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Last data update: 2014.03.03
rtracklayer

Package: rtracklayer
Title: R interface to genome browsers and their annotation tracks
Version: 1.32.1
Author: Michael Lawrence, Vince Carey, Robert Gentleman
Depends: R (>= 3.3), methods, GenomicRanges (>= 1.21.20)
Imports: XML (>= 1.98-0), BiocGenerics (>= 0.13.8), S4Vectors (>=
0.9.33), IRanges (>= 2.3.7), XVector (>= 0.9.4), GenomeInfoDb
(>= 1.3.14), Biostrings (>= 2.37.1), zlibbioc, RCurl (>=
1.4-2), Rsamtools (>= 1.17.8), GenomicAlignments (>= 1.5.4),
tools
Suggests: BSgenome (>= 1.33.4), humanStemCell, microRNA (>= 1.1.1),
genefilter, limma, org.Hs.eg.db, hgu133plus2.db,
BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene
LinkingTo: S4Vectors, IRanges, XVector
Description: Extensible framework for interacting with multiple genome
browsers (currently UCSC built-in) and manipulating
annotation tracks in various formats (currently GFF, BED, bedGraph, BED15,
WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the
supported browsers, as well as query and modify the browser state, such as the
current viewport.
Maintainer: Michael Lawrence <michafla@gene.com>
License: Artistic-2.0 + file LICENSE
Collate: io.R web.R ranges.R trackDb.R browser.R ucsc.R readGFF.R gff.R
bed.R wig.R utils.R bigWig.R chain.R quickload.R twobit.R
fasta.R tabix.R bam.R trackTable.R index.R compression.R
test_rtracklayer_package.R ncbi.R
biocViews: Annotation,Visualization,DataImport
NeedsCompilation: yes
Packaged: 2016-06-13 01:57:07 UTC; biocbuild
● BiocViews: Annotation, DataImport, Visualization
● 1 images, 50 functions, 2 datasets
● Reverse Depends: 16
Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'rtracklayer' ...
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for OPENSSL... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c XVector_stubs.c -o XVector_stubs.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c R_init_rtracklayer.c -o R_init_rtracklayer.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c readGFF.c -o readGFF.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c bigWig.c -o bigWig.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c chain_io.c -o chain_io.o
chain_io.c: In function 'read_chain_file':
chain_io.c:119:9: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
         fgets(linebuf, LINEBUF_SIZE, stream); /* skip empty line */
         ^
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c twoBit.c -o twoBit.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c handlers.c -o handlers.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c utils.c -o utils.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/bbiRead.c -o ucsc/bbiRead.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/cirTree.c -o ucsc/cirTree.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/common.c -o ucsc/common.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/dnautil.c -o ucsc/dnautil.o
ucsc/dnautil.c: In function 'reverseComplementSlashSeparated':
ucsc/dnautil.c:496:9: warning: implicit declaration of function 'isAllNt' [-Wimplicit-function-declaration]
     if (isAllNt(allele, alLen))
         ^
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/errAbort.c -o ucsc/errAbort.o
ucsc/errAbort.c: In function 'getThreadVars':
ucsc/errAbort.c:331:5: warning: ignoring return value of 'write', declared with attribute warn_unused_result [-Wunused-result]
     write(STDERR_FILENO, errMsg, strlen(errMsg)); 
     ^
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/hash.c -o ucsc/hash.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/linefile.c -o ucsc/linefile.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/localmem.c -o ucsc/localmem.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/zlibFace.c -o ucsc/zlibFace.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/dystring.c -o ucsc/dystring.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/hmmstats.c -o ucsc/hmmstats.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/obscure.c -o ucsc/obscure.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/rangeTree.c -o ucsc/rangeTree.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/rbTree.c -o ucsc/rbTree.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/memalloc.c -o ucsc/memalloc.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/dlist.c -o ucsc/dlist.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/udc.c -o ucsc/udc.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/net.c -o ucsc/net.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/bits.c -o ucsc/bits.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/twoBit.c -o ucsc/twoBit.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/internet.c -o ucsc/internet.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/https.c -o ucsc/https.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/base64.c -o ucsc/base64.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/verbose.c -o ucsc/verbose.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/os.c -o ucsc/os.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/S4Vectors/include" -I"/home/ddbj/local/lib64/R/library/IRanges/include" -I"/home/ddbj/local/lib64/R/library/XVector/include"   -fpic  -g -O2  -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o rtracklayer.so S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_rtracklayer.o readGFF.o bigWig.o chain_io.o twoBit.o handlers.o utils.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/errAbort.o ucsc/hash.o ucsc/linefile.o ucsc/localmem.o ucsc/sqlNum.o ucsc/zlibFace.o ucsc/dystring.o ucsc/hmmstats.o ucsc/obscure.o ucsc/pipeline.o ucsc/rangeTree.o ucsc/rbTree.o ucsc/memalloc.o ucsc/dlist.o ucsc/udc.o ucsc/net.o ucsc/bits.o ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -lz -pthread -lssl -lcrypto -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/rtracklayer/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
Creating a generic function for 'offset' from package 'stats' in package 'rtracklayer'
Creating a generic function from function 'uri' in package 'rtracklayer'
** help
*** installing help indices
  converting help for package 'rtracklayer'
    finding HTML links ... done
    BEDFile-class                           html  
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/BEDFile-class.Rd:113: missing file link 'findOverlaps'
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/BEDFile-class.Rd:175: missing file link 'BamFile'
    BamFile-methods                         html  
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/BamFile-methods.Rd:11: missing file link 'GAlignments'
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/BamFile-methods.Rd:12: missing file link 'GAlignmentPairs'
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/BamFile-methods.Rd:13: missing file link 'BamFile'
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/BamFile-methods.Rd:28: missing file link 'ScanBamParam'
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/BamFile-methods.Rd:40: missing file link 'filterBam'
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/BamFile-methods.Rd:45: missing file link 'readGAlignmentPairs'
    Bed15TrackLine-class                    html  
    BigWigFile                              html  
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/BigWigFile.Rd:143: missing file link 'Seqinfo'
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/BigWigFile.Rd:158: missing file link 'RleList-class'
    BigWigSelection-class                   html  
    finding level-2 HTML links ... done

Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/BigWigSelection-class.Rd:15: missing file link 'RangedSelection'
    BrowserViewList-class                   html  
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/BrowserViewList-class.Rd:13: missing file link 'Vector'
    Chain-class                             html  
    FastaFile-class                         html  
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/FastaFile-class.Rd:50: missing file link 'writeXStringSet'
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/FastaFile-class.Rd:51: missing file link 'readDNAStringSet'
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/FastaFile-class.Rd:58: missing file link 'writeXStringSet'
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/FastaFile-class.Rd:59: missing file link 'readDNAStringSet'
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/FastaFile-class.Rd:63: missing file link 'BSgenome'
    GFFFile-class                           html  
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/GFFFile-class.Rd:124: missing file link 'findOverlaps'
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/GFFFile-class.Rd:189: missing file link 'BamFile'
    GRangesForUCSCGenome                    html  
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/GRangesForUCSCGenome.Rd:12: missing file link 'Seqinfo'
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/GRangesForUCSCGenome.Rd:35: missing file link 'GRanges'
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/GRangesForUCSCGenome.Rd:54: missing file link 'seqlengths'
    GenomicData                             html  
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/GenomicData.Rd:46: missing file link 'GRanges'
    GenomicSelection                        html  
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/GenomicSelection.Rd:7: missing file link 'RangedSelection'
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/GenomicSelection.Rd:26: missing file link 'RangedSelection'
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/GenomicSelection.Rd:33: missing file link 'RangedSelection'
    Quickload-class                         html  
    QuickloadGenome-class                   html  
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/QuickloadGenome-class.Rd:60: missing file link 'BSgenome'
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/QuickloadGenome-class.Rd:61: missing file link 'GenomeDescription'
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/QuickloadGenome-class.Rd:83: missing file link 'Seqinfo'
    RTLFile-class                           html  
    RangesList-methods                      html  
    TabixFile-methods                       html  
    TrackDb-class                           html  
    TwoBitFile-class                        html  
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/TwoBitFile-class.Rd:99: missing file link 'Seqinfo'
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/TwoBitFile-class.Rd:108: missing file link 'BSgenome'
    UCSCData-class                          html  
    UCSCFile-class                          html  
    UCSCSchema-class                        html  
    UCSCTableQuery-class                    html  
    WIGFile-class                           html  
    activeView-methods                      html  
    asBED                                   html  
    asGFF                                   html  
    basicTrackLine-class                    html  
    blocks-methods                          html  
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/blocks-methods.Rd:9: missing file link 'GRanges'
    browseGenome                            html  
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/browseGenome.Rd:19: missing file link 'GRanges'
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/browseGenome.Rd:20: missing file link 'GRanges'
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/browseGenome.Rd:21: missing file link 'GenomicRangesList'
    browserSession-class                    html  
    browserSession-methods                  html  
    browserView-class                       html  
    browserView-methods                     html  
    browserViews-methods                    html  
    cpneTrack                               html  
    export                                  html  
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/export.Rd:138: missing file link 'BamFile'
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/export.Rd:148: missing file link 'FaFile'
    genomeBrowsers                          html  
    laySequence-methods                     html  
    layTrack-methods                        html  
    liftOver                                html  
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/liftOver.Rd:22: missing file link 'GRanges'
    readGFF                                 html  
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/readGFF.Rd:11: missing file link 'DataFrame'
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/readGFF.Rd:65: missing file link 'GRanges'
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/readGFF.Rd:69: missing file link 'GRanges'
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/readGFF.Rd:70: missing file link 'DataFrame'
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/readGFF.Rd:74: missing file link 'TxDb'
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/readGFF.Rd:76: missing file link 'DataFrame'
    targets                                 html  
    tracks-methods                          html  
    ucscGenomes                             html  
    ucscSession-class                       html  
Rd warning: /tmp/RtmpkcpT5l/R.INSTALL62eb923a875/rtracklayer/man/ucscSession-class.Rd:62: missing file link 'Seqinfo'
    ucscTrackLine-class                     html  
    ucscTrackModes-class                    html  
    ucscTrackModes-methods                  html  
    ucscView-class                          html  
    wigToBigWig                             html  
    wigTrackLine-class                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rtracklayer)
Making 'packages.html' ... done