244.6 seconds
RetCode: 0
Status:   WARNINGS   
CheckDir: RTCGA.mutations.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.mutations.install-out.txt --library=D:\biocbuild\bbs-3.13-bioc\R\library --no-vignettes --timings RTCGA.mutations_20151101.21.0.tar.gz
###
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* using log directory 'D:/biocbuild/bbs-3.13-data-experiment/meat/RTCGA.mutations.Rcheck'
* using R Under development (unstable) (2021-02-08 r79971)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RTCGA.mutations/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'RTCGA.mutations' 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.mutations' can be installed ... WARNING
Found the following significant warnings:
  Rd warning: cannot open file 'D:/biocbuild/bbs-3.13-data-experiment/meat/RTCGA.mutations.buildbin-libdir/00LOCK-RTCGA.mutations/00new/RTCGA.mutations/help/ACC.mutations,BLCA.mutations,BRCA.mutations,CESC.mutations,CHOL.mutations,COAD.mutations,COADREAD.mutations,DLBC.mutations,ESCA.mutations,GBMLGG.mutations,GBM.mutations,HNSC.mutations,KICH.mutations,KIPAN.mutations,KIRC.mutations,KIRP.mutations,LAML.mutations,LGG.mutations,LIHC.mutations,LUAD.mutations,LUSC.mutations,OV.mutations,PAAD.mutations,PCPG.mutations,PRAD.mutations,READ.mutations,SARC.mutations,SKCM.mutations,STAD.mutations,STES.mutations,TGCT.mutations,THCA.mutations,UCEC.mutations,UCS.mutations,UVM.mutations.html': No such file or directory
See 'D:/biocbuild/bbs-3.13-data-experiment/meat/RTCGA.mutations.Rcheck/00install.out' for details.
* checking installed package size ... NOTE
  installed size is 201.3Mb
  sub-directories of 1Mb or more:
    data  201.1Mb
* 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 ... 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.mutations.Rcheck/00check.log'
for details.



Installation output

RTCGA.mutations.Rcheck/00install.out

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###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O http://155.52.173.35/BBS/3.13/data-experiment/src/contrib/RTCGA.mutations_20151101.21.0.tar.gz && rm -rf RTCGA.mutations.buildbin-libdir && mkdir RTCGA.mutations.buildbin-libdir && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=RTCGA.mutations.buildbin-libdir RTCGA.mutations_20151101.21.0.tar.gz && D:\biocbuild\bbs-3.13-bioc\R\bin\R.exe CMD INSTALL RTCGA.mutations_20151101.21.0.zip && rm RTCGA.mutations_20151101.21.0.tar.gz RTCGA.mutations_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
  0  103M    0 95602    0     0   804k      0  0:02:12 --:--:--  0:02:12  797k
 14  103M   14 14.9M    0     0  13.5M      0  0:00:07  0:00:01  0:00:06 13.5M
 30  103M   30 31.2M    0     0  14.9M      0  0:00:06  0:00:02  0:00:04 14.8M
 44  103M   44 46.3M    0     0  14.9M      0  0:00:06  0:00:03  0:00:03 14.9M
 50  103M   50 52.3M    0     0  12.7M      0  0:00:08  0:00:04  0:00:04 12.7M
 54  103M   54 56.2M    0     0  11.0M      0  0:00:09  0:00:05  0:00:04 11.2M
 58  103M   58 60.8M    0     0   9.9M      0  0:00:10  0:00:06  0:00:04 9414k
 62  103M   62 64.7M    0     0  9342k      0  0:00:11  0:00:07  0:00:04 6864k
 64  103M   64 67.3M    0     0  8521k      0  0:00:12  0:00:08  0:00:04 4310k
 68  103M   68 70.9M    0     0  7987k      0  0:00:13  0:00:09  0:00:04 3824k
 72  103M   72 75.1M    0     0  7621k      0  0:00:13  0:00:10  0:00:03 3861k
 75  103M   75 78.4M    0     0  7242k      0  0:00:14  0:00:11  0:00:03 3606k
 80  103M   80 83.4M    0     0  7066k      0  0:00:15  0:00:12  0:00:03 3835k
 84  103M   84 88.0M    0     0  6878k      0  0:00:15  0:00:13  0:00:02 4223k
 89  103M   89 93.3M    0     0  6782k      0  0:00:15  0:00:14  0:00:01 4591k
 95  103M   95 99.5M    0     0  6753k      0  0:00:15  0:00:15 --:--:-- 5001k
100  103M  100  103M    0     0  6793k      0  0:00:15  0:00:15 --:--:-- 5696k

install for i386

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

Rd warning: cannot open file 'D:/biocbuild/bbs-3.13-data-experiment/meat/RTCGA.mutations.buildbin-libdir/00LOCK-RTCGA.mutations/00new/RTCGA.mutations/help/ACC.mutations,BLCA.mutations,BRCA.mutations,CESC.mutations,CHOL.mutations,COAD.mutations,COADREAD.mutations,DLBC.mutations,ESCA.mutations,GBMLGG.mutations,GBM.mutations,HNSC.mutations,KICH.mutations,KIPAN.mutations,KIRC.mutations,KIRP.mutations,LAML.mutations,LGG.mutations,LIHC.mutations,LUAD.mutations,LUSC.mutations,OV.mutations,PAAD.mutations,PCPG.mutations,PRAD.mutations,READ.mutations,SARC.mutations,SKCM.mutations,STAD.mutations,STES.mutations,TGCT.mutations,THCA.mutations,UCEC.mutations,UCS.mutations,UVM.mutations.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.mutations' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RTCGA.mutations' as RTCGA.mutations_20151101.21.0.zip
* DONE (RTCGA.mutations)
* installing to library 'D:/biocbuild/bbs-3.13-bioc/R/library'
package 'RTCGA.mutations' successfully unpacked and MD5 sums checked

Tests output


Example timings