oligo

Package: oligo
Version: 1.36.1
Title: Preprocessing tools for oligonucleotide arrays
Author: Benilton Carvalho and Rafael Irizarry
Contributors: Ben Bolstad, Vincent Carey, Wolfgang Huber, Harris
Jaffee, Jim MacDonald, Matt Settles
Maintainer: Benilton Carvalho <benilton@unicamp.br>
Depends: R (>= 3.2.0), BiocGenerics (>= 0.13.11), oligoClasses (>=
1.29.6), Biobase (>= 2.27.3), Biostrings (>= 2.35.12)
Imports: affyio (>= 1.35.0), affxparser (>= 1.39.4), DBI (>= 0.3.1),
ff, graphics, methods, preprocessCore (>= 1.29.0), RSQLite (>=
1.0.0), splines, stats, stats4, utils, zlibbioc
Enhances: ff, doMC, doMPI
LinkingTo: preprocessCore
Suggests: BSgenome.Hsapiens.UCSC.hg18, hapmap100kxba, pd.hg.u95av2,
pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr,
pd.hugene.1.0.st.v1, maqcExpression4plex, genefilter, limma,
RColorBrewer, oligoData, BiocStyle, knitr, RUnit, biomaRt,
AnnotationDbi, GenomeGraphs, RCurl, ACME, biomaRt,
AnnotationDbi, GenomeGraphs, RCurl
VignetteBuilder: knitr
Description: A package to analyze oligonucleotide arrays
(expression/SNP/tiling/exon) at probe-level. It currently
supports Affymetrix (CEL files) and NimbleGen arrays (XYS
files).
License: LGPL (>= 2)
Collate: AllGenerics.R methods-GenericArrays.R methods-GeneFeatureSet.R
methods-ExonFeatureSet.R methods-ExpressionFeatureSet.R
methods-ExpressionSet.R methods-LDS.R methods-FeatureSet.R
methods-SnpFeatureSet.R methods-SnpCnvFeatureSet.R
methods-TilingFeatureSet.R methods-HtaFeatureSet.R
methods-DBPDInfo.R methods-background.R methods-normalization.R
methods-summarization.R read.celfiles.R read.xysfiles.R
utils-general.R utils-selectors.R todo-snp.R functions-crlmm.R
functions-snprma.R justSNPRMA.R justCRLMM.R methods-snp6.R
methods-genotype.R methods-PLMset.R zzz.R
LazyLoad: Yes
biocViews: Microarray, OneChannel, TwoChannel, Preprocessing, SNP,
DifferentialExpression, ExonArray, GeneExpression, DataImport
NeedsCompilation: yes
Packaged: 2016-05-16 01:34:34 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'oligo' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c DABG.c -o DABG.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c ParserGzXYS.c -o ParserGzXYS.o
ParserGzXYS.c: In function 'gzcountLines':
ParserGzXYS.c:18:17: warning: passing argument 1 of 'gzeof' from incompatible pointer type [-Wincompatible-pointer-types]
   while (!gzeof(file)){
                 ^
In file included from ParserGzXYS.c:4:0:
/usr/include/zlib.h:1475:21: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
 ZEXTERN int ZEXPORT gzeof OF((gzFile file));
                     ^
ParserGzXYS.c:19:12: warning: passing argument 1 of 'gzgets' from incompatible pointer type [-Wincompatible-pointer-types]
     gzgets(file, buffer, 1000);
            ^
In file included from ParserGzXYS.c:4:0:
/usr/include/zlib.h:1372:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
 ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
                        ^
ParserGzXYS.c: In function 'gzxys_header_field':
ParserGzXYS.c:46:6: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   fp = gzopen(currentFile, "rb");
      ^
ParserGzXYS.c:50:10: warning: passing argument 1 of 'gzgets' from incompatible pointer type [-Wincompatible-pointer-types]
   gzgets(fp, buffer, LINEMAX);
          ^
In file included from ParserGzXYS.c:4:0:
/usr/include/zlib.h:1372:24: note: expected 'gzFile {aka struct gzFile_s *}' but argument is of type 'struct gzFile_s **'
 ZEXTERN char * ZEXPORT gzgets OF((gzFile file, char *buf, int len));
                        ^
ParserGzXYS.c:51:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
   gzclose(fp);
           ^
In file included from ParserGzXYS.c:4:0:
/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));
                        ^
ParserGzXYS.c: In function 'R_read_gzxys_files':
ParserGzXYS.c:134:6: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
   fp = gzopen(CHAR(STRING_ELT(filenames, 0)), "rb");
      ^
ParserGzXYS.c:138:11: warning: passing argument 1 of 'gzclose' from incompatible pointer type [-Wincompatible-pointer-types]
   gzclose(fp);
           ^
In file included from ParserGzXYS.c:4:0:
/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 -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c ParserXYS.c -o ParserXYS.o
ParserXYS.c: In function 'xys_header_field':
ParserXYS.c:145:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   fgets(buffer, LINEMAX, fp);
   ^
ParserXYS.c: In function 'R_read_xys_header':
ParserXYS.c:320:3: warning: ignoring return value of 'fgets', declared with attribute warn_unused_result [-Wunused-result]
   fgets(buffer, LINEMAX, fp);
   ^
