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BioC 3.4: INSTALL report for DiffBind on zin1

This page was generated on 2016-09-21 03:37:32 -0700 (Wed, 21 Sep 2016).

Package 316/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
DiffBind 2.1.5
Rory Stark
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/DiffBind
Last Changed Rev: 121127 / Revision: 121152
Last Changed Date: 2016-09-19 04:54:06 -0700 (Mon, 19 Sep 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64 [ OK ] OK  OK YES, new version is higher than in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK YES, new version is higher than in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK YES, new version is higher than in internal repository

Summary

Package: DiffBind
Version: 2.1.5
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD INSTALL DiffBind
StartedAt: 2016-09-19 20:24:22 -0700 (Mon, 19 Sep 2016)
EndedAt: 2016-09-19 20:24:59 -0700 (Mon, 19 Sep 2016)
EllapsedTime: 37.2 seconds
RetCode: 0
Status:  OK 

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD INSTALL DiffBind
###
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* installing to library ‘/home/biocbuild/bbs-3.4-bioc/R/library’
* installing *source* package ‘DiffBind’ ...
** libs
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c RcppExports.cpp -o RcppExports.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c bamReader.cpp -o bamReader.o
bamReader.cpp: In member function ‘bool bode::BamReader::isBam(const string&)’:
bamReader.cpp:14:7: warning: variable ‘rd’ set but not used [-Wunused-but-set-variable]
   int rd;
       ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c bedReader.cpp -o bedReader.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c bitBucket.cpp -o bitBucket.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c croi_func.cpp -o croi_func.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c croi_main.cpp -o croi_main.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c densitySet.cpp -o densitySet.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c iBucket.cpp -o iBucket.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c interval.cpp -o interval.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c intervalDensity.cpp -o intervalDensity.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c intervalNode.cpp -o intervalNode.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c intervalSet.cpp -o intervalSet.o
intervalSet.cpp: In destructor ‘virtual bode::IntervalSet::˜IntervalSet()’:
intervalSet.cpp:14:16: warning: deleting object of polymorphic class type ‘bode::IntervalTree’ which has non-virtual destructor might cause undefined behaviour [-Wdelete-non-virtual-dtor]
     delete it->second;
                ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c intervalTree.cpp -o intervalTree.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c merge.cpp -o merge.o
merge.cpp: In function ‘int mergeSet(PeakSet, PeakSet, int)’:
merge.cpp:15:8: warning: unused variable ‘wasMerge’ [-Wunused-variable]
   bool wasMerge = false;
        ^
merge.cpp: In function ‘bool validData(Rcpp::DataFrame, bool)’:
merge.cpp:36:8: warning: unused variable ‘okay’ [-Wunused-variable]
   bool okay = true;
        ^
gcc -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c mergeOne.c -o mergeOne.o
mergeOne.c: In function ‘mo_mergeTwo’:
mergeOne.c:351:7: warning: variable ‘keepAll’ set but not used [-Wunused-but-set-variable]
   int keepAll,minOverlap;
       ^
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c nodeGroup.cpp -o nodeGroup.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c peakOrder.cpp -o peakOrder.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c reader.cpp -o reader.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c sequence.cpp -o sequence.o
g++ -I/home/biocbuild/bbs-3.4-bioc/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/include" -I"/home/biocbuild/bbs-3.4-bioc/R/library/Rcpp/include"   -fpic  -g -O2  -Wall -c util.cpp -o util.o
g++ -shared -L/home/biocbuild/bbs-3.4-bioc/R/lib -L/usr/local/lib -o DiffBind.so RcppExports.o bamReader.o bedReader.o bitBucket.o croi_func.o croi_main.o densitySet.o iBucket.o interval.o intervalDensity.o intervalNode.o intervalSet.o intervalTree.o merge.o mergeOne.o nodeGroup.o peakOrder.o reader.o sequence.o util.o /home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/usrlib//libbam.a /home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/usrlib//libbcf.a /home/biocbuild/bbs-3.4-bioc/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/biocbuild/bbs-3.4-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.4-bioc/R/library/DiffBind/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DiffBind)