qrqc

Package: qrqc
Version: 1.26.0
Date: 2012-04-17
Title: Quick Read Quality Control
Author: Vince Buffalo
Maintainer: Vince Buffalo <vsbuffalo@ucdavis.edu>
Imports: reshape, ggplot2, Biostrings, biovizBase, graphics, methods,
plyr, stats
Depends: reshape, ggplot2, Biostrings, biovizBase, brew, xtable,
Rsamtools (>= 1.19.38), testthat
LinkingTo: Rsamtools
Description: Quickly scans reads and gathers statistics on base and
quality frequencies, read length, k-mers by position, and
frequent sequences. Produces graphical output of statistics for
use in quality control pipelines, and an optional HTML quality
report. S4 SequenceSummary objects allow specific tests and
functionality to be written around the data collected.
License: GPL (>=2)
URL: http://github.com/vsbuffalo/qrqc
biocViews: Sequencing, QualityControl, DataImport, Preprocessing,
Visualization
NeedsCompilation: yes
Packaged: 2016-05-04 04:01:43 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'qrqc' ...
** 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"   -fpic  -g -O2  -c R_init_io.c -o R_init_io.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"   -fpic  -g -O2  -c io.c -o io.o
io.c: In function 'summarize_file':
io.c:32:25: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types]
 #define FILE_OPEN(x, m) (gzopen(x, m))
                         ^
io.c:347:19: note: in expansion of macro 'FILE_OPEN'
   FILE_TYPE *fp = FILE_OPEN(CHAR(STRING_ELT(filename, 0)), "r");
                   ^
io.c:350:21: warning: passing argument 1 of 'kseq_init' from incompatible pointer type [-Wincompatible-pointer-types]
   block = kseq_init(fp);
                     ^
In file included from io.c:11:0:
/home/ddbj/local/lib64/R/library/Rsamtools/include/samtools/kseq.h:152:16: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
  SCOPE kseq_t *kseq_init(type_t fd)         
                ^
/home/ddbj/local/lib64/R/library/Rsamtools/include/samtools/kseq.h:223:2: note: in expansion of macro '__KSEQ_BASIC'
  __KSEQ_BASIC(SCOPE, type_t)     
  ^
/home/ddbj/local/lib64/R/library/Rsamtools/include/samtools/kseq.h:226:35: note: in expansion of macro 'KSEQ_INIT2'
 #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                   ^
io.c:34:1: note: in expansion of macro 'KSEQ_INIT'
 KSEQ_INIT(gzFile, gzread)
 ^
io.c:452:21: warning: passing argument 1 of 'kseq_init' from incompatible pointer type [-Wincompatible-pointer-types]
   block = kseq_init(fp);
                     ^
In file included from io.c:11:0:
/home/ddbj/local/lib64/R/library/Rsamtools/include/samtools/kseq.h:152:16: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
  SCOPE kseq_t *kseq_init(type_t fd)         
                ^
/home/ddbj/local/lib64/R/library/Rsamtools/include/samtools/kseq.h:223:2: note: in expansion of macro '__KSEQ_BASIC'
  __KSEQ_BASIC(SCOPE, type_t)     
  ^
/home/ddbj/local/lib64/R/library/Rsamtools/include/samtools/kseq.h:226:35: note: in expansion of macro 'KSEQ_INIT2'
 #define KSEQ_INIT(type_t, __read) KSEQ_INIT2(static, type_t, __read)
                                   ^
io.c:34:1: note: in expansion of macro 'KSEQ_INIT'
 KSEQ_INIT(gzFile, gzread)
 ^
io.c:453:14: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
   FILE_CLOSE(fp);
              ^
io.c:33:32: note: in definition of macro 'FILE_CLOSE'
 #define FILE_CLOSE(x) (gzclose(x))
                                ^
In file included from io.c:30:0:
/usr/include/zlib.h:1511:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
 ZEXTERN int ZEXPORT    gzclose OF((gzFile file));
                        ^
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o qrqc.so R_init_io.o io.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/qrqc/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'qrqc'
    finding HTML links ... done
    FASTASummary-class                      html  
    FASTQSummary-class                      html  
    SequenceSummary-class                   html  
    basePlot-methods                        html  
    calcKL                                  html  
    gcPlot-methods                          html  
    geom_qlinerange                         html  
    getBase-methods                         html  
    getBaseProp-methods                     html  
    getGC-methods                           html  
    getKmer-methods                         html  
    getMCQual-methods                       html  
    getQual-methods                         html  
    getSeqlen-methods                       html  
    kmerEntropyPlot                         html  
    kmerKLPlot                              html  
    list2df                                 html  
    makeReport                              html  
    plotBases                               html  
    plotGC                                  html  
    plotQuals                               html  
    plotSeqLengths                          html  
    qualPlot-methods                        html  
    readSeqFile                             html  
    scale_color_dna                         html  
    scale_color_iupac                       html  
    seqlenPlot-methods                      html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (qrqc)
Making 'packages.html' ... done