Back to Multiple platform build/check report for BioC 3.14
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

This page was generated on 2022-04-13 12:06:55 -0400 (Wed, 13 Apr 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 20.04.4 LTS)x86_644.1.3 (2022-03-10) -- "One Push-Up" 4324
tokay2Windows Server 2012 R2 Standardx644.1.3 (2022-03-10) -- "One Push-Up" 4077
machv2macOS 10.14.6 Mojavex86_644.1.3 (2022-03-10) -- "One Push-Up" 4137
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

BUILD BIN results for mitoClone2 on tokay2


To the developers/maintainers of the mitoClone2 package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/mitoClone2.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? for more information.
- Make sure to use the following settings in order to reproduce any error or warning you see on this page.

raw results

Package 1177/2083HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
mitoClone2 1.0.0  (landing page)
Benjamin Story
Snapshot Date: 2022-04-12 01:55:07 -0400 (Tue, 12 Apr 2022)
git_url: https://git.bioconductor.org/packages/mitoClone2
git_branch: RELEASE_3_14
git_last_commit: 2b6203f
git_last_commit_date: 2021-10-26 13:11:28 -0400 (Tue, 26 Oct 2021)
nebbiolo2Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
tokay2Windows Server 2012 R2 Standard / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
machv2macOS 10.14.6 Mojave / x86_64  OK    OK    OK    OK  UNNEEDED, same version is already published

Summary

Package: mitoClone2
Version: 1.0.0
Command: rm -rf mitoClone2.buildbin-libdir && mkdir mitoClone2.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mitoClone2.buildbin-libdir mitoClone2_1.0.0.tar.gz
StartedAt: 2022-04-13 06:37:38 -0400 (Wed, 13 Apr 2022)
EndedAt: 2022-04-13 06:39:30 -0400 (Wed, 13 Apr 2022)
EllapsedTime: 111.7 seconds
RetCode: 0
Status:   OK  
PackageFile: mitoClone2_1.0.0.zip
PackageFileSize: 4.971 MiB

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf mitoClone2.buildbin-libdir && mkdir mitoClone2.buildbin-libdir && C:\Users\biocbuild\bbs-3.14-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=mitoClone2.buildbin-libdir mitoClone2_1.0.0.tar.gz
###
##############################################################################
##############################################################################



install for i386

* installing *source* package 'mitoClone2' ...
** using staged installation
** libs
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -D_FILE_OFFSET_BITS=64 ../inst/SCITEpkg/*.cpp -o scite
../inst/SCITEpkg/findBestTrees.cpp:56:8: warning: built-in function 'gamma' declared as non-function [-Wbuiltin-declaration-mismatch]
 double gamma = 1;
        ^~~~~
../inst/SCITEpkg/mcmcBinTreeMove.cpp: In function 'int pickNodeToMove(int*, int)':
../inst/SCITEpkg/mcmcBinTreeMove.cpp:75:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
mkdir -p "C:/Users/biocbuild/bbs-3.14-bioc/meat/mitoClone2.buildbin-libdir/00LOCK-mitoClone2/00new/mitoClone2/SCITE/"
cp scite "C:/Users/biocbuild/bbs-3.14-bioc/meat/mitoClone2.buildbin-libdir/00LOCK-mitoClone2/00new/mitoClone2/SCITE/"
rm scite
"C:/rtools40/mingw32/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c bam2R_10x.cpp -o bam2R_10x.o
bam2R_10x.cpp:6:2: warning: "/*" within comment [-Wcomment]
  /**************************************************************************************
   
bam2R_10x.cpp:8:1: warning: "/*" within comment [-Wcomment]
 /**********************************************************************
  
bam2R_10x.cpp: In function 'void bam2R_pileup_function(const bam_pileup1_t*, int, int, nttable_t&, std::map<std::__cxx11::basic_string<char>, std::vector<int> >&)':
bam2R_10x.cpp:75:10: warning: unused variable 'bc_absent' [-Wunused-variable]
      int bc_absent;
          ^~~~~~~~~
bam2R_10x.cpp: In function 'SEXPREC* bam2R_10x(SEXP, SEXP, SEXP, SEXP, int*, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
bam2R_10x.cpp:158:16: warning: unused variable 'iter' [-Wunused-variable]
     hts_itr_t *iter = NULL;
                ^~~~
bam2R_10x.cpp:161:9: warning: unused variable 'c' [-Wunused-variable]
     int c = 0;
         ^
C:/rtools40/mingw32/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o mitoClone2.dll tmp.def bam2R_10x.o C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/usrlib/i386/libhts.a -LC:/extsoft/lib/i386 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -lidn -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/mitoClone2.buildbin-libdir/00LOCK-mitoClone2/00new/mitoClone2/libs/i386
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'mitoClone2'
    finding HTML links ... done
    bam2R_10x                               html  
    baseCountsFromBamList                   html  
    clusterMetaclones                       html  
    data                                    html  
    getAlleleCount                          html  
    getCloneLikelihood                      html  
    getVarsCandidate                        html  
    mitoPlot                                html  
    mut2GR                                  html  
    mutationCalls-class                     html  
    mutationCallsFromCohort                 html  
    mutationCallsFromExclusionlist          html  
    mutationCallsFromMatrix                 html  
    overwriteMetaclones                     html  
    plotClones                              html  
    pullcountsVars                          html  
    quick_cluster                           html  
    removeWindow                            html  
    setVarsCandidate                        html  
    varCluster                              html  
*** copying figures
** 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 'mitoClone2' ...
** libs
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -D_FILE_OFFSET_BITS=64 ../inst/SCITEpkg/*.cpp -o scite
../inst/SCITEpkg/findBestTrees.cpp:56:8: warning: built-in function 'gamma' declared as non-function [-Wbuiltin-declaration-mismatch]
 double gamma = 1;
        ^~~~~
../inst/SCITEpkg/mcmcBinTreeMove.cpp: In function 'int pickNodeToMove(int*, int)':
../inst/SCITEpkg/mcmcBinTreeMove.cpp:75:1: warning: control reaches end of non-void function [-Wreturn-type]
 }
 ^
mkdir -p "C:/Users/biocbuild/bbs-3.14-bioc/meat/mitoClone2.buildbin-libdir/mitoClone2/SCITE/"
cp scite "C:/Users/biocbuild/bbs-3.14-bioc/meat/mitoClone2.buildbin-libdir/mitoClone2/SCITE/"
rm scite
"C:/rtools40/mingw64/bin/"g++ -std=gnu++11  -I"C:/Users/BIOCBU~1/BBS-3~1.14-/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign  -c bam2R_10x.cpp -o bam2R_10x.o
bam2R_10x.cpp:6:2: warning: "/*" within comment [-Wcomment]
  /**************************************************************************************
   
bam2R_10x.cpp:8:1: warning: "/*" within comment [-Wcomment]
 /**********************************************************************
  
bam2R_10x.cpp: In function 'void bam2R_pileup_function(const bam_pileup1_t*, int, int, nttable_t&, std::map<std::__cxx11::basic_string<char>, std::vector<int> >&)':
bam2R_10x.cpp:75:10: warning: unused variable 'bc_absent' [-Wunused-variable]
      int bc_absent;
          ^~~~~~~~~
bam2R_10x.cpp: In function 'SEXPREC* bam2R_10x(SEXP, SEXP, SEXP, SEXP, int*, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
bam2R_10x.cpp:158:16: warning: unused variable 'iter' [-Wunused-variable]
     hts_itr_t *iter = NULL;
                ^~~~
bam2R_10x.cpp:161:9: warning: unused variable 'c' [-Wunused-variable]
     int c = 0;
         ^
C:/rtools40/mingw64/bin/g++ -std=gnu++11 -shared -s -static-libgcc -o mitoClone2.dll tmp.def bam2R_10x.o C:/Users/biocbuild/bbs-3.14-bioc/R/library/Rhtslib/usrlib/x64/libhts.a -LC:/extsoft/lib/x64 -lcurl -lrtmp -lssl -lssh2 -lcrypto -lgdi32 -lz -lws2_32 -lwldap32 -lwinmm -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU~1/BBS-3~1.14-/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.14-bioc/meat/mitoClone2.buildbin-libdir/mitoClone2/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'mitoClone2' as mitoClone2_1.0.0.zip
* DONE (mitoClone2)