Back to Multiple platform build/check report for BioC 3.9
ABCDEFGHIJKL[M]NOPQRSTUVWXYZ

INSTALL report for methylKit on tokay2

This page was generated on 2019-04-09 12:26:54 -0400 (Tue, 09 Apr 2019).

Package 964/1703HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
methylKit 1.9.3
Altuna Akalin , Alexander Gosdschan
Snapshot Date: 2019-04-08 17:01:18 -0400 (Mon, 08 Apr 2019)
URL: https://git.bioconductor.org/packages/methylKit
Branch: master
Last Commit: 21fb06e
Last Changed Date: 2019-02-05 04:13:38 -0400 (Tue, 05 Feb 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64 [ OK ] OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK 

Summary

Package: methylKit
Version: 1.9.3
Command: C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/methylKit_1.9.3.tar.gz && rm -rf methylKit.buildbin-libdir && mkdir methylKit.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=methylKit.buildbin-libdir methylKit_1.9.3.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL methylKit_1.9.3.zip && rm methylKit_1.9.3.tar.gz methylKit_1.9.3.zip
StartedAt: 2019-04-08 20:17:49 -0400 (Mon, 08 Apr 2019)
EndedAt: 2019-04-08 20:20:20 -0400 (Mon, 08 Apr 2019)
EllapsedTime: 151.7 seconds
RetCode: 0
Status:  OK  

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   C:\cygwin\bin\curl.exe -O https://malbec2.bioconductor.org/BBS/3.9/bioc/src/contrib/methylKit_1.9.3.tar.gz && rm -rf methylKit.buildbin-libdir && mkdir methylKit.buildbin-libdir && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL --merge-multiarch --build --library=methylKit.buildbin-libdir methylKit_1.9.3.tar.gz && C:\Users\biocbuild\bbs-3.9-bioc\R\bin\R.exe CMD INSTALL methylKit_1.9.3.zip && rm methylKit_1.9.3.tar.gz methylKit_1.9.3.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
 63  629k   63  400k    0     0   400k      0  0:00:01 --:--:--  0:00:01  403k
100  629k  100  629k    0     0   629k      0  0:00:01  0:00:01 --:--:--  633k

install for i386

* installing *source* package 'methylKit' ...
** libs
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_32/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c methCall.cpp -o methCall.o
methCall.cpp: In function 'int process_sam(std::istream*, std::string&, std::string&, std::string&, int&, int&, int&, int, int)':
methCall.cpp:708:84: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
                                                                                    ^
methCall.cpp:707:84: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
                                                                                    ^
methCall.cpp:706:81: 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_bam(std::string&, std::string&, std::string&, std::string&, int&, int&, int&, int)':
methCall.cpp:1027:84: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
                                                                                    ^
methCall.cpp:1026:84: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
                                                                                    ^
methCall.cpp:1025:81: 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::string&, std::string&, std::string&, int&, int&, int&)':
methCall.cpp:1254:84: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
                                                                                    ^
methCall.cpp:1253:84: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
                                                                                    ^
methCall.cpp:1252:81: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CpGstatus) { processCGmethHash(CGmethHash,out,mincov);     std::fclose(out); }
                                                                                 ^
C:/Rtools/mingw_32/bin/g++ -shared -s -static-libgcc -o methylKit.dll tmp.def RcppExports.o methCall.o -LC:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib/i386 -lhts -lz -lm -lws2_32 -lpthread -LC:/extsoft/lib/i386 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/i386 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/methylKit.buildbin-libdir/00LOCK-methylKit/00new/methylKit/libs/i386
** 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  
    genomation-deprecated                   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  
    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  
    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

install for x64

* installing *source* package 'methylKit' ...
** libs
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c RcppExports.cpp -o RcppExports.o
C:/Rtools/mingw_64/bin/g++  -std=gnu++11 -I"C:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/include" -DNDEBUG  -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rcpp/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/include" -I"C:/Users/biocbuild/bbs-3.9-bioc/R/library/zlibbioc/include"   -I"C:/extsoft/include"     -O2 -Wall  -mtune=generic -c methCall.cpp -o methCall.o
methCall.cpp: In function 'int process_sam(std::istream*, std::string&, std::string&, std::string&, int&, int&, int&, int, int)':
methCall.cpp:708:84: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
                                                                                    ^
methCall.cpp:707:84: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
                                                                                    ^
methCall.cpp:706:81: 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_bam(std::string&, std::string&, std::string&, std::string&, int&, int&, int&, int)':
methCall.cpp:1027:84: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
                                                                                    ^
methCall.cpp:1026:84: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
                                                                                    ^
methCall.cpp:1025:81: 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::string&, std::string&, std::string&, int&, int&, int&)':
methCall.cpp:1254:84: warning: 'CHGout' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CHGstatus) { processCHmethHash(CHGmethHash,CHGout,mincov); std::fclose(CHGout); }
                                                                                    ^
methCall.cpp:1253:84: warning: 'CHHout' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CHHstatus) { processCHmethHash(CHHmethHash,CHHout,mincov); std::fclose(CHHout); }
                                                                                    ^
methCall.cpp:1252:81: warning: 'out' may be used uninitialized in this function [-Wmaybe-uninitialized]
   if(CpGstatus) { processCGmethHash(CGmethHash,out,mincov);     std::fclose(out); }
                                                                                 ^
C:/Rtools/mingw_64/bin/g++ -shared -s -static-libgcc -o methylKit.dll tmp.def RcppExports.o methCall.o -LC:/Users/biocbuild/bbs-3.9-bioc/R/library/Rhtslib/usrlib/x64 -lhts -lz -lm -lws2_32 -lpthread -LC:/extsoft/lib/x64 -LC:/extsoft/lib -LC:/Users/BIOCBU˜1/BBS-3˜1.9-B/R/bin/x64 -lR
installing to C:/Users/biocbuild/bbs-3.9-bioc/meat/methylKit.buildbin-libdir/methylKit/libs/x64
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'methylKit' as methylKit_1.9.3.zip
* DONE (methylKit)
* installing to library 'C:/Users/biocbuild/bbs-3.9-bioc/R/library'
package 'methylKit' successfully unpacked and MD5 sums checked