ShortRead

Package: ShortRead
Type: Package
Title: FASTQ input and manipulation
Version: 1.30.0
Author: Martin Morgan, Michael Lawrence, Simon Anders
Maintainer: Bioconductor Package Maintainer
<maintainer@bioconductor.org>
Description: This package implements sampling, iteration, and input of
FASTQ files. The package includes functions for filtering and
trimming reads, and for generating a quality assessment report.
Data are represented as DNAStringSet-derived objects, and
easily manipulated for a diversity of purposes. The package
also contains legacy support for early single-end, ungapped
alignment formats.
License: Artistic-2.0
LazyLoad: yes
Depends: BiocGenerics (>= 0.11.3), BiocParallel, Biostrings (>=
2.37.1), Rsamtools (>= 1.21.4), GenomicAlignments (>= 1.5.4)
Imports: Biobase, S4Vectors (>= 0.7.1), IRanges (>= 2.3.7),
GenomeInfoDb (>= 1.1.19), GenomicRanges (>= 1.21.6), hwriter,
methods, zlibbioc, lattice, latticeExtra,
Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi
LinkingTo: S4Vectors, IRanges, XVector, Biostrings
biocViews: DataImport, Sequencing, QualityControl
NeedsCompilation: yes
Packaged: 2016-05-04 03:09:08 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'ShortRead' ...
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for gzeof in -lz... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking size of unsigned long... 8
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -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" -I"/home/ddbj/local/lib64/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -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" -I"/home/ddbj/local/lib64/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -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" -I"/home/ddbj/local/lib64/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -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" -I"/home/ddbj/local/lib64/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -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" -I"/home/ddbj/local/lib64/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -c XVector_stubs.c -o XVector_stubs.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -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" -I"/home/ddbj/local/lib64/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -c alphabet.c -o alphabet.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -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" -I"/home/ddbj/local/lib64/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -c io.c -o io.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -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" -I"/home/ddbj/local/lib64/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -c io_bowtie.c -o io_bowtie.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -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" -I"/home/ddbj/local/lib64/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -c io_soap.c -o io_soap.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -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" -I"/home/ddbj/local/lib64/R/library/Biostrings/include"  -DPACKAGE_NAME="" -DPACKAGE_TARNAME="" -DPACKAGE_VERSION="" -DPACKAGE_STRING="" -DPACKAGE_BUGREPORT="" -DPACKAGE_URL="" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fpic  -g -O2  -c readBfaToc.cc -o readBfaToc.o
g++ -I/home/ddbj/local/lib64/R/include -DNDEBUG  -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" -I"/home/ddbj/local/lib64/R/library/Biostrings/include"  -DPACKAGE_NAME="" -DPACKAGE_TARNAME="" -DPACKAGE_VERSION="" -DPACKAGE_STRING="" -DPACKAGE_BUGREPORT="" -DPACKAGE_URL="" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fpic  -g -O2  -c read_maq_map.cc -o read_maq_map.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -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" -I"/home/ddbj/local/lib64/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -c sampler.c -o sampler.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -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" -I"/home/ddbj/local/lib64/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -c trim.c -o trim.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -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" -I"/home/ddbj/local/lib64/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -c util.c -o util.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -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" -I"/home/ddbj/local/lib64/R/library/Biostrings/include"  -fopenmp -fpic  -g -O2  -c xsnap.c -o xsnap.o
g++ -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o S4Vectors_stubs.o XVector_stubs.o alphabet.o io.o io_bowtie.o io_soap.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -lz -fopenmp -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/ShortRead/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'ShortRead'
    finding HTML links ... done
    AlignedDataFrame-class                  html  
    AlignedDataFrame                        html  
    AlignedRead-class                       html  
Rd warning: /tmp/RtmpqSjMZL/R.INSTALL68706ee2afc8/ShortRead/man/AlignedRead-class.Rd:119: missing file link 'RangesList'
Rd warning: /tmp/RtmpqSjMZL/R.INSTALL68706ee2afc8/ShortRead/man/AlignedRead-class.Rd:120: missing file link 'RangedData'
Rd warning: /tmp/RtmpqSjMZL/R.INSTALL68706ee2afc8/ShortRead/man/AlignedRead-class.Rd:121: missing file link 'GRanges'
Rd warning: /tmp/RtmpqSjMZL/R.INSTALL68706ee2afc8/ShortRead/man/AlignedRead-class.Rd:124: missing file link 'Ranges'
Rd warning: /tmp/RtmpqSjMZL/R.INSTALL68706ee2afc8/ShortRead/man/AlignedRead-class.Rd:182: file link 'IntervalTree-class' in package 'IRanges' does not exist and so has been treated as a topic
    AlignedRead                             html  
    BowtieQA-class                          html  
    ExperimentPath-class                    html  
    FastqQA-class                           html  
    Intensity-class                         html  
    MAQMapQA-class                          html  
    QA-class                                html  
    QualityScore-class                      html  
    QualityScore                            html  
    RochePath-class                         html  
    RocheSet-class                          html  
    RtaIntensity-class                      html  
    RtaIntensity                            html  
    SRFilter-class                          html  
Rd warning: /tmp/RtmpqSjMZL/R.INSTALL68706ee2afc8/ShortRead/man/SRFilter-class.Rd:76: file link 'FilterRules' in package 'IRanges' does not exist and so has been treated as a topic
Rd warning: /tmp/RtmpqSjMZL/R.INSTALL68706ee2afc8/ShortRead/man/SRFilter-class.Rd:80: file link 'FilterRules' in package 'IRanges' does not exist and so has been treated as a topic
    SRFilterResult-class                    html  
    SRSet-class                             html  
    finding level-2 HTML links ... done

    SRUtil-class                            html  
    Sampler-class                           html  
    ShortRead-class                         html  
    ShortRead-deprecated                    html  
    ShortRead-package                       html  
    ShortReadQ-class                        html  
    Snapshot-class                          html  
    SnapshotFunction-class                  html  
    SolexaExportQA-class                    html  
    SolexaIntensity-class                   html  
    SolexaIntensity                         html  
    SolexaPath-class                        html  
    SolexaSet-class                         html  
    SpTrellis-class                         html  
    accessors                               html  
    alphabetByCycle                         html  
    alphabetScore                           html  
    clean                                   html  
    countLines                              html  
    deprecated                              html  
    dotQA-class                             html  
    dustyScore                              html  
    filterFastq                             html  
    polyn                                   html  
    qa                                      html  
    qa2                                     html  
    readAligned                             html  
    readBaseQuality                         html  
    readBfaToc                              html  
    readFasta                               html  
    readFastq                               html  
    readIntensities                         html  
    readPrb                                 html  
    readQseq                                html  
    readXStringColumns                      html  
    renew                                   html  
    report                                  html  
    spViewPerFeature                        html  
    srFilter                                html  
    srdistance                              html  
    srduplicated                            html  
    tables                                  html  
    trimTails                               html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (ShortRead)
Making 'packages.html' ... done