rSFFreader

Package: rSFFreader
Type: Package
Title: rSFFreader reads in sff files generated by Roche 454 and Life
Sciences Ion Torrent sequencers
Version: 0.20.0
Date: 2011-10-02
Author: Matt Settles <mattsettles@gmail.com>, Sam Hunter, Brice Sarver,
Ilia Zhbannikov, Kyu-Chul Cho
Maintainer: Matt Settles <mattsettles@gmail.com>
Description: rSFFreader reads sequence, qualities and clip point values
from sff files generated by Roche 454 and Life Sciences Ion
Torrent sequencers into similar classes as are present for fastq files.
License: Artistic-2.0
Depends: ShortRead (>= 1.23.17)
Imports: methods, Biostrings, IRanges
Suggests: xtable
LinkingTo: S4Vectors, IRanges, XVector, Biostrings
Collate: allClasses.R allGenerics.R methods-Misc.R methods-SffHeader.R
methods-SffReads.R methods-SffReadsQ.R readSFF.R
biocViews: DataImport, Sequencing
NeedsCompilation: yes
Packaged: 2016-05-04 04:46:02 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'rSFFreader' ...
** 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"   -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"   -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"   -fpic  -g -O2  -c R_init_rSFFreader.c -o R_init_rSFFreader.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"   -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"   -fpic  -g -O2  -c SFF-io.c -o SFF-io.o
SFF-io.c: In function 'readCommonHeader':
SFF-io.c:262:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
     fread( &commonHeader.magic_number, sizeof(uint32_t), 1, file);
     ^
SFF-io.c:265:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
     fread( commonHeader.version, sizeof(char), 4, file);
     ^
SFF-io.c:267:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
     fread( &commonHeader.index_offset, sizeof(uint64_t), 1, file);
     ^
SFF-io.c:270:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
     fread( &commonHeader.index_length, sizeof(uint32_t), 1, file);
     ^
SFF-io.c:273:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
     fread( &commonHeader.number_of_reads, sizeof(uint32_t), 1, file);
     ^
SFF-io.c:276:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
     fread( &commonHeader.commonHeader_length, sizeof(uint16_t), 1, file);
     ^
SFF-io.c:279:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
     fread( &commonHeader.key_length, sizeof(uint16_t), 1, file);
     ^
SFF-io.c:282:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
     fread( &commonHeader.number_of_flows_per_read, sizeof(uint16_t), 1, file);
     ^
SFF-io.c:285:5: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
     fread( &commonHeader.flowgram_format_code, sizeof(uint8_t),1, file);
     ^
SFF-io.c:297:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
         fread(&ch, sizeof(char), 1, file);
         ^
SFF-io.c:309:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
         fread(&ch, sizeof(char), 1, file);
         ^
SFF-io.c: In function 'sff_geometry':
SFF-io.c:778:13: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
             fread( &header.read_header_length, sizeof(uint16_t), 1, file);
             ^
SFF-io.c:780:13: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
             fread( &header.name_length, sizeof(uint16_t), 1, file);
             ^
SFF-io.c:782:13: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
             fread( &header.number_of_bases, sizeof(uint32_t), 1, file);
             ^
SFF-io.c:784:13: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
             fread( &header.clip_qual_left, sizeof(uint16_t), 1, file);
             ^
SFF-io.c:786:13: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
             fread( &header.clip_qual_right, sizeof(uint16_t), 1, file);
             ^
SFF-io.c:788:13: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
             fread( &header.clip_adapter_left, sizeof(uint16_t), 1, file);
             ^
SFF-io.c:790:13: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
             fread( &header.clip_adapter_right, sizeof(uint16_t), 1, file);
             ^
SFF-io.c: In function 'readSFF':
SFF-io.c:628:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
         fread( &header.read_header_length, sizeof(uint16_t), 1, file);
         ^
SFF-io.c:630:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
         fread( &header.name_length, sizeof(uint16_t), 1, file);
         ^
SFF-io.c:632:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
         fread( &header.number_of_bases, sizeof(uint32_t), 1, file);
         ^
SFF-io.c:634:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
         fread( &header.clip_qual_left, sizeof(uint16_t), 1, file);
         ^
SFF-io.c:636:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
         fread( &header.clip_qual_right, sizeof(uint16_t), 1, file);
         ^
SFF-io.c:638:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
         fread( &header.clip_adapter_left, sizeof(uint16_t), 1, file);
         ^
SFF-io.c:640:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
         fread( &header.clip_adapter_right, sizeof(uint16_t), 1, file);
         ^
SFF-io.c:656:9: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
         fread( data.name, sizeof(char),header.name_length, file);
         ^
SFF-io.c:674:13: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
             fread( &uint16, sizeof(uint16_t), 1, file);
             ^
SFF-io.c:682:13: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
             fread( &uint8, sizeof(uint8_t), 1, file);
             ^
SFF-io.c:691:13: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
             fread( &ch, sizeof(char), 1, file);
             ^
SFF-io.c:708:13: warning: ignoring return value of 'fread', declared with attribute warn_unused_result [-Wunused-result]
             fread( &uint8, sizeof(uint8_t), 1, file);
             ^
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"   -fpic  -g -O2  -c XVector_stubs.c -o XVector_stubs.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o rSFFreader.so Biostrings_stubs.o IRanges_stubs.o R_init_rSFFreader.o S4Vectors_stubs.o SFF-io.o XVector_stubs.o -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/rSFFreader/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'rSFFreader'
    finding HTML links ... done
    SffHeader-class                         html  
    SffReads-class                          html  
    finding level-2 HTML links ... done

    SffReadsQ-class                         html  
    availableClipModes                      html  
    load454SampleData                       html  
    loadIonSampleData                       html  
    rSFFreader-internals                    html  
    rSFFreader-package                      html  
    readsff                                 html  
    readsffgeometry                         html  
    readsffheader                           html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (rSFFreader)
Making 'packages.html' ... done