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This page was generated on 2022-03-18 11:08:00 -0400 (Fri, 18 Mar 2022).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo1Linux (Ubuntu 20.04.4 LTS)x86_64R Under development (unstable) (2022-02-17 r81757) -- "Unsuffered Consequences" 4334
riesling1Windows Server 2019 Standardx64R Under development (unstable) (2021-11-21 r81221) -- "Unsuffered Consequences" 4097
palomino3Windows Server 2022 Datacenterx64R Under development (unstable) (2022-02-17 r81757 ucrt) -- "Unsuffered Consequences" 4083
merida1macOS 10.14.6 Mojavex86_64R Under development (unstable) (2022-03-02 r81842) -- "Unsuffered Consequences" 4134
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 methylKit on riesling1


To the developers/maintainers of the methylKit package:
- Please allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/methylKit.git to
reflect on this report. See How and When does the builder pull? When will my changes propagate? here 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 1127/2090HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylKit 1.21.0  (landing page)
Altuna Akalin , Alexander Gosdschan
Snapshot Date: 2022-03-17 13:55:23 -0400 (Thu, 17 Mar 2022)
git_url: https://git.bioconductor.org/packages/methylKit
git_branch: master
git_last_commit: ba376aa
git_last_commit_date: 2021-10-26 12:29:01 -0400 (Tue, 26 Oct 2021)
nebbiolo1Linux (Ubuntu 20.04.4 LTS) / x86_64  OK    OK    WARNINGS  UNNEEDED, same version is already published
riesling1Windows Server 2019 Standard / x64  OK    OK    WARNINGS    OK  
palomino3Windows Server 2022 Datacenter / x64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published
merida1macOS 10.14.6 Mojave / x86_64  OK    OK    WARNINGS    OK  UNNEEDED, same version is already published

Summary

Package: methylKit
Version: 1.21.0
Command: rm -rf methylKit.buildbin-libdir && mkdir methylKit.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=methylKit.buildbin-libdir methylKit_1.21.0.tar.gz
StartedAt: 2022-03-17 21:20:27 -0400 (Thu, 17 Mar 2022)
EndedAt: 2022-03-17 21:21:57 -0400 (Thu, 17 Mar 2022)
EllapsedTime: 89.5 seconds
RetCode: 0
Status:   OK  
PackageFile: methylKit_1.21.0.zip
PackageFileSize: 3.718 MiB

Command output

##############################################################################
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###
### Running command:
###
###   rm -rf methylKit.buildbin-libdir && mkdir methylKit.buildbin-libdir && D:\biocbuild\bbs-3.15-bioc\R\bin\R.exe CMD INSTALL --build --library=methylKit.buildbin-libdir methylKit_1.21.0.tar.gz
###
##############################################################################
##############################################################################


* installing *source* package 'methylKit' ...
** using staged installation
** libs
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c RcppExports.cpp -o RcppExports.o
"C:/rtools40/mingw64/bin/"g++  -std=gnu++11 -I"D:/biocbuild/bbs-3.15-bioc/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rcpp/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/Rhtslib/include' -I'D:/biocbuild/bbs-3.15-bioc/R/library/zlibbioc/include'   -I"C:/extsoft/include"     -O2 -Wall  -mfpmath=sse -msse2 -mstackrealign -fno-reorder-blocks-and-partition  -c methCall.cpp -o methCall.o
methCall.cpp: In function 'int process_sam(std::istream*, std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, int&, int&, int&, int, int, size_t&)':
methCall.cpp:687:39: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:686:39: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:685:39: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp: In function 'int process_bam(std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, int&, int&, int&, int, size_t&)':
methCall.cpp:1014:39: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1013:39: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1042:76: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CpGstatus) { processCGmethHash(CGmethHash,out,mincov);     std::fclose(out); }
                                                                 ~~~~~~~~~~~^~~~~
methCall.cpp: In function 'int process_single_bismark(std::istream*, std::__cxx11::string&, std::__cxx11::string&, std::__cxx11::string&, int&, int&, int&, size_t&)':
methCall.cpp:1244:39: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHGstatus){ processCHmethHash(CHGmethHash,CHGout,mincov);}
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1243:39: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CHHstatus){ processCHmethHash(CHHmethHash,CHHout,mincov); }
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~
methCall.cpp:1242:39: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized]
       if(CpGstatus){ processCGmethHash(CGmethHash,out,mincov);}
                      ~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~
C:/rtools40/mingw64/bin/g++ -shared -s -static-libgcc -o methylKit.dll tmp.def RcppExports.o methCall.o D:/biocbuild/bbs-3.15-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 -LD:/biocbuild/bbs-3.15-bioc/R/bin/x64 -lR
installing to D:/biocbuild/bbs-3.15-bioc/meat/methylKit.buildbin-libdir/00LOCK-methylKit/00new/methylKit/libs/x64
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
  converting help for package 'methylKit'
    finding HTML links ... done
    PCASamples-methods                      html  
    adjustMethylC                           html  
    assocComp-methods                       html  
    bedgraph-methods                        html  
    calculateDiffMeth-methods               html  
    calculateDiffMethDSS-methods            html  
    clusterSamples-methods                  html  
    dataSim-methods                         html  
    diffMethPerChr-methods                  html  
    extract-methods                         html  
    filterByCoverage-methods                html  
    getAssembly-methods                     html  
    getContext-methods                      html  
    getCorrelation-methods                  html  
    getCoverageStats-methods                html  
    getDBPath-methods                       html  
    getData-methods                         html  
    getMethylDiff-methods                   html  
    getMethylationStats-methods             html  
    getSampleID-methods                     html  
    getTreatment-methods                    html  
    joinSegmentNeighbours                   html  
    makeMethylDB-methods                    html  
    methRead-methods                        html  
    methSeg                                 html  
    finding level-2 HTML links ... done

    methSeg2bed                             html  
    methylBase-class                        html  
    methylBase.obj                          html  
    methylBaseDB-class                      html  
    methylDiff-class                        html  
    methylDiff.obj                          html  
    methylDiffDB-class                      html  
    methylKit-defunct                       html  
    methylRaw-class                         html  
    methylRawDB-class                       html  
    methylRawList-class                     html  
    methylRawList.obj                       html  
    methylRawListDB-class                   html  
    normalizeCoverage-methods               html  
    percMethylation-methods                 html  
    pool-methods                            html  
    processBismarkAln-methods               html  
    readMethylDB-methods                    html  
    reconstruct-methods                     html  
    regionCounts                            html  
    removeComp-methods                      html  
    reorganize-methods                      html  
    select-methods                          html  
    selectByOverlap-methods                 html  
    show-methods                            html  
    tileMethylCounts-methods                html  
    unite-methods                           html  
    updateMethObject                        html  
** 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
* MD5 sums
packaged installation of 'methylKit' as methylKit_1.21.0.zip
* DONE (methylKit)