[med-svn] [r-cran-seqinr] 08/15: Updated version 3.3-3 from 'upstream/3.3-3'

Andreas Tille tille at debian.org
Sat Sep 23 06:55:20 UTC 2017


This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository r-cran-seqinr.

commit 3d31e70f0ea67eb954522184a1b341f9966be1ba
Merge: 86323a2 b00b2c4
Author: Andreas Tille <tille at debian.org>
Date:   Sat Sep 23 08:24:23 2017 +0200

    Updated version 3.3-3 from 'upstream/3.3-3'
    
    with Debian dir 3dd4e834211d19f504227dc7543fbc4495faa056

 DESCRIPTION                                 |   32 +
 MD5                                         |  343 +++
 NAMESPACE                                   |   80 +
 R/AAstat.R                                  |   31 +
 R/ClassSeq.R                                |   84 +
 R/GC.R                                      |  182 ++
 R/PI.R                                      |   47 +
 R/R_socket.R                                |   27 +
 R/acnucclose.R                              |   30 +
 R/acnucopen.R                               |   52 +
 R/al2bp.R                                   |    9 +
 R/allistranks.R                             |   61 +
 R/amb.R                                     |   30 +
 R/as.alignment.R                            |    9 +
 R/as.matrix.alignment.R                     |    8 +
 R/autosocket.R                              |   41 +
 R/baselineabif.R                            |   19 +
 R/bma.R                                     |   20 +
 R/cai.R                                     |   11 +
 R/choosebank.R                              |  153 ++
 R/circle.R                                  |   10 +
 R/clfcd.R                                   |   90 +
 R/clientid.R                                |   21 +
 R/closebank.R                               |   25 +
 R/col2alpha.R                               |    4 +
 R/comp.R                                    |   44 +
 R/consensus.R                               |   42 +
 R/count.R                                   |   38 +
 R/countfreelists.R                          |   31 +
 R/countsubseqs.R                            |   36 +
 R/db.growth.R                               |   89 +
 R/dia.bactgensize.R                         |  208 ++
 R/dist.alignment.R                          |   41 +
 R/dotPlot.R                                 |   32 +
 R/draw.oriloc.R                             |   73 +
 R/draw.rearranged.oriloc.R                  |   57 +
 R/draw.recstat.R                            |  185 ++
 R/extract.breakpoints.R                     |   99 +
 R/extractseqs.R                             |  113 +
 R/fastacc.R                                 |   29 +
 R/gb2fasta.R                                |   39 +
 R/gbk2g2.R                                  |   86 +
 R/gbk2g2.euk.R                              |  153 ++
 R/get.ncbi.R                                |  388 +++
 R/getAnnot.R                                |   44 +
 R/getFrag.R                                 |   47 +
 R/getKeyword.R                              |   51 +
 R/getLength.R                               |   34 +
 R/getLocation.R                             |   56 +
 R/getName.R                                 |   22 +
 R/getSequence.R                             |   73 +
 R/getTrans.R                                |   35 +
 R/getType.R                                 |   31 +
 R/getlistrank.R                             |   47 +
 R/getliststate.R                            |   38 +
 R/gfrag.R                                   |   42 +
 R/ghelp.R                                   |   36 +
 R/isenum.R                                  |   80 +
 R/kaks.R                                    |   81 +
 R/knowndbs.R                                |   48 +
 R/lseqinr.R                                 |    7 +
 R/modifylist.R                              |   90 +
 R/move.R                                    |    9 +
 R/oriloc.R                                  |  234 ++
 R/parser.socket.R                           |   26 +
 R/peakabif.R                                |   68 +
 R/permutation.R                             |   44 +
 R/plot.SeqAcnucWeb.R                        |  110 +
 R/plotPanels.R                              |   22 +
 R/plotabif.R                                |   54 +
 R/plotladder.R                              |   35 +
 R/pmw.R                                     |    1 +
 R/prepgetannots.R                           |   81 +
 R/prettyseq.R                               |   47 +
 R/query.r                                   |  137 +
 R/quitacnuc.R                               |   12 +
 R/read.abif.R                               |  156 ++
 R/read.alignment.R                          |   35 +
 R/read.fasta.R                              |  150 ++
 R/readBins.R                                |   36 +
 R/readPanels.R                              |   42 +
 R/readfirstrec.R                            |   46 +
 R/readsmj.R                                 |   91 +
