Back to Multiple platform build/check report for BioC 3.8
ABCDEFGHIJ[K]LMNOPQRSTUVWXYZ

INSTALL report for kebabs on malbec1

This page was generated on 2019-04-16 11:50:56 -0400 (Tue, 16 Apr 2019).

Package 815/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
kebabs 1.16.0
Ulrich Bodenhofer
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/kebabs
Branch: RELEASE_3_8
Last Commit: 726b350
Last Changed Date: 2018-10-30 11:41:56 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64 [ OK ] OK  OK UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: kebabs
Version: 1.16.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL kebabs
StartedAt: 2019-04-15 18:06:00 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 18:07:57 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 116.4 seconds
RetCode: 0
Status:  OK 

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL kebabs
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘kebabs’ ...
** libs
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c ByteStringVector.c -o ByteStringVector.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c ExplicitRepC.cpp -o ExplicitRepC.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c FeatureWeightsPosDepC.cpp -o FeatureWeightsPosDepC.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c GappyPairC.cpp -o GappyPairC.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c KernelUtils.cpp -o KernelUtils.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c PredictionC.cpp -o PredictionC.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c PredictionProfileC.cpp -o PredictionProfileC.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c Rsvm.c -o Rsvm.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c SparseMatrixHash.cpp -o SparseMatrixHash.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c SpectrumC.cpp -o SpectrumC.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c SymmetricPairC.cpp -o SymmetricPairC.o
g++  -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/S4Vectors/include" -I/usr/local/include   -fpic  -g -O2  -Wall -c Utils.cpp -o Utils.o
gcc -I"/home/biocbuild/bbs-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-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-3.8-bioc/R/include" -DNDEBUG  -I"/home/biocbuild/bbs-3.8-bioc/R/library/IRanges/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/XVector/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Biostrings/include" -I"/home/biocbuild/bbs-3.8-bioc/R/library/Rcpp/include" -I"/home/biocbuild/bbs-3.8-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-3.8-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-3.8-bioc/R/lib -lR
installing to /home/biocbuild/bbs-3.8-bioc/R/library/kebabs/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (kebabs)