DECIPHER

Package: DECIPHER
Type: Package
Title: Tools for curating, analyzing, and manipulating biological
sequences
Version: 2.0.2
Date: 2016-06-07
Author: Erik Wright
Maintainer: Erik Wright <DECIPHER@cae.wisc.edu>
biocViews: Clustering, Genetics, Sequencing, DataImport, Visualization,
Microarray, QualityControl, qPCR, Alignment, WholeGenome,
Microbiome
Description: A toolset for deciphering and managing biological sequences.
Depends: R (>= 3.3.0), Biostrings (>= 2.35.12), RSQLite (>= 1.0.0),
stats, parallel
Imports: methods, DBI, S4Vectors, IRanges, XVector
LinkingTo: Biostrings, RSQLite, S4Vectors, IRanges, XVector
License: GPL-3
NeedsCompilation: yes
Packaged: 2016-06-08 03:03:29 UTC; biocbuild

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'DECIPHER' ...
** libs
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c AlignProfiles.c -o AlignProfiles.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c AppendXStringSets.c -o AppendXStringSets.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c AssignIndels.c -o AssignIndels.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -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/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c CalculateDeltaG.c -o CalculateDeltaG.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c CalculateFISH.c -o CalculateFISH.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c ChainSegments.c -o ChainSegments.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c ClusterML.c -o ClusterML.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c ClusterNJ.c -o ClusterNJ.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c ClusterUPGMA.c -o ClusterUPGMA.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c CommonGaps.c -o CommonGaps.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c Compositions.c -o Compositions.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c Compression.c -o Compression.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c ConsensusSequence.c -o ConsensusSequence.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c ConsolidateGaps.c -o ConsolidateGaps.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c DesignProbes.c -o DesignProbes.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c Diff.c -o Diff.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c DistanceMatrix.c -o DistanceMatrix.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c EnumerateSequence.c -o EnumerateSequence.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c ExpandAmbiguities.c -o ExpandAmbiguities.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c FindFrameshifts.c -o FindFrameshifts.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c Import.c -o Import.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c InsertGaps.c -o InsertGaps.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c IntDist.c -o IntDist.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c MeltPolymer.c -o MeltPolymer.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c MultiMatch.c -o MultiMatch.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c NNLS.c -o NNLS.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c Order.c -o Order.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c PredictHEC.c -o PredictHEC.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c R_init_decipher.c -o R_init_decipher.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c RemoveGaps.c -o RemoveGaps.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c ReplaceChars.c -o ReplaceChars.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c SubsetXStringSet.c -o SubsetXStringSet.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c TerminalMismatch.c -o TerminalMismatch.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -fpic  -g -O2  -c Translate.c -o Translate.o
gcc -I/home/ddbj/local/lib64/R/include -DNDEBUG  -I/usr/local/include -I"/home/ddbj/local/lib64/R/library/Biostrings/include" -I"/home/ddbj/local/lib64/R/library/RSQLite/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"  -fopenmp -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 DECIPHER.so AlignProfiles.o AppendXStringSets.o AssignIndels.o Biostrings_stubs.o CalculateDeltaG.o CalculateFISH.o ChainSegments.o ClusterML.o ClusterNJ.o ClusterUPGMA.o CommonGaps.o Compositions.o Compression.o ConsensusSequence.o ConsolidateGaps.o DesignProbes.o Diff.o DistanceMatrix.o EnumerateSequence.o ExpandAmbiguities.o FindFrameshifts.o Import.o InsertGaps.o IntDist.o MeltPolymer.o MultiMatch.o NNLS.o Order.o PredictHEC.o R_init_decipher.o RemoveGaps.o ReplaceChars.o SubsetXStringSet.o TerminalMismatch.o Translate.o XVector_stubs.o -fopenmp -L/home/ddbj/local/lib64/R/lib -lR
installing to /home/ddbj/local/lib64/R/library/DECIPHER/libs
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'DECIPHER'
    finding HTML links ... done
    Add2DB                                  html  
    AdjustAlignment                         html  
    AlignDB                                 html  
    AlignProfiles                           html  
    AlignSeqs                               html  
    AlignSynteny                            html  
    AlignTranslation                        html  
    AmplifyDNA                              html  
    Array2Matrix                            html  
    BrowseDB                                html  
    BrowseSeqs                              html  
    CalculateEfficiencyArray                html  
    CalculateEfficiencyFISH                 html  
    CalculateEfficiencyPCR                  html  
    Codec                                   html  
    ConsensusSequence                       html  
    CorrectFrameshifts                      html  
    CreateChimeras                          html  
    DB2Seqs                                 html  
    DECIPHER-package                        html  
    DesignArray                             html  
    DesignPrimers                           html  
    DesignProbes                            html  
    DesignSignatures                        html  
    DigestDNA                               html  
    Disambiguate                            html  
    DistanceMatrix                          html  
    FindChimeras                            html  
    FindSynteny                             html  
    FormGroups                              html  
    HEC_MI                                  html  
    IdClusters                              html  
    IdConsensus                             html  
    IdLengths                               html  
    IdentifyByRank                          html  
    MIQS                                    html  
    MODELS                                  html  
    MaskAlignment                           html  
    MeltDNA                                 html  
    NNLS                                    html  
    OrientNucleotides                       html  
    PredictHEC                              html  
    RESTRICTION_ENZYMES                     html  
    ReadDendrogram                          html  
    SearchDB                                html  
    Seqs2DB                                 html  
    StaggerAlignment                        html  
    Synteny-class                           html  
    TerminalChar                            html  
    TileSeqs                                html  
    WriteDendrogram                         html  
    deltaGrules                             html  
    deltaHrules                             html  
    deltaSrules                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (DECIPHER)
Making 'packages.html' ... done