Package: release.debian.org
Severity: normal
User: release.debian.org@packages.debian.org
Usertags: unblock
Please unblock package debian-med
As of
[0] https://lists.debian.org/debian-release/2012/06/msg00323.html
I now uploaded debian-med metapackages targeting at Wheezy. These are
created using the latest blends-dev package to prevent the problem
described in #694896.
The changes in the debian-med package are to a large extend auto
generated by blends-dev and the full debdiff (attached
debian-med_1.13.2.debdiff.gz) is a bit hard to read because the files in
tasks/ are serving at the same time used as documentation for the Debian
Med web sentinel[1]. There is no reasonable way to maintain this in a
separate source so the diff is larger than you would usually accept
these days. However, this was explained in [0] and was done this way
in the last releases as well.
To enable you concentrating on the *relevant* changes which are caused
due to changes in the package pool (some packages became removed and
some became accepted since the last generation of the metapackages) I
have split of the parts of the debdiff which are more easy to inspect to
see what relevant changes in the dependencies have actually happended.
Please feel free to inspect:
debian-med_1.13.2.debdiff_tasks:
--- debian-med-1.11/debian-med-tasks.desc 2012-04-17 10:05:09.000000000 +0200
+++ debian-med-1.13.2/debian-med-tasks.desc 2012-12-20 09:30:47.000000000 +0100
This shows in the most simple way what recommends were added / removed
debian-med_1.13.2.debdiff_control:
--- debian-med-1.11/debian/changelog 2012-04-17 10:04:12.000000000 +0200
+++ debian-med-1.13.2/debian/changelog 2012-12-20 09:30:16.000000000 +0100
--- debian-med-1.11/debian/control 2012-04-17 10:05:13.000000000 +0200
+++ debian-med-1.13.2/debian/control 2012-12-20 09:30:51.000000000 +0100
--- debian-med-1.11/debian/control.stub 2012-04-05 08:30:36.000000000 +0200
+++ debian-med-1.13.2/debian/control.stub 2012-12-20 09:30:36.000000000 +0100
This extract from debdiff shows the changes inside debian/.
debian-med_control_1.11-1.13.2.wdiff:
This was created using
wdiff debian-med-1.11/debian/control debian-med-1.13.2/debian/control
and is a better way to see the differences in the list of Recommends / Suggests
inside the metapackages than a plain diff.
Feel free to ask for any further information if needed.
Kind regards and thanksa for working on the Wheezy release
Andreas.
[1] http://debian-med.debian.net/tasks
unblock debian-med/1.13.2
-- System Information:
Debian Release: 6.0.6
Architecture: i386 (i686)
Kernel: Linux 2.6.36-xenU-4814-i386 (SMP w/1 CPU core)
Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
# This file is autogenerated via make -f debian/rules dist. Do not edit!
Source: debian-med
Section: misc
Priority: extra
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
DM-Upload-Allowed: yes
Uploaders: Andreas Tille <tille@debian.org>
Build-Depends-Indep: blends-dev (>= [-0.6.15)-] {+0.6.16.2)+}
Standards-Version: 3.9.3
Vcs-Browser: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/
Vcs-Svn: svn://svn.debian.org/blends/projects/med/trunk/debian-med/
Package: med-tasks
Architecture: all
Depends: tasksel
Description: Debian Med tasks for tasksel
This package provides Debian Med tasks in tasksel.
.
These tasks are described in detail at
http://debian-med.alioth.debian.org/tasks/
Package: med-config
Architecture: all
Depends: adduser, ${misc:Depends}, menu, blends-common (>= 0.6.15)
Conflicts: med-common
Replaces: med-common
Provides: med-common
Description: Debian Med general config package
This package provides the basic infrastructure of all [-med-* packages and is
needed-] {+metapackages assembled+}
by [-them.-] {+the Debian Med team.+}
.
This [-package-] {+metapackage+} provides [-some files which are-] common [-to all med-* packages.-] {+features shared between the different
metapackages of the project.+} Moreover it introduces a method to handle {+a
'med'+} system users [-in a-] group
[-med-] using debconf.
.
[-Other packages in-]
{+The+} Debian Med Project {+include metapackages for different tasks, which+} are:
[-.-]
* [-med-bio biological research
* med-bio-dev developing-] applications [-in biological-] {+for microbiological+} research
[-* med-cloud command line biol. applications-] {+and support+} for {+development of
biological applications
*+} cloud computing {+in microbiological research+}
* [-med-data-] drug databases
* [-med-dental helping tools for dentists-] {+dental surgery practice+}
* [-med-epi-] epidemiology {+and medical statistics+}
* [-med-imaging-] image processing
[-* med-imaging-dev developing applications-] {+and support+} for [-image processing-] {+imaging application development+}
* [-med-pharmacy pharmaceutical-] {+pharmacological+} research
* [-med-physics-] radiation oncology, diagnostic [-imaging,-] {+imaging and+} related fields
* [-med-practice general practitioners-] {+medical practice+}
* [-med-psychology-] psychological research {+and practice+}
* [-med-statistics miscellaneous tools medical for statistics-] {+rehabilitation+}
* [-med-tools contains miscellaneous tools-] {+typesetting and publishing+}
* [-med-typesetting depends from useful-] {+miscellaneous+} tools [-for typesetting-]
.