 R/rearranged.oriloc.R                       |   65 +
 R/recstat.R                                 |   65 +
 R/residuecount.R                            |   33 +
 R/reverse.align.R                           |   86 +
 R/rho.R                                     |   16 +
 R/rot13.R                                   |    6 +
 R/s2n.R                                     |   23 +
 R/savelist.R                                |   71 +
 R/setlistname.R                             |   31 +
 R/splitseq.R                                |   15 +
 R/stresc.R                                  |   21 +
 R/stutterabif.R                             |  109 +
 R/swap.R                                    |    9 +
 R/synonymous.R                              |   74 +
 R/tablecode.R                               |  147 ++
 R/test.co.recstat.R                         |  205 ++
 R/test.li.recstat.R                         |  180 ++
 R/translate.R                               |   74 +
 R/trimSpace.R                               |   11 +
 R/uco.R                                     |  121 +
 R/util.R                                    |   93 +
 R/where.is.this.acc.R                       |   55 +
 R/words.R                                   |    7 +
 R/words.pos.R                               |   14 +
 R/write.fasta.R                             |   39 +
 R/zscore.R                                  |   63 +
 data/AnoukResult.RData                      |  Bin 0 -> 319 bytes
 data/ECH.RData                              |  Bin 0 -> 38356 bytes
 data/EXP.RData                              |  Bin 0 -> 1066 bytes
 data/JLO.RData                              |  Bin 0 -> 39576 bytes
 data/SEQINR.UTIL.RData                      |  Bin 0 -> 1775 bytes
 data/aacost.RData                           |  Bin 0 -> 638 bytes
 data/aaindex.RData                          |  Bin 0 -> 81845 bytes
 data/caitab.RData                           |  Bin 0 -> 941 bytes
 data/chargaff.RData                         |  Bin 0 -> 351 bytes
 data/clustal.RData                          |  Bin 0 -> 422 bytes
 data/datalist                               |   26 +
 data/dinucl.RData                           |  Bin 0 -> 65740 bytes
 data/ec999.RData                            |  Bin 0 -> 317767 bytes
 data/fasta.RData                            |  Bin 0 -> 1028 bytes
 data/gcO2.rda                               |  Bin 0 -> 6076 bytes
 data/gcT.rda                                |  Bin 0 -> 17828 bytes
 data/gs500liz.RData                         |  Bin 0 -> 176 bytes
 data/identifiler.RData                      |  Bin 0 -> 554 bytes
 data/m16j.RData                             |  Bin 0 -> 418892 bytes
 data/mase.RData                             |  Bin 0 -> 543 bytes
 data/msf.RData                              |  Bin 0 -> 838 bytes
 data/pK.RData                               |  Bin 0 -> 322 bytes
 data/phylip.RData                           |  Bin 0 -> 276 bytes
 data/prochlo.RData                          |  Bin 0 -> 412468 bytes
 data/revaligntest.RData                     |  Bin 0 -> 435 bytes
 data/sysdata.rda                            |  Bin 0 -> 1775 bytes
 data/toyaa.RData                            |  Bin 0 -> 164 bytes
 data/toycodon.RData                         |  Bin 0 -> 195 bytes
 data/waterabs.RData                         |  Bin 0 -> 568 bytes
 inst/CITATION                               |   15 +
 inst/abif/1_0000206138_C01_005.fsa          |  Bin 0 -> 109299 bytes
 inst/abif/1_FAC321_0000205983_B02_004.fsa   |  Bin 0 -> 111777 bytes
 inst/abif/2_0000206138_C01_005.fsa          |  Bin 0 -> 109387 bytes
 inst/abif/2_FAC321_0000205983_B02_004.fsa   |  Bin 0 -> 114833 bytes
 inst/abif/AmpFLSTR_Bins_v1.txt              |    1 +
 inst/abif/AmpFLSTR_Panels_v1.txt            |    1 +
 inst/abif/NGM_Bins.txt                      | 3689 +++++++++++++++++++++++++++
 inst/abif/NGM_Pa.txt                        |  215 ++
 inst/abif/Promega_Bins_v1.txt               |    1 +
 inst/abif/Promega_Panels_v1.txt             |    1 +
 inst/abif/Prototype_PowerPlex_EP01_Bins.txt |    1 +
 inst/abif/Prototype_PowerPlex_EP01_Pa.txt   |    1 +
 inst/abif/samplefsa2ps.fsa                  |  Bin 0 -> 218313 bytes
 inst/sequences/Anouk.fasta                  |   70 +
 inst/sequences/DarrenObbard.fasta           |    6 +
 inst/sequences/ECOUNC.fsa                   |  133 +
 inst/sequences/UBIQUITIN.mase               |   19 +
 inst/sequences/ame1.gbk                     |  581 +++++
 inst/sequences/bb.acc                       |   20 +
 inst/sequences/bb.kwd                       |   20 +
 inst/sequences/bb.mne                       |   20 +
 inst/sequences/bb.sp                        |   20 +
 inst/sequences/bordetella.fasta             |   38 +
 inst/sequences/bordetella.pep.aln           |   22 +
 inst/sequences/ct.bfa                       |  Bin 0 -> 521283 bytes
 inst/sequences/ct.fasta.gz                  |  Bin 0 -> 325963 bytes
