seqbias

Package: seqbias
Version: 1.20.0
Date: 25-12-2010
Title: Estimation of per-position bias in high-throughput sequencing
data
Description: This package implements a model of per-position sequencing
bias in high-throughput sequencing data using a simple Bayesian
network, the structure and parameters of which are trained on a
set of aligned reads and a reference genome sequence.
Author: Daniel Jones <dcjones@cs.washington.edu>
Maintainer: Daniel Jones <dcjones@cs.washington.edu>
Depends: R (>= 2.13.0), GenomicRanges (>= 0.1.0), Biostrings (>=
2.15.0), methods
LinkingTo: Rsamtools (>= 1.19.38)
Imports: zlibbioc
Suggests: Rsamtools, ggplot2
LazyLoad: yes
License: LGPL-3
biocViews: Sequencing
NeedsCompilation: yes
Packaged: 2016-05-04 03:54:59 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'seqbias' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c common.c -o common.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c miscmath.c -o miscmath.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c pos_table.c -o pos_table.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c samtools_extra.c -o samtools_extra.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c kmer_matrix.cpp -o kmer_matrix.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c logger.cpp -o logger.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c motif.cpp -o motif.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c seqbias.cpp -o seqbias.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c sequencing_bias.cpp -o sequencing_bias.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c twobitseq.cpp -o twobitseq.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c yaml-cpp/aliasmanager.cpp -o yaml-cpp/aliasmanager.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c yaml-cpp/conversion.cpp -o yaml-cpp/conversion.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c yaml-cpp/directives.cpp -o yaml-cpp/directives.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c yaml-cpp/emitfromevents.cpp -o yaml-cpp/emitfromevents.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c yaml-cpp/emitter.cpp -o yaml-cpp/emitter.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c yaml-cpp/emitterstate.cpp -o yaml-cpp/emitterstate.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c yaml-cpp/emitterutils.cpp -o yaml-cpp/emitterutils.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c yaml-cpp/exp.cpp -o yaml-cpp/exp.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c yaml-cpp/iterator.cpp -o yaml-cpp/iterator.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c yaml-cpp/nodebuilder.cpp -o yaml-cpp/nodebuilder.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c yaml-cpp/node.cpp -o yaml-cpp/node.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c yaml-cpp/nodeownership.cpp -o yaml-cpp/nodeownership.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c yaml-cpp/null.cpp -o yaml-cpp/null.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c yaml-cpp/ostream.cpp -o yaml-cpp/ostream.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c yaml-cpp/parser.cpp -o yaml-cpp/parser.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c yaml-cpp/regex.cpp -o yaml-cpp/regex.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c yaml-cpp/scanner.cpp -o yaml-cpp/scanner.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c yaml-cpp/scanscalar.cpp -o yaml-cpp/scanscalar.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c yaml-cpp/scantag.cpp -o yaml-cpp/scantag.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c yaml-cpp/scantoken.cpp -o yaml-cpp/scantoken.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c yaml-cpp/simplekey.cpp -o yaml-cpp/simplekey.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c yaml-cpp/singledocparser.cpp -o yaml-cpp/singledocparser.o
In file included from yaml-cpp/singledocparser.cpp:2:0:
yaml-cpp/collectionstack.h:28:48: warning: unused parameter 'type' [-Wunused-parameter]
   void PopCollectionType(CollectionType::value type) { assert(type == GetCurCollectionType()); collectionStack.pop(); }
                                                ^
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c yaml-cpp/stream.cpp -o yaml-cpp/stream.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG -D_USE_KNETFILE -DBGZF_CACHE -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Rsamtools/include"  -Wall -Wextra -I. -fpic  -g -O2  -c yaml-cpp/tag.cpp -o yaml-cpp/tag.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o seqbias.so common.o miscmath.o pos_table.o samtools_extra.o kmer_matrix.o logger.o motif.o seqbias.o sequencing_bias.o twobitseq.o yaml-cpp/aliasmanager.o yaml-cpp/conversion.o yaml-cpp/directives.o yaml-cpp/emitfromevents.o yaml-cpp/emitter.o yaml-cpp/emitterstate.o yaml-cpp/emitterutils.o yaml-cpp/exp.o yaml-cpp/iterator.o yaml-cpp/nodebuilder.o yaml-cpp/node.o yaml-cpp/nodeownership.o yaml-cpp/null.o yaml-cpp/ostream.o yaml-cpp/parser.o yaml-cpp/regex.o yaml-cpp/scanner.o yaml-cpp/scanscalar.o yaml-cpp/scantag.o yaml-cpp/scantoken.o yaml-cpp/simplekey.o yaml-cpp/singledocparser.o yaml-cpp/stream.o yaml-cpp/tag.o /home/ddbj/local/lib64/R/library/Rsamtools/usrlib//libbam.a /home/ddbj/local/lib64/R/library/Rsamtools/usrlib//libbcf.a /home/ddbj/local/lib64/R/library/Rsamtools/usrlib//libtabix.a -lz -pthread -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/seqbias/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'seqbias'
    finding HTML links ... done
    count_reads                             html  
    kmer_freq                               html  
    random_intervals                        html  
    seqbias-class                           html  
    seqbias-package                         html  
    seqbias_fit                             html  
    seqbias_load                            html  
    seqbias_predict                         html  
    seqbias_save                            html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (seqbias)
Making 'packages.html' ... done