Back to Multiple platform build/check report for BioC 3.12
AB[C]DEFGHIJKLMNOPQRSTUVWXYZ

INSTALL report for chimera on tokay1

This page was generated on 2020-08-13 11:37:09 -0400 (Thu, 13 Aug 2020).

TO THE DEVELOPERS/MAINTAINERS OF THE chimera PACKAGE: Please make sure to use the following settings in order to reproduce any error or warning you see on this page.
Package 268/1885HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chimera 1.31.1
Raffaele A Calogero
Snapshot Date: 2020-08-12 14:52:00 -0400 (Wed, 12 Aug 2020)
URL: https://git.bioconductor.org/packages/chimera
Branch: master
Last Commit: f48abc1
Last Changed Date: 2020-06-01 10:00:40 -0400 (Mon, 01 Jun 2020)
malbec1 Linux (Ubuntu 18.04.4 LTS) / x86_64  OK  OK  WARNINGS UNNEEDED, same version exists in internal repository
nebbiolo1 Linux (Ubuntu 20.04.1 LTS) / x86_64  OK  OK  WARNINGS 
tokay1 Windows Server 2012 R2 Standard / x64 [ OK ] ERROR  skipped  skipped 
merida1 macOS 10.14.6 Mojave / x86_64  OK  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: chimera
Version: 1.31.1
Command: C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/chimera_1.31.1.tar.gz && rm -rf chimera.buildbin-libdir && mkdir chimera.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=chimera.buildbin-libdir chimera_1.31.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL chimera_1.31.1.zip && rm chimera_1.31.1.tar.gz chimera_1.31.1.zip
StartedAt: 2020-08-12 18:43:27 -0400 (Wed, 12 Aug 2020)
EndedAt: 2020-08-12 18:45:53 -0400 (Wed, 12 Aug 2020)
EllapsedTime: 146.2 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec1.bioconductor.org/BBS/3.12/bioc/src/contrib/chimera_1.31.1.tar.gz && rm -rf chimera.buildbin-libdir && mkdir chimera.buildbin-libdir && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=chimera.buildbin-libdir chimera_1.31.1.tar.gz && C:\Users\biocbuild\bbs-3.12-bioc\R\bin\R.exe CMD INSTALL chimera_1.31.1.zip && rm chimera_1.31.1.tar.gz chimera_1.31.1.zip
###
##############################################################################
##############################################################################


  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 2016k  100 2016k    0     0  19.3M      0 --:--:-- --:--:-- --:--:-- 20.0M

install for i386

* installing *source* package 'chimera' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c StarParser.cpp -o StarParser.o
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o chimera.dll tmp.def StarParser.o -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/chimera.buildbin-libdir/00LOCK-chimera/00new/chimera/libs/i386
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'chimera'
    finding HTML links ... done
    MHmakeRandomString                      html  
    bam2fastq                               html  
    breakpointOverlaps                      html  
    chimera-package                         html  
    chimeraSeqSet                           html  
    chimeraSeqs                             html  
    class.fSet                              html  
    defuseTPTN                              html  
    filterList                              html  
    filterSamReads                          html  
    fusionName                              html  
    fusionPeptides                          html  
    gapfillerInstallation                   html  
    gapfillerRun                            html  
    gapfillerWrap                           html  
    importFusionData                        html  
    is.fSet                                 html  
    newfSet                                 html  
    oncofuseInstallation                    html  
    oncofuseRun                             html  
    picardInstallation                      html  
    plotCoverage                            html  
    prettyPrint                             html  
    removingErrorLine                       html  
    starInstallation                        html  
    starReads                               html  
    starRun                                 html  
    subreadRun                              html  
    supportingReads                         html  
    tophatInstallation                      html  
    tophatRun                               html  
    validateSamFile                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: Package 'chimera' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package can be loaded from final location
Warning: Package 'chimera' is deprecated and will be removed from Bioconductor
  version 3.13
** testing if installed package keeps a record of temporary installation path

install for x64

* installing *source* package 'chimera' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.12-/R/include" -DNDEBUG     -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -c StarParser.cpp -o StarParser.o
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o chimera.dll tmp.def StarParser.o -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.12-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.12-bioc/meat/chimera.buildbin-libdir/chimera/libs/x64
** testing if installed package can be loaded
Warning: Package 'chimera' is deprecated and will be removed from Bioconductor
  version 3.13
* MD5 sums
packaged installation of 'chimera' as chimera_1.31.1.zip
* DONE (chimera)
* installing to library 'C:/Users/biocbuild/bbs-3.12-bioc/R/library'
package 'chimera' successfully unpacked and MD5 sums checked