 inst/sequences/ct.gbk.gz                    |  Bin 0 -> 678534 bytes
 inst/sequences/ct.predict                   |  948 +++++++
 inst/sequences/ecolicgpe5.fasta             |    6 +
 inst/sequences/gopher.fasta                 |   56 +
 inst/sequences/gopher.names                 |    8 +
 inst/sequences/hannah.txt                   | 1784 +++++++++++++
 inst/sequences/humanMito.fasta              |  283 ++
 inst/sequences/input.dat                    | 2835 ++++++++++++++++++++
 inst/sequences/input.out                    |  112 +
 inst/sequences/legacy.fasta                 |   30 +
 inst/sequences/louse.fasta                  |   57 +
 inst/sequences/louse.names                  |    8 +
 inst/sequences/malM.fasta                   |   17 +
 inst/sequences/ortho.fasta                  |   30 +
 inst/sequences/scuco.txt                    |  112 +
 inst/sequences/seqAA.fasta                  |    5 +
 inst/sequences/smallAA.fasta                |    2 +
 inst/sequences/smallAA.fasta.gz             |  Bin 0 -> 85 bytes
 inst/sequences/someORF.fsa                  |  453 ++++
 inst/sequences/test.aln                     |   27 +
 inst/sequences/test.mase                    |   19 +
 inst/sequences/test.msf                     |   57 +
 inst/sequences/test.phylip                  |   12 +
 man/AAstat.Rd                               |   33 +
 man/AnoukResult.Rd                          |   29 +
 man/ECH.Rd                                  |   37 +
 man/EXP.Rd                                  |   99 +
 man/GC.Rd                                   |  202 ++
 man/JLO.Rd                                  |   49 +
 man/SEQINR.UTIL.Rd                          |   27 +
 man/SeqAcnucWeb.Rd                          |   38 +
 man/SeqFastaAA.Rd                           |   41 +
 man/SeqFastadna.Rd                          |   43 +
 man/SeqFrag.Rd                              |   37 +
 man/a.Rd                                    |   55 +
 man/aaa.Rd                                  |   53 +
 man/aacost.Rd                               |   70 +
 man/aaindex.Rd                              |  618 +++++
 man/acnucopen.Rd                            |   79 +
 man/al2bp.Rd                                |   69 +
 man/alllistranks.Rd                         |   55 +
 man/amb.Rd                                  |   53 +
 man/as.alignment.Rd                         |   38 +
 man/as.matrix.alignment.Rd                  |   26 +
 man/autosocket.Rd                           |   28 +
 man/baselineabif.Rd                         |   36 +
 man/bma.Rd                                  |   42 +
 man/c2s.Rd                                  |   26 +
 man/cai.Rd                                  |   95 +
 man/caitab.Rd                               |   73 +
 man/chargaff.Rd                             |  131 +
 man/choosebank.Rd                           |   97 +
 man/circle.Rd                               |   45 +
 man/closebank.Rd                            |   27 +
 man/clustal.Rd                              |   13 +
 man/col2alpha.Rd                            |   49 +
 man/comp.Rd                                 |   64 +
 man/computePI.Rd                            |   41 +
 man/consensus.Rd                            |  103 +
 man/count.Rd                                |   95 +
 man/countfreelists.Rd                       |   41 +
 man/countsubseqs.Rd                         |   39 +
 man/crelistfromclientdata.Rd                |   93 +
 man/dia.bactgensize.Rd                      |   83 +
 man/dinucl.Rd                               |   65 +
 man/dist.alignment.Rd                       |   41 +
 man/dotPlot.Rd                              |   88 +
 man/dotchart.uco.Rd                         |   60 +
 man/draw.oriloc.Rd                          |   69 +
 man/draw.rearranged.oriloc.Rd               |   66 +
 man/draw.recstat.Rd                         |   34 +
 man/ec999.Rd                                |   36 +
 man/extract.breakpoints.Rd                  |   91 +
 man/extractseqs.Rd                          |   89 +
 man/fasta.Rd                                |   10 +
 man/fastacc.Rd                              |  196 ++
 man/figures/aka.pdf                         |  Bin 0 -> 17307 bytes
 man/figures/chargaff.png                    |  Bin 0 -> 79475 bytes
 man/figures/gcskewmbe96.pdf                 |  Bin 0 -> 29632 bytes
 man/figures/introduction-dbg.pdf            |  Bin 0 -> 12554 bytes
 man/figures/lncs2004.pdf                    |  Bin 0 -> 54378 bytes
 man/figures/waterabs.jpg                    |  Bin 0 -> 59360 bytes
 man/gb2fasta.Rd                             |   40 +
 man/gbk2g2.Rd                               |   38 +
 man/gbk2g2.euk.Rd                           |   38 +
 man/gcO2.Rd                                 |   21 +
 man/gcT.Rd                                  |   34 +
 man/get.db.growth.Rd                        |   61 +
 man/get.ncbi.Rd                             |   41 +
