[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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