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BioC 3.5: INSTALL report for kebabs on malbec2

This page was generated on 2017-08-16 13:16:12 -0400 (Wed, 16 Aug 2017).

Package 700/1382HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
kebabs 1.10.0
Ulrich Bodenhofer
Snapshot Date: 2017-08-15 17:17:57 -0400 (Tue, 15 Aug 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_5/madman/Rpacks/kebabs
Last Changed Rev: 129126 / Revision: 131943
Last Changed Date: 2017-04-24 15:25:24 -0400 (Mon, 24 Apr 2017)
malbec2 Linux (Ubuntu 16.04.1 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
veracruz2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: kebabs
Version: 1.10.0
Command: /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD INSTALL kebabs
StartedAt: 2017-08-15 18:02:46 -0400 (Tue, 15 Aug 2017)
EndedAt: 2017-08-15 18:04:05 -0400 (Tue, 15 Aug 2017)
EllapsedTime: 79.1 seconds
RetCode: 0
Status:  OK 

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.5-bioc/R/bin/R CMD INSTALL kebabs
###
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* installing to library ‘/home/biocbuild/bbs-3.5-bioc/R/library’
* installing *source* package ‘kebabs’ ...
** libs
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c ByteStringVector.c -o ByteStringVector.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c ExplicitRepC.cpp -o ExplicitRepC.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c GappyPairC.cpp -o GappyPairC.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c IRanges_stubs.c -o IRanges_stubs.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c KernelUtils.cpp -o KernelUtils.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c MismatchC.cpp -o MismatchC.o
MismatchC.cpp: In function ‘SEXPREC* getMismatchKernelMatrix(Rcpp::NumericMatrix, ByteStringVector, ByteStringVector, int, int, Rcpp::IntegerVector, Rcpp::IntegerVector, bool, int, bool, bool, int, int, bool, bool, int, alphaInfo*)’:
MismatchC.cpp:432:41: warning: ‘currValSqrt’ may be used uninitialized in this function [-Wmaybe-uninitialized]
                     km(i,j) = kernelVal / currValSqrt;
                                         ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c MotifC.cpp -o MotifC.o
MotifC.cpp: In function ‘void genPredProfileMotif(Rcpp::NumericMatrix, ByteStringVector, Rcpp::IntegerVector, int, ByteStringVector, ByteStringVector, int, bool, int, int, int, int, Rcpp::NumericMatrix, int, ByteStringVector, Rcpp::IntegerVector*, int, int, ByteStringVector, Rcpp::IntegerVector*, int, int, int, bool, bool, bool)’:
MotifC.cpp:3677:27: warning: ‘keyPool’ may be used uninitialized in this function [-Wmaybe-uninitialized]
         pKeypool = keyPool;
                           ^
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c PredictionC.cpp -o PredictionC.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c PredictionProfileC.cpp -o PredictionProfileC.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c R_init_kebabs.cpp -o R_init_kebabs.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c Rsvm.c -o Rsvm.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c SparseMatrixHash.cpp -o SparseMatrixHash.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c SpectrumC.cpp -o SpectrumC.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c SymmetricPairC.cpp -o SymmetricPairC.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c Utils.cpp -o Utils.o
gcc -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c XVector_stubs.c -o XVector_stubs.o
g++  -I/home/biocbuild/bbs-3.5-bioc/R/include -DNDEBUG  -I"/home/biocbuild/bbs-3.5-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.5-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c svm.cpp -o svm.o
g++ -shared -L/home/biocbuild/bbs-3.5-bioc/R/lib -L/usr/local/lib -o kebabs.so Biostrings_stubs.o ByteStringVector.o ExplicitRepC.o FeatureWeightsPosDepC.o GappyPairC.o IRanges_stubs.o KernelUtils.o MismatchC.o MotifC.o PredictionC.o PredictionProfileC.o R_init_kebabs.o Rsvm.o SparseMatrixHash.o SpectrumC.o SymmetricPairC.o Utils.o XVector_stubs.o svm.o -L/home/biocbuild/bbs-3.5-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.5-bioc/R/library/kebabs/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 (kebabs)