 man/getAnnot.Rd                             |   88 +
 man/getFrag.Rd                              |   59 +
 man/getKeyword.Rd                           |   53 +
 man/getLength.Rd                            |   58 +
 man/getLocation.Rd                          |   54 +
 man/getName.Rd                              |   57 +
 man/getSequence.Rd                          |   79 +
 man/getTrans.Rd                             |  118 +
 man/getType.Rd                              |   30 +
 man/getlistrank.Rd                          |   46 +
 man/getliststate.Rd                         |   51 +
 man/gfrag.Rd                                |   37 +
 man/ghelp.Rd                                |   43 +
 man/gs500liz.Rd                             |   43 +
 man/identifiler.Rd                          |   27 +
 man/isenum.Rd                               |   61 +
 man/kaks.Rd                                 |  101 +
 man/knowndbs.Rd                             |   52 +
 man/lseqinr.Rd                              |   23 +
 man/m16j.Rd                                 |  101 +
 man/mase.Rd                                 |   10 +
 man/modifylist.Rd                           |   85 +
 man/move.Rd                                 |   43 +
 man/msf.Rd                                  |    9 +
 man/n2s.Rd                                  |   40 +
 man/oriloc.Rd                               |  147 ++
 man/pK.Rd                                   |   88 +
 man/parser.socket.Rd                        |   28 +
 man/peakabif.Rd                             |   68 +
 man/permutation.Rd                          |   67 +
 man/phylip.Rd                               |   10 +
 man/plot.SeqAcnucWeb.Rd                     |   35 +
 man/plotPanels.Rd                           |   26 +
 man/plotabif.Rd                             |   75 +
 man/plotladder.Rd                           |   59 +
 man/pmw.Rd                                  |   80 +
 man/prepgatannots.Rd                        |   73 +
 man/prettyseq.Rd                            |   35 +
 man/print.SeqAcnucWeb.Rd                    |   32 +
 man/print.qaw.Rd                            |   30 +
 man/prochlo.Rd                              |  119 +
 man/query.Rd                                |  116 +
 man/read.abif.Rd                            |   80 +
 man/read.alignment.Rd                       |  116 +
 man/read.fasta.Rd                           |  177 ++
 man/readBins.Rd                             |   56 +
 man/readPanels.Rd                           |   59 +
 man/readfirstrec.Rd                         |   56 +
 man/readsmj.Rd                              |   40 +
 man/rearranged.oriloc.Rd                    |   97 +
 man/recstat.Rd                              |   62 +
 man/residuecount.Rd                         |   36 +
 man/revaligntest.Rd                         |   22 +
 man/reverse.align.Rd                        |  111 +
 man/rot13.Rd                                |   34 +
 man/s2c.Rd                                  |   27 +
 man/s2n.Rd                                  |   65 +
 man/savelist.Rd                             |   45 +
 man/seqinr-package.Rd                       |   20 +
 man/setlistname.Rd                          |   45 +
 man/splitseq.Rd                             |   41 +
 man/stresc.Rd                               |   27 +
 man/stutterabif.Rd                          |   83 +
 man/swap.Rd                                 |   54 +
 man/syncodons.Rd                            |  113 +
 man/synsequence.Rd                          |   29 +
 man/tablecode.Rd                            |   46 +
 man/test.co.recstat.Rd                      |   48 +
 man/test.li.recstat.Rd                      |   49 +
 man/toyaa.Rd                                |   29 +
 man/toycodon.Rd                             |   20 +
 man/translate.Rd                            |  128 +
 man/trimSpace.Rd                            |   74 +
 man/uco.Rd                                  |  124 +
 man/ucoweight.Rd                            |   28 +
 man/waterabs.Rd                             |   95 +
 man/where.is.this.acc.Rd                    |   31 +
 man/words.Rd                                |   49 +
 man/words.pos.Rd                            |   49 +
 man/write.fasta.Rd                          |   44 +
 man/zscore.Rd                               |  106 +
 src/Makevars                                |    2 +
 src/Makevars.win                            |    2 +
 src/alignment.c                             |  917 +++++++
 src/alignment.h                             |   33 +
 src/fastacc.c                               |   39 +
 src/getzlibsock.c                           |  244 ++
 src/kaks.c                                  | 1125 ++++++++
 src/util.c                                  |   72 +
 src/zsockr.c                                |  169 ++
 344 files changed, 30458 insertions(+)

-- 
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