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c baseProfile.c -o baseProfile.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c basecontent.c -o basecontent.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c chipbackground.c -o chipbackground.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c mas5calls.c -o mas5calls.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c rma2.c -o rma2.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c rma_common.c -o rma_common.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/preprocessCore/include"   -fpic  -g -O2  -c trimmed.c -o trimmed.o
gcc -shared -L/home/ddbj/local/lib64/R/lib -L/usr/local/lib64 -o oligo.so DABG.o ParserGzXYS.o ParserXYS.o baseProfile.o basecontent.o chipbackground.o mas5calls.o rma2.o rma_common.o trimmed.o -lz -lgfortran -lm -lquadmath -L/home/ddbj/local/lib64/R/lib -lRlapack -L/home/ddbj/local/lib64/R/lib -lRblas -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/oligo/libs
** R
** inst
** preparing package for lazy loading
Note: in method for 'pm<-' with signature
'object="TilingFeatureSet",subset="ANY",target="ANY",value="array"':
expanding the signature to include omitted arguments in definition: =
"missing"
Note: in method for 'mm<-' with signature
'object="TilingFeatureSet",subset="ANY",target="ANY",value="array"':
expanding the signature to include omitted arguments in definition: =
"missing"
** help
*** installing help indices
  converting help for package 'oligo'
    finding HTML links ... done
    Index-methods                           html  
    IntensityMatrix-methods                 html  
    MAplot-methods                          html  
    Sequences-methods                       html  
    basecontent                             html  
    basicPLM                                html  
Rd warning: /tmp/Rtmp8Kjns9/R.INSTALL6b7835840c78/oligo/man/basicPLM.Rd:42: missing file link 'rcModelPLM'
Rd warning: /tmp/Rtmp8Kjns9/R.INSTALL6b7835840c78/oligo/man/basicPLM.Rd:44: missing file link 'rcModelPLMrr'
Rd warning: /tmp/Rtmp8Kjns9/R.INSTALL6b7835840c78/oligo/man/basicPLM.Rd:45: missing file link 'rcModelPLMrc'
    basicRMA                                html  
    boxplot                                 html  
    chromosome                              html  
    colors                                  html  
    coordinates                             html  
    crlmm                                   html  
    fitProbeLevelModel                      html  
Rd warning: /tmp/Rtmp8Kjns9/R.INSTALL6b7835840c78/oligo/man/fitProbeLevelModel.Rd:9: missing file link 'FeatureSet'
Rd warning: /tmp/Rtmp8Kjns9/R.INSTALL6b7835840c78/oligo/man/fitProbeLevelModel.Rd:17: missing file link 'FeatureSet'
Rd warning: /tmp/Rtmp8Kjns9/R.INSTALL6b7835840c78/oligo/man/fitProbeLevelModel.Rd:50: missing file link 'rma'
Rd warning: /tmp/Rtmp8Kjns9/R.INSTALL6b7835840c78/oligo/man/fitProbeLevelModel.Rd:50: missing file link 'summarizationMethods'
    getAffinitySplineCoefficients           html  
    getBaseProfile                          html  
    getContainer                            html  
    getCrlmmSummaries                       html  
    getNetAffx                              html  
    getNgsColorsInfo                        html  
    getPlatformDesign                       html  
    getProbeInfo                            html  
    hist                                    html  
    image                                   html  
    justSNPRMA                              html  
    list.xysfiles                           html  
    oligo-package                           html  
    oligoDefunct                            html  
    oligoPLM-class                          html  
Rd warning: /tmp/Rtmp8Kjns9/R.INSTALL6b7835840c78/oligo/man/oligoPLM-class.Rd:122: missing file link 'rma'
Rd warning: /tmp/Rtmp8Kjns9/R.INSTALL6b7835840c78/oligo/man/oligoPLM-class.Rd:122: missing file link 'summarize'
    paCalls                                 html  
    plotM-methods                           html  
    pmAllele                                html  
    pmFragmentLength                        html  
    pmPosition                              html  
    pmStrand                                html  
    preprocessTools                         html  
    probeNames                              html  
    read.celfiles                           html  
    read.xysfiles                           html  
    readSummaries                           html  
    rma-methods                             html  
    runDate                                 html  
    sequenceDesignMatrix                    html  
    snprma                                  html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (oligo)
Making 'packages.html' ... done