[-Note: All these packages are so called metapackages. This means they are-]
{+Each task is represented by a metapackage. Metapackages do+} not {+contain+}
executable programs, but [-only links to-] {+rather dependencies from+} other packages. This way
you will conveniently get all [-the non-commercial-] {+free+} medical software which is available for
Debian [-GNU/Linux.-] {+by simply installing the relevant metapackage+}
Package: med-bio
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: abacas, acedb-other, acedb-other-belvu, acedb-other-dotter, adun.app, alien-hunter, altree, amap-align, ampliconnoise, autodock, autodock-vina, autogrid, ballview, bedtools, biomaj, blast2, bowtie, bowtie2, boxshade, bwa, cd-hit, clonalframe, clustalo, clustalw, clustalx, dialign, dialign-tx, disulfinder, dotur, {+dssp,+} embassy-domainatrix, embassy-domalign, embassy-domsearch, emboss, exonerate, fastdnaml, fastlink, {+fasttree,+} fastx-toolkit, ffindex, figtree, filo, gamgi, garlic, [-gassst,-] gbrowse, gdpc, {+gentle,+} gff2aplot, gff2ps, ghemical, glam2, grinder, gromacs, hhsuite, hmmer, infernal, jalview, jellyfish, jmol, kalign, last-align, librg-utils-perl, loki, mafft, maq, maqview, massxpert, melting, mipe, mira-assembler, mlv-smile, mothur, mrbayes, mummer, muscle, mustang, ncbi-blast+, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, ncoils, {+neobio,+} njplot, perlprimer, phyml, picard-tools, plasmidomics, plink, poa, populations, primer3, probalign, probcon
s, proda, profnet-bval, profnet-chop, profnet-con, profnet-isis, profnet-md, profnet-norsnet, profnet-prof, profnet-snapfun, profphd, profphd-net, profphd-utils, proftmb, pymol, pynast, python-cogent, qiime, r-bioc-cummerbund, r-bioc-hilbertvis, {+r-cran-genabel,+} r-cran-qtl, r-other-bio3d, r-other-mott-happy, rasmol, raster3d, raxml, readseq, reprof, rnahybrid, samtools, sibsim4, sigma-align, sim4, squizz, {+sra-toolkit,+} ssake, staden-io-lib-utils, t-coffee, tabix, theseus, tigr-glimmer, tm-align, transtermhp, tree-puzzle | tree-ppuzzle, treeviewx, vcftools, velvet, wise
Suggests: abyss, act, [-agdbnet,-] amos-assembler, amoscmp, anfo, apollo, arachne, arb, artemis, asap, augustus, autodocktools, axparafit, axpcoords, bagphenotype, bambus, {+bamtools,+} beads, beast-mcmc, big-blast, [-bio-mauve,-] {+bigsdb,+} blimps-utils, blixem, btk-core, cactus, caftools, cain, cap3, {+cdbfasta,+} cdna-db, [-chado,-] cinema, circos, clonalorigin, clustalw-mpi, cluster3, cmap, coalesce, codonw, compclust, {+concavity, conservation-code,+} contralign, coot, copycat, crossbow, cufflinks, cytoscape, das-proserver, dazzle, decipher, e-hive, ecell, {+edtsurf,+} eigensoft, elph, embassy-phylip, emboss-explorer, [-emboss-kaptain,-] ensembl, est-db, estferret, estscan, exalt, excavator, fas, fasta, [-fasttree,-] {+fastqc,+} figaro, finex, fluctuate, forester, forge, galaxy, {+gassst,+} gbioseq, gbrowse-syn, genemark, genesplicer, genetrack, genezilla, genographer, [-gentle,-] {+genometools,+} glimmerhmm, gmap, gmv, grogui, haploview, hawkeye, hexamer, hilbertvisgui
, {+hmmer2,+} igv, jbrowse, jigsaw, jstreeview, [-jtreeview,-] kempbasu, lagan, lamarc, {+logol-bin,+} logomat-m, {+ltrsift,+} lucy, {+macs,+} mage2tab, maker2, martj, maude, mauvealigner, maxd, melting-gui, meme, mesquite, metarep, microbiomeutil, migrate, minimus, mirbase, mobyle, molekel, [-molphy,-] {+mosaik-aligner,+} mozilla-biofox, {+mpsqed,+} msatfinder, mugsy, mummergpu, murasaki, mview, [-neobio,-] {+ncbi-seg,+} ngila, {+norsnet, norsp, nw-align, oases,+} obo-edit, oligoarrayaux, omegamap, operondb, pal2nal, paml, partigene, patman, {+patristic,+} pcma, pdb2pqr, pfaat, pftools, phagefinder, phpphylotree, phy-spread, phylip, phylographer, {+phyloviz-core,+} phylowin, plato, prank, {+predictnls, predictprotein,+} proalign, {+profbval, profisis,+} profit, prot4est, {+pscan-tfbs, psipred,+} pyrophosphate-tools, python-orange, python-rdkit, python-reaper, qtlcart, r-ape, [-r-other-genabel,-] r-other-valdar-bagphenotype.library, raccoon, ray-denovoassembler, rbs-finder,
rdp-classifier, recombine, [-repeatfinder,-] repeatