Change log for debian-med package in Ubuntu

debian-med (3.8.1) unstable; urgency=medium

  * Standards-Version: 4.6.2
  * Update dependencies to fit Bookworm release status

  * start of automatic changelog entry *
  
  * Changes in metapackage dependencies
   -med-bio-dev
    added:
      Recommends:  libwfa2-dev

 -- Andreas Tille <email address hidden>  Mon, 22 May 2023 14:04:33 +0200

Available diffs

• diff from 3.8 to 3.8.1 (12.6 KiB)

debian-med (3.8) unstable; urgency=medium

  * nifti2dicom, qnifti2dicom, libsimpleitk1-dev, python3-simpleitk removed
    from Debian thus removed from tasks
  * Suggests: libgatk-native-bindings-java
  * Replace: msxpertsuite by massxpert, minexpert2 (see #1024780)

  * start of automatic changelog entry * 
  
  * Changes in metapackage dependencies
   -med-bio
    added:
      Recommends:  minexpert2, snippy, metaeuk, any2fasta, btllib-tools,
                   savvy-util, comet-ms, muscle3, pyfastx, seqan-needle,
                   seqan-raptor, massxpert
    removed:
      Recommends:  sequenceconverter.app, msxpertsuite
   -med-bio-dev
    added:
      Recommends:  libbio-db-seqfeature-perl, python3-pyfastx,
                   libbiojava6-java, python3-bioframe
      Suggests:    libsavvy-dev, libgatk-native-bindings-java, libbtllib-dev,
                   python3-cgelib, python3-conda-package-streaming
    removed:
      Recommends:  libbiojava5-java
   -med-bio-phylogeny
    added:
      Recommends:  muscle3
   -med-cloud
    added:
      Recommends:  muscle3
   -med-covid-19
    added:
      Recommends:  muscle3
   -med-imaging
    removed:
      Recommends:  qnifti2dicom, nifti2dicom
   -med-imaging-dev
    added:
      Recommends:  python3-bioxtasraw
    removed:
      Recommends:  python3-simpleitk, libsimpleitk1-dev
   -med-psychology
    added:
      Recommends:  python3-bioxtasraw

 -- Andreas Tille <email address hidden>  Wed, 08 Feb 2023 11:04:38 +0100

Available diffs

• diff from 3.7.3 to 3.8 (17.1 KiB)

debian-med (3.7.3) unstable; urgency=medium

  * Build-Depends-Indep: blends-dev (>= 0.7.5~)
    Closes: #1012341
  * dicompyler removed from Debian thus from oncology task
  * zalign removed from Debian
  * Standards-Version: 4.6.1

  * start of automatic changelog entry * 
  
  * Changes in metapackage dependencies
   -med-bio
    added:
      Recommends:  ska, genomicsdb-tools, nxtrim, fastq-pair, unikmer,
                   xpore, abpoa, surpyvor, metaphlan, pullseq, pyensembl,
                   terraphast
    removed:
      Recommends:  metaphlan2, zalign, falcon
   -med-bio-dev
    added:
      Recommends:  python3-pyabpoa, libbiojava5-java, ont-fast5-api,
                   python3-slow5, python3-gtfparse, libslow5-dev,
                   python3-propka, python3-pyspoa
      Suggests:   libgatk-fermilite-java, libgatk-fermilite-jni,
                  libvbz-hdf-plugin-dev, libterraces-dev,
                  libcapsule-maven-nextflow-java, libgatk-bwamem-java,
                  libicb-utils-java, libgatk-bwamem-jni, python3-bioblend,
                  libgenomicsdb-dev, libgenomicsdb-java, capsule-nextflow,
                  libbiosoup-dev
   -med-cloud
    removed:
      Recommends:  zalign
   -med-imaging
    added:
      Recommends:  heudiconv
      Suggests:  orthanc-neuro
   -med-imaging-dev
    added:
      Recommends:  python3-dcmstack
    removed:
      Suggests:  libvtk7-dev
   -med-oncology
    removed:
      Recommends:  dicompyler
   -med-psychology
    added:
      Recommends:  orthanc-neuro
   -med-tools
    added:
      Recommends:  cycle
    removed:
      Suggests:  cycle

 -- Andreas Tille <email address hidden>  Fri, 28 Oct 2022 10:12:35 +0200

Available diffs

• diff from 3.7.2 to 3.7.3 (17.1 KiB)

debian-med (3.7.2) unstable; urgency=medium

  * opensurgsim is removed from Debian
  * substitute r-cran-gprofiler by r-cran-gprofiler2 (see #994212)

  * start of automatic changelog entry * 
  
  * Changes in metapackage dependencies
   -med-bio
    added:
      Recommends:  megan-ce, twopaco, lamassemble, ntcard, snpsift, mcaller,
                   dnarrange, megadepth, r-bioc-megadepth, provean,
                   libpwiz-tools, rockhopper, diann
      Suggests:  r-cran-gprofiler2
    removed:
      Suggests:  mcaller, r-cran-gprofiler
   -med-bio-dev
    added:
      Recommends:  libpwiz-dev, python3-cogent3, r-cran-gprofiler2
    removed:
      Recommends:  r-cran-gprofiler
      Suggests:  python3-cogent3, python3-mcaller
   -med-covid-19
    added:
      Recommends:  nf-core-artic
    removed:
      Recommends:  artic
   -med-epi
    added:
      Recommends:  r-cran-prevalence
   -med-imaging
    removed:
      Recommends:  python3-mvpa2
   -med-imaging-dev
    added:
      Recommends:  libopencv-dev, python3-torchvision
    removed:
      Recommends:  python3-mvpa2, pytorch-vision, libopensurgsim-dev, libcv-dev

 -- Andreas Tille <email address hidden>  Fri, 03 Jun 2022 12:04:09 +0200

Available diffs

• diff from 3.7.1 to 3.7.2 (15.6 KiB)

debian-med (3.7.1) unstable; urgency=medium

  * Remove libbiod-dev
  * Remove r-cran-rsgcc (see #1002794)
  * Remove r-other-hms-dbmi-spp since it is r-cran-spp
  * Standards-Version: 4.6.0

  * start of automatic changelog entry * 
  
  * Changes in metapackage dependencies
   -med-bio
    added:
      Recommends: r-bioc-mofa2, igblast, tipp, haploview, cutesv,
                  python3-cogent3
      Suggests:  r-bioc-isoformswitchanalyzer, catfishq, nano-snakemake,
                 tandem-genotypes, illustrate
    removed:
      Recommends: hinge, r-bioc-pcamethods, python3-cogent,
                  r-other-hms-dbmi-spp, haploview-cran-amap, compclust,
                  gassst, ccs, ncbi-igblast
      Suggests:  r-cran-rsgcc, r-bioc-org.ce.eg.db, r-bioc-org.rn.eg.db
   -med-bio-dev
    added:
      Recommends: goby-java, python3-cigar, python3-pangolearn,
                  python3-compclust
    removed:
      Recommends: libgoby-java, r-other-hms-dbmi-spp, pangolearn, libbiod-dev,
                  python3-hyphy
      Suggests:  r-cran-rsgcc
   -med-bio-ngs
    added:
      Recommends:  q2cli
      Suggests:  r-bioc-mofa2, r-bioc-isoformswitchanalyzer
   -med-covid-19
    added:
      Recommends:  tipp, python3-idseq-dag, r-cran-kernelheaping
    removed:
      Recommends:  idseq-dag
   -med-epi
    added:
      Recommends:  r-cran-kernelheaping
   -med-imaging
    added:
      Suggests:  illustrate
   -med-imaging-dev
    added:
      Recommends:  libvtk9-dev, libinsighttoolkit5-dev
      Suggests:  libvtk7-dev
    removed:
      Recommends:  libvtk7-dev, libinsighttoolkit4-dev
      Suggests:  libvtk6-dev

 -- Andreas Tille <email address hidden>  Wed, 12 Jan 2022 20:44:28 +0100

Available diffs

• diff from 3.7 to 3.7.1 (16.1 KiB)

debian-med (3.7) unstable; urgency=medium

  * Re-render metapackages according the package pool in bullseye

  * start of automatic changelog entry * 
  
  * Changes in metapackage dependencies
   -med-bio
    added:
      Recommends:  bio-vcf, uncalled, covpipe, fastani, bioawk, bamclipper
      Suggests:  r-bioc-structuralvariantannotation
   -med-bio-dev
    added:
      Recommends:  libbio-db-ncbihelper-perl, libbio-variation-perl,
                   python3-scanpy, libbio-db-biofetch-perl, libbio-db-embl-perl,
                   python3-wdlparse, pangolearn, libpdb-redo-dev
      Suggests:  r-bioc-structuralvariantannotation
   -med-covid-19
    added:
      Recommends:  uncalled, covpipe, fastani, python3-scanpy, nthash,
                   bamclipper
   -med-epi
    added:
      Suggests:  python3-epimodels
   -med-imaging
    added:
      Recommends:  python3-nipype, bart-cuda
    removed:
      Suggests:  python-nipype
   -med-imaging-dev
    added:
      Recommends:  python3-nipype, python3-brian, python3-vigra
    removed:
      Suggests:  python-vigra, python-nipype

 -- Andreas Tille <email address hidden>  Mon, 03 May 2021 21:28:56 +0200

Available diffs

• diff from 3.5.1ubuntu1 (in Ubuntu) to 3.7 (71.6 KiB)

debian-med (3.5.1ubuntu1) groovy; urgency=medium

  * debian/control: tifffile is now available as python3-tifffile.

 -- Łukasz 'sil2100' Zemczak <email address hidden>  Tue, 16 Jun 2020 16:31:53 +0200

Available diffs

• diff from 3.5.1 (in Debian) to 3.5.1ubuntu1 (792 bytes)

debian-med (3.5.1) unstable; urgency=medium

  * Drop fastx-toolkit and libgtextutils since unmaintained and
    libgtextutils has issued with gcc9
  * Drop mgltools-pmv which is constantly broken for several years

  * start of automatic changelog entry * 
  
  * Changes in metapackage dependencies
   -med-bio
    added:
      Recommends:  r-bioc-geoquery, r-cran-wgcna
    removed:
      Recommends:  mgltools-pmv, r-other-wgcna, fastx-toolkit
   -med-bio-dev
    added:
      Suggests:  r-bioc-geoquery
    removed:
      Suggests:  libgtextutils-dev
   -med-bio-ngs
    removed:
      Recommends:  fastx-toolkit
   -med-cloud
    removed:
      Recommends:  fastx-toolkit

 -- Andreas Tille <email address hidden>  Fri, 06 Dec 2019 18:24:39 +0100

Available diffs

• diff from 3.5 to 3.5.1 (10.3 KiB)

debian-med (3.5) unstable; urgency=medium

  * Python2 packages only suggested
    Closes: #945659
  * Remove tophat since deprecated by upstream
  * giira from Recommends to Suggests since it needs tophat
  * lintian-override for field-too-long Recommends

  * start of automatic changelog entry * 
  
  * Changes in metapackage dependencies
   -med-bio
    added:
      Recommends: idefix, resfinder, purple, pufferfish
      Suggests:   skewer, giira
    removed:
      Recommends: giira, tophat
      Suggests:   mobyle-programs, mobyle-tutorials, mobyle
   -med-bio-dev
    added:
      Recommends: python3-dnaio, python3-pyani, biobambam2, libcdk-java
      Suggests:   r-bioc-dada2, python-pbcommand, python-pbh5tools,
                  r-cran-dt, r-cran-proc, python-kineticstools, libfast-perl,
                  python-corepywrap, libmaus2-dev, python-pbcore,
                  r-cran-pcapp, r-cran-dynamictreecut, python-cogent,
                  r-cran-kaos
    removed:
      Recommends: python-pbh5tools, python-pbcommand, python-kineticstools,
                  python-corepywrap, libmaus2-dev, python-pbcore,
                  r-cran-dynamictreecut, python-cogent
   -med-bio-ngs
    removed:
      Recommends: tophat
   -med-cloud
    added:
      Recommends: hisat2
      Suggests:   python-cogent
    removed:
      Recommends: python-cogent, tophat
   -med-imaging
    added:
      Suggests:   python-nipype, python-nitime, python-dipy, python-nipy
    removed:
      Recommends: python-nipype, python-nitime, python-dipy, python-nipy
      Suggests:   tifffile
   -med-imaging-dev
    added:
      Suggests:   python-vigra, python-nipype, python-cfflib, python-nitime,
                  python-pyxnat, python-nipy, python-vmtk, python-dipy
    removed:
      Recommends: python-vigra, python-nipype, python-cfflib, python-nitime,
                  python-pyxnat, python-nipy, python-vmtk, python-dipy
   -med-psychology
    added:
      Suggests:  python-pyepl
    removed:
      Recommends:  python-pypsignifit, python-pyepl

 -- Andreas Tille <email address hidden>  Thu, 28 Nov 2019 09:25:44 +0100

Available diffs

• diff from 3.4 to 3.5 (14.6 KiB)

debian-med (3.4) unstable; urgency=medium

  * Standards-Version: 4.4.1
  * Use debhelper-compat
  * Re-render dependencies without Python2 packages

  * start of automatic changelog entry * 
  
  * Changes in metapackage dependencies
   -med-bio
    added:
      Recommends:  python3-deeptoolsintervals, skesa, python3-orange, vg,
                   mmseqs2, mindthegap, kaptive, r-cran-tsne,
                   python3-deeptools, r-cran-seurat, python3-cogent,
                   kleborate, python3-reaper, python3-treetime, pizzly,
                   trim-galore, pigx-scrnaseq, pigx-rnaseq,
                   r-bioc-multiassayexperiment, wham-align, r-other-wgcna,
                   r-bioc-mofa, seqcluster, r-cran-kaos, r-cran-drinsight
      Suggests:  r-bioc-tximport, r-bioc-qusage, python3-pyflow,
                 python3-alignlib, r-cran-corrplot, r-cran-fitdistrplus,
                 r-cran-dynamictreecut, python3-loompy, strelka,
                 r-cran-gprofiler, python3-py2bit, r-cran-sctransform
    removed:
      Recommends:  python-orange, python-treetime, python-reaper, python-cogent
   -med-bio-dev
    added:
      Recommends:  python3-roadrunner, python3-deeptoolsintervals,
                   r-other-hms-dbmi-spp, python3-loompy, python3-py2bit,
                   r-cran-rotl, r-cran-seqinr, libseqan2-dev, r-cran-boolnet,
                   r-other-apmswapp, r-cran-vegan, r-cran-tsne, gffread,
                   python3-deeptools, r-cran-seurat, r-cran-corrplot,
                   r-cran-fitdistrplus, r-cran-qqman, r-cran-metamix,
                   r-cran-pscbs, r-cran-pheatmap, r-cran-sctransform,
                   r-cran-adephylo, r-cran-phangorn, r-cran-distory,
                   python3-htseq, libmaus2-dev, python3-rdkit, r-cran-samr,
                   r-cran-webgestaltr, python3-freecontact, libseqan3-dev,
                   r-cran-rentrez, r-cran-adegenet, r-cran-dynamictreecut,
                   r-cran-gprofiler, r-cran-forecast, libgclib,
                   python3-biom-format, r-cran-drinsight
      Suggests:  r-cran-rann, r-bioc-biostrings, r-bioc-deseq2,
                 r-bioc-mergeomics, r-cran-metap, r-bioc-qusage,
                 python3-pyflow, python3-pycosat, r-bioc-metagenomeseq,
                 r-bioc-annotate, r-bioc-cner, r-bioc-geneplotter,
                 r-bioc-ensembldb, r-bioc-rentrez, r-bioc-tximport,
                 r-bioc-rtracklayer, r-bioc-annotationhub, r-bioc-ebseq,
                 r-bioc-go.db, r-bioc-limma, r-cran-ica, r-bioc-pcamethods,
                 r-bioc-savr, r-cran-rsvd, python3-alignlib,
                 r-cran-future.batchtools, r-bioc-tfbstools, r-bioc-bitseq,
                 r-bioc-cummerbund, r-bioc-multiassayexperiment, r-bioc-gviz,
                 r-bioc-genefilter, r-bioc-phyloseq, r-bioc-impute,
                 r-bioc-aroma.light, r-cran-future.apply, r-bioc-mofa,
                 r-bioc-dnacopy
    removed:
      Recommends:  python-htseq, python-mmtk, python-rdkit, python-screed,
                   python-biom-format, python-roadrunner, python-freecontact
      Suggests:  python-pyflow, r-cran-rentrez
   -med-bio-ngs
    added:
      Recommends:  wham-align
   -med-cloud
    removed:
      Recommends:  python-biopython
   -med-data
    added:
      Recommends:  python3-hl7
      Suggests:  oscar
    removed:
      Recommends:  python-hl7
   -med-epi
    added:
      Recommends:  python3-treetime
    removed:
      Recommends:  python-treetime
   -med-imaging
    added:
      Recommends:  python3-nibabel, python3-mvpa2, python3-dicom,
                   python3-surfer, tifffile
    removed:
      Recommends:  python-surfer, python-mvpa2, python-dicom,
                   python-nibabel, python-tifffile
   -med-imaging-dev
    added:
      Recommends:  python3-mia, python3-mvpa2, python3-dicom,
                   python3-openslide, python3-gdcm, python3-imageio,
                   python3-mne, python3-nibabel
      Suggests:  tifffile
    removed:
      Recommends:  python-mia | python3-mia, python-gdcm, python-mne,
                   python-mvpa2, python-dicom, python-nibabel,
                   python-imageio, python-openslide
      Suggests:  python-libavg, python-tifffile
   -med-physics
    added:
      Suggests:  python3-multipletau
    removed:
      Suggests:  python-multipletau
   -med-practice
    added:
      Recommends:  oscar
   -med-psychology
    removed:
      Suggests:  python-visionegg
   -med-tools
    added:
      Recommends:  python3-fitbit
      Suggests:  oscar
    removed:
      Recommends:  python-clips, python-fitbit

 -- Andreas Tille <email address hidden>  Sat, 05 Oct 2019 12:02:38 +0200

Available diffs

• diff from 3.3 to 3.4 (18.6 KiB)

debian-med (3.3) unstable; urgency=medium

  * Re-render tasks with Buster release state

  * start of automatic changelog entry * 
  
  * Changes in metapackage dependencies
   -med-bio
    added:
      Recommends: pilercr, mosdepth, quast, r-cran-webgestaltr, ragout,
                  kraken2, gffread, filtlong, umis, sailfish, sibelia,
                  atropos, braker, virulencefinder, vcfanno, biobambam2,
                  python3-pybel, kmerresistance, optitype, spaln, kma,
                  stringtie, oncofuse, optimir, kallisto, sina, dendroscope,
                  multiqc, python3-geneimpacts, bismark
      Suggests:   r-cran-forecast
    removed:
      Recommends: pybel
      Suggests:   melting-gui
   -med-bio-dev
    added:
      Recommends: libbio-samtools-perl, libbio-asn1-entrezgene-perl,
                  libnexml-java, libbio-tools-run-alignment-clustalw-perl,
                  libbigwig-dev, libbio-tools-phylo-paml-perl,
                  libbio-chado-schema-perl, python3-cgecore, libbio-scf-perl,
                  python3-mirtop, libbio-tools-run-alignment-tcoffee-perl,
                  python3-pybel
      Ignore:     golang-github-biogo-hts-dev
   -med-bio-ngs
    added:
      Recommends: kraken2, stringtie
   -med-cms
    added:
      Recommends: xnat
    removed:
      Suggests:   xnat
   -med-imaging
    added:
      Recommends: xnat
    removed:
      Suggests:   xnat
   -med-imaging-dev
    added:
      Recommends: libvtk7-dev
      Suggests:   libvtk6-dev
    removed:
      Recommends:  libvtk6-dev
   -med-psychology
    added:
      Recommends:  r-cran-psychometric, r-cran-psych, r-cran-psyphy,
                   r-cran-psychotree
    removed:
      Recommends:  psychotree, psychometric, miscpsycho, psyphy, psych

 -- Andreas Tille <email address hidden>  Fri, 25 Jan 2019 14:49:50 +0100

Available diffs

• diff from 3.2 to 3.3 (16.0 KiB)

debian-med (3.2) unstable; urgency=medium

  * Fix broken reference to alioth
  * Standards-Version: 4.3.0
  * debhelper 12
  * Versioned Build-Depends: blends-dev (>= 0.7.2~)
  * Add missing ${misc:Depends}

  * start of automatic changelog entry * 
  
  * Changes in metapackage dependencies
   -med-bio
    added:
      Recommends:  r-cran-sdmtools, delly, python3-pybedtools, r-cran-tcr,
                   qutemol, r-cran-tigger, bax2bam, python3-gffutils,
                   vdjtools, r-cran-shazam, r-cran-alakazam, gramalign,
                   igor, deepbinner, python3-sqt, minimap2, sourmash,
                   samblaster, murasaki | murasaki-mpi, biosyntax, paipline,
                   pyvcf, r-bioc-cner, igdiscover, fastp, ncbi-igblast,
                   pybel, jellyfish1, minimac4, lambda-align2, sweed,
                   viewmol, seq-seq-pan, yaha, python3-biomaj3-daemon,
                   changeo, mirtop, python3-presto, cct, unanimity,
                   plasmidseeker
    removed:
      Recommends:  hilbertvisgui, decipher, hyphygui, jstreeview,
                   biosyntax-gedit, python3-biomaj3, spice, rosetta,
                   hexamer, murasaki, gbioseq, finex, das-proserver, est-db
   -med-bio-dev
    added:
      Recommends:  python3-screed, python3-misopy, python3-pyvcf,
                   python3-biomaj3, python3-ngs, toil, python3-cutadapt,
                   python3-ruffus, python3-biotools, python3-sqt,
                   libmems-dev, python3-hyphy, libstatgen-dev, python3-cobra,
                   python3-biopython, python3-pysam, python3-airr,
                   python3-dendropy, libgenome-dev, python3-fast5,
                   python3-cyvcf2, libpll-dev, python3-bx, libmuscle-dev,
                   python3-treetime, python3-presto, python3-pbconsensuscore,
                   python3-csb, python3-intervaltree-bio, python3-seqcluster,
                   python3-ete3, python3-bcbio, python3-pyfaidx, galaxy-lib,
                   python3-consensuscore2, snakemake
      Suggests:    ctdconverter, libmodhmm-dev, libsvmloc-dev, vdjtools,
                   python3-ctdopts, python3-biopython-sql, libmilib-java
    removed:
      Recommends:  python3-biotools | python-biotools, octave-bioinfo,
                   python3-pyvcf | python-pyvcf,
                   python3-biomaj3 | python-biomaj3,
                   python3-pbconsensuscore | python-pbconsensuscore,
                   libmuscle-3.7-dev, python3-pyfaidx | python-pyfaidx,
                   python3-consensuscore2 | python-consensuscore2,
                   python-bd2k, python3-bx | python-bx,
                   python3-ete3 | python-ete3, python3-ruffus | python-ruffus,
                   python3-fast5 | python-fast5,
                   python3-dendropy | python-dendropy, python-pysam,
                   python3-cutadapt | python-cutadapt, libgff-perl,
                   python3-ngs | python-ngs, python3-pyfasta | python-pyfasta,
                   python3-csb | python-csb, libgenome-1.3-dev,
                   python3-biopython | python-biopython,
                   python3-hyphy | python-hyphy, python-cobra,
                   libmems-1.6-dev,
                   python3-intervaltree-bio | python-intervaltree-bio,
                   python3-misopy | python-misopy
      Suggests:    python3-biopython-sql | python-biopython-sql
   -med-bio-ngs
    added:
      Recommends:  python3-presto, changeo, bcbio, igor, python3-pybedtools,
                   igdiscover, python3-airr, r-cran-tcr, r-cran-tigger,
                   python3-sqt, python3-gffutils, fastp, vdjtools,
                   samblaster, r-cran-shazam, r-cran-alakazam
   -med-bio-phylogeny
    added:
      Suggests:    python3-treetime
   -med-epi
    added:
      Recommends:  epifire
   -med-imaging
    added:
      Recommends:  mrtrix3, odil
      Suggests:    orthanc-mysql, tifffile
   -med-imaging-dev
    added:
      Recommends:  libsimpleitk1-dev, python3-biosig, libodil-dev,
                   python3-simpleitk, libxdf-dev
    removed:
      Recommends:  libodil0-dev
   -med-pharmacy
    added:
      Recommends:  r-cran-rpact
   -med-physics
    added:
      Suggests:    python3-biosig
    removed:
      Suggests:    python-biosig
   -med-research
    added:
      Recommends:  r-cran-rpact
   -med-typesetting
    removed:
      Suggests:    referencer

 -- Andreas Tille <email address hidden>  Thu, 24 Jan 2019 15:07:55 +0100

Available diffs

• diff from 3.1 to 3.2 (26.0 KiB)

debian-med (3.1) unstable; urgency=medium

  * Versioned Build-Depends bumped to 0.6.99 to enable Recommends in tasks
    files
  * s/Depends/Recommends/
    (leave out list of changed metapackage dependencies which is messed up
     due to this change)
  * Moved to Salsa
  * Standards-Version: 4.1.4
  * Bumped versioned Build-Depends blends-dev to >= 0.7~
  * Priotity: optional (as per policy 4.0.1.0 - see #759260)

 -- Andreas Tille <email address hidden>  Thu, 26 Apr 2018 22:33:08 +0200

Available diffs

• diff from 3.0.1ubuntu1 (in Ubuntu) to 3.1 (65.8 KiB)

debian-med (3.0.1ubuntu1) artful; urgency=medium

  * Merge from Debian unstable.  Remaining changes:
    - Regenerate control file for artful.

Available diffs

• diff from 2.1ubuntu6 to 3.0.1ubuntu1 (38.7 KiB)

debian-med (2.1ubuntu6) yakkety; urgency=medium

  * Replace libmia-2.2-dev with libmia-2.4-dev.

 -- Matthias Klose <email address hidden>  Fri, 30 Sep 2016 21:05:45 +0200

Available diffs

• diff from 2.1ubuntu5 to 2.1ubuntu6 (7.6 KiB)

debian-med (2.1ubuntu5) yakkety; urgency=medium

  * Drop python-mvpa2.

 -- Matthias Klose <email address hidden>  Fri, 02 Sep 2016 13:26:37 +0200

Available diffs

• diff from 2.1ubuntu4 to 2.1ubuntu5 (7.1 KiB)

debian-med (2.1ubuntu4) xenial; urgency=medium

  * Drop odin for now, doesn't build with new gsl.

 -- Iain Lane <email address hidden>  Wed, 11 Nov 2015 16:29:39 +0000

Available diffs

• diff from 2.1ubuntu3 to 2.1ubuntu4 (924 bytes)

debian-med (2.1ubuntu3) wily; urgency=medium

  * debian-med-imaging: Suggest minc-tools instead of depending on them.
    Currently not built.

 -- Matthias Klose <email address hidden>  Sun, 27 Sep 2015 06:37:12 +0200

Available diffs

• diff from 2.1ubuntu2 to 2.1ubuntu3 (965 bytes)

debian-med (2.1ubuntu2) wily; urgency=medium

  * libfreecontact0-dev -> libfreecontact0-dev.

 -- Matthias Klose <email address hidden>  Tue, 01 Sep 2015 12:36:31 +0200

Available diffs

• diff from 2.1ubuntu1 to 2.1ubuntu2 (3.9 KiB)

debian-med (2.1ubuntu1) wily; urgency=medium

  * Merge from Debian unstable. Remaining changes:
    - Regenerate control file.

Available diffs

• diff from 2.0ubuntu1 to 2.1ubuntu1 (7.8 KiB)

debian-med (2.0ubuntu1) wily; urgency=medium

  * Merge from Debian unstable. Remaining changes:
    - Regenerate control file.

Available diffs

• diff from 1.99ubuntu1 to 2.0ubuntu1 (8.0 KiB)

debian-med (1.99ubuntu1) vivid; urgency=medium

  * Regenerate control file.
 -- Logan Rosen <email address hidden>   Sun, 14 Dec 2014 04:38:29 -0500

Available diffs

• diff from 1.13.2ubuntu3 to 1.99ubuntu1 (47.3 KiB)

debian-med (1.13.2ubuntu3) trusty; urgency=medium

  * s/libgenome-1.3-0-dev/libgenome-1.3/ due to changes in libegnome, this
    should resolve NBS.
 -- Dimitri John Ledkov <email address hidden>   Mon, 14 Apr 2014 20:26:18 +0100

Available diffs

• diff from 1.13.2ubuntu2 to 1.13.2ubuntu3 (1.1 KiB)

debian-med (1.13.2ubuntu2) saucy; urgency=low

  * s/pixelmed-java/libpixelmed-java/ due to changes in pixelmed packaging
    - update debian/control
 -- Micah Gersten <email address hidden>   Mon, 22 Jul 2013 22:47:59 -0500

Available diffs

• diff from 1.13.2ubuntu1 to 1.13.2ubuntu2 (1.2 KiB)

debian-med (1.13.2ubuntu1) raring; urgency=low

  * Merge from Debian unstable.  Remaining changes:
    - sources.list.quantal → sources.list.raring
    - regenerate debian/control.
    - Change libteem1-dev in Recommends to libteem-dev
      for libteem1-dev -> libteem-dev transition.
 -- Vibhav Pant <email address hidden>   Tue, 26 Mar 2013 13:52:45 +0530

Available diffs

• diff from 1.13.1ubuntu1 to 1.13.2ubuntu1 (5.9 KiB)

debian-med (1.13.1ubuntu1) raring; urgency=low

  * Merge from Debian unstable (LP: #1089907).  Remaining changes:
    - sources.list.quantal → sources.list.raring
    - regenerate debian/control.
    - Change libteem1-dev in Recommends to libteem-dev
      for libteem1-dev -> libteem-dev transition.
 -- Vibhav Pant <email address hidden>   Thu, 13 Dec 2012 18:19:52 +0530

Available diffs

• diff from 1.13ubuntu1 to 1.13.1ubuntu1 (5.8 KiB)

debian-med (1.13ubuntu1) raring; urgency=low

  * Merge from Debian unstable.  Remaining changes:
    - sources.list.quantal → sources.list.raring
    - regenerate debian/control.
    - Change libteem1-dev in Recommends to libteem-dev
      for libteem1-dev -> libteem-dev transition.

Available diffs

• diff from 1.11ubuntu2 to 1.13ubuntu1 (53.6 KiB)

debian-med (1.11ubuntu2) quantal; urgency=low

  * debian/control:
    - Change libteem1-dev in Recommends to libteem-dev
      for libteem1-dev -> libteem-dev transition.
      (LP: #1019485)
 -- Vibhav Pant <email address hidden>   Sat, 30 Jun 2012 09:46:02 +0530

Available diffs

• diff from 1.11ubuntu1 to 1.11ubuntu2 (859 bytes)

debian-med (1.11ubuntu1) quantal; urgency=low

  * Merge from Debian unstable. Remaining changes:
    - sources.list.precise → sources.list.quantal
    - regenerate debian/control.

Available diffs

• diff from 1.10ubuntu1 to 1.11ubuntu1 (26.2 KiB)

debian-med (1.10ubuntu1) precise; urgency=low

  * sources.list.oneiric → sources.list.precise
  * regenerate debian/control.
 -- Charlie Smotherman <email address hidden>   Tue, 27 Dec 2011 11:14:18 -0500

Available diffs

• diff from 1.8ubuntu4 to 1.10ubuntu1 (74.9 KiB)

debian-med (1.8ubuntu4) oneiric; urgency=low

  * tasks/imaging-dev, debian-med-tasks.desc: Drop libvxl1-dev, it's gone from
    oneiric.
  * sources.list.natty → sources.list.oneiric
  * regenerate debian/control.
 -- Martin Pitt <email address hidden>   Fri, 30 Sep 2011 06:20:19 +0200

Available diffs

• diff from 1.8ubuntu3 to 1.8ubuntu4 (4.2 KiB)

debian-med (1.8ubuntu3) natty; urgency=low

  * med-bio-dev: change depends from libajax6-dev -> emboss-lib for
    emboss-lib transition
    - update debian/control
 -- Bhavani Shankar <email address hidden>   Sat, 25 Dec 2010 16:20:32 +0530

Available diffs

• diff from 1.8ubuntu2 to 1.8ubuntu3 (833 bytes)

debian-med (1.8ubuntu2) natty; urgency=low

  * debian-med-tasks.desc: Change dependency for libajax6-dev ->
    emboss-lib transition.
 -- Bilal Akhtar <email address hidden>   Sat, 11 Dec 2010 15:48:36 +0300

Available diffs

• diff from 1.8ubuntu1 to 1.8ubuntu2 (475 bytes)

debian-med (1.8ubuntu1) natty; urgency=low

  * Merge from debian unstable. Remaining change:
  * Add a sources.list file for Natty, the packagelists will update.

Available diffs

• diff from 1.7ubuntu1 to 1.8ubuntu1 (17.4 KiB)

debian-med (1.7ubuntu1) maverick; urgency=low

  * Merge from Debian unstable (LP: #614263). Remaining change:
    - Add a sources.list file for Maverick, the packagelists will update.

Available diffs

• diff from 1.6ubuntu1 to 1.7ubuntu1 (24.1 KiB)

debian-med (1.6ubuntu1) maverick; urgency=low

  * Merge from debian unstable (LP: #590820). No remaining changes.
  * Add a sources.list file for Maverick, the packagelists will update.
 -- Jean-Louis Dupond <email address hidden>   Wed, 05 May 2010 03:48:59 +0100

Available diffs

• diff from 1.5ubuntu1 to 1.6ubuntu1 (13.2 KiB)

debian-med (1.5ubuntu1) lucid; urgency=low

  * Merge with Debian (LP: #521438):
    - Add a sources.list file for Lucid, the packagelists will update.

Available diffs

• diff from 1.4ubuntu1 to 1.5ubuntu1 (2.8 KiB)

debian-med (1.4ubuntu1) lucid; urgency=low

  * Add a sources.list file for Lucid, the packagelists will update.

Available diffs

• diff from 1.3ubuntu1 to 1.4ubuntu1 (24.7 KiB)

debian-med (1.3ubuntu1) karmic; urgency=low

  * Merge from debian unstable, Ubuntu remaining changes:
    - Add a sources.list file for karmic, the packagelists will update.
  * We will rebuild this after closing Ubuntu bug #418574.

Available diffs

• diff from 1.2ubuntu1 to 1.3ubuntu1 (28.2 KiB)

debian-med (1.2ubuntu1) karmic; urgency=low

  * Merge from debian unstable, remaining changes: (LP: #371394)
    - add a sources.list for karmic, so the packagelists will
      update.

Available diffs

• diff from 1.0ubuntu1 to 1.2ubuntu1 (52.3 KiB)

debian-med (1.0ubuntu1) jaunty; urgency=low

  * Replace libgenome-1.3-1 with libgenome-1.3-0 in the depends of the
    med-bio-dev task.
    - Add a sources.list for jaunty so that the package lists can be updated.

 -- James Westby <email address hidden>   Fri, 16 Jan 2009 12:50:44 +0000

Available diffs

• diff from 1.0 to 1.0ubuntu1 (2.5 KiB)

debian-med (1.0) unstable; urgency=low

  * tasks/bio-dev
    - Added libgenome
    - Added libmems as prospective package
    - Moved bioconductor from bio to bio-dev
    - Added prospective projects where Steffen Möller started some
      packaging work
    - libqsearch -> libqsearch-dev
  * tasks/bio
    - Added prospective projects where Steffen Möller started some
      packaging work
    - Suggests: texlive-latex-extra (because of TeXShade)
    - Removed line breaks in Dependencies, because cdd-gen-control
      is not compliant to RFC 822 and requires '\' at the end of
      lines to continue parsing the tasks files.  To simply circumvent
      this problem the relevant lines were concatenated to not miss
      the dependencies in the resulting control file
    - Renamed dialign-t to dialign-tx
  * tasks/tools
    - Added mssstest
    - Added wgerman-medical, hunspell-de-med (remark: these are not
      really tools but we have no better section, typesetting might be
      an option but does also fit not really good)
  * tasks/imaging
    - Added prospective packages from static page
  * tasks/imaging-dev
    - Removed libgtkimreg
    - Added libvtk5
    - Added prospective packages from static page
    - libminc0-dev | libminc-dev -> libminc-dev
    - insighttoolkit -> insighttoolkit3
  * tasks/physics
    - octave | octave2.1 -> octave3.0
  * debian/control.stub: XS-DM-Upload-Allowed -> DM-Upload-Allowed
  * Standards-Version: 3.8.0 (no changes needed)
  * Fixed typing of Debian Med: sed -i 's/Debian-Med/Debian Med/' *

 -- Ubuntu Archive Auto-Sync <email address hidden>   Tue,  04 Nov 2008 21:18:20 +0000

Available diffs

• diff from 0.17 to 1.0 (44.3 KiB)

debian-med (0.17) unstable; urgency=low

  * tasks/bio:
    - Added emboss-kaptain as prospective package
    - Added agdbnet as prospective package
    - Added autodock, exonerate
    - Suggests biococoa.app: Only suggests because status is
      questionable
    - Removed bugsx which is not really biology related
    - Added gamgi as prospective package
    - Moved unoffical and prospective packages from static
      web pages to tasks file
  * tasks/bio-dev:
    - Added aceperl as prospective package
    - Added libgff-perl as prospective package
    - Added Recommends: libqsearch
  * tasks/imaging
    - Removed paul
    - pngquant: Recommends -> Suggests
    - Added gdmc as prospective package
    - Added dicom4j as prospective package
  * tasks/epi: New meta package: med-epi for epidemiology
    research
  * tasks/tools:
    - Moved NetEpi prospective package to epi where it really
      belongs to
    - Added pondus
  * Removed remark about recommended and suggested packages
    from description or meta packages
  * Build-Depends-Indep: cdd-dev (>= 0.5.0) which ensures that the
    source tarball is builded properly and no network access is neede
    to build the package
    Closes: #470271

debian-med (0.15) unstable; urgency=low

  * med-imaging-dev: Added
    Depends: libinsighttoolkit-dev
    Suggests: insighttoolkit-examples
  * med-imaging(-dev): Depend from libniftiio1(-dev) instead of
    libniftiio0(-dev)
    Closes: #448903
  * Increased Build-Dep version cdd-dev (>= 0.4.4)
  * Standards-Version: 3.7.3 (no changes needed)
  * Added several prospective packages in tasks

 -- Ubuntu Archive Auto-Sync <email address hidden>   Thu,  06 Dec 2007 09:47:50 +0000

debian-med (0.14) unstable; urgency=low

  * Builded using new cdd-dev 0.4
    - med-common is now renamed to med-config
    - additional package med-tasks
  * med-bio: added emboss
  * med-imaging: amide, dicomnifti, imagej, python-nifti
                 decreased paul from Recommends to Suggests
  * med-imaging-dev: cimg-dev
                 decreased libgtkimreg-dev from Recommends to Suggests
  * med-practice: libchipcard3c1, libchipcard3d0
  

debian-med (0.12) unstable; urgency=low

  * Changed med-practice menu
    Closes: #385584
    Use menu entry for gnumed-client-debug that regards #389932.
    Note: gnumed-client-debug is not in the med-practice dependency
    list but it is suggested by gnumed-client.  So *if* the package
    is installed at the box then an additional menu item occures correctly
    in the Debian-Med menu.  If it is not installed, only gnumed-client
    is shown in the menu.
  * med-bio: Added alternative to tree-puzzle as tree-ppuzzle
  * Drop med-dent because odontolinux was removed from Debian
  * med-bio: Added poa
             Moved vrom Suggests to Depends: seaview (now really free)
             Suggests: wise-doc
  * med-imaging: Depends: libfslio0, libniftiio0, nifti-bin
                 Suggests: 
  * med-imaging-dev: Depends: libfslio0-dev, libniftiio0-dev
                     Suggests: libnifti-doc

debian-med (0.10.1) unstable; urgency=low


  * Make med-common depend from ${misc:Depends}
    Closes: #331797
  * Now med-practice really depends from gnumed-client which is now
    awailable at Debian mirror

 -- Andreas Tille <email address hidden>  Wed,  5 Oct 2005 07:55:13 +0200

debian-med (0.9) unstable; urgency=low


  * Removed gnutrion from tools because it was removed from Debian at all
  * Rebuilded with cdd-dev 0.3.10 version
  * med-bio: 
     Depends: muscle, gff2aplot, t-coffee, gff2ps, gdpc
     Suggests: arb
  * med-bio-dev
     Recommends: libvibrant6-dev
     Why: libmotif-dev conflicts lesstif-dev, so if someone wants to
          install libmotif-dev it must be possible to deinstall
	  libvibrant6-dev without beeing forced to deinstall med-bio-dev
	  as well
     Depends: python-biopython
  * med-imaging:
     paul now Recommends not Depends
     Depends: dcmtk
     Recommends: pngquant
  * med-tools: 
     Depends: cycle
     Suggests: cl-pubmed
               Strong dependency would cost installing a large amount
	       of Common Lisp tools which in most cases is not worth
	       the effort
  * Added user menu entries: bio/gff2aplot.txt, bio/gff2ps.txt,
    bio/muscle.txt, bio/t-coffee.txt, bio/boxshade.txt,
    bio-dev/python-biopython.txt, imaging/dcmtk.txt
  * Added charset to debian/po.stub/de.po

 -- Andreas Tille <email address hidden>  Sun, 24 Oct 2004 20:59:03 +0200

debian-med (0.8.3) unstable; urgency=high


  * Rebuilded again against cdd-dev 0.3.4 which really closes the
    mentioned bug.
  * Urgency set to high because it *really* fixes a grave bug.

 -- Andreas Tille <email address hidden>  Thu, 15 Jul 2004 10:59:25 +0200

debian-med (0.7) unstable; urgency=low


  * Switched to new version of cdd package (0.3) which has many
    enhancements (no really important changes to the Debian-Med stuff
    except that the packages have to be rebuilded with cdd-dev).
  * New cdd-dev package cares for versioned dependency on med-common
    Closes: #244903

 -- Andreas Tille <email address hidden>  Tue, 20 Apr 2004 11:21:16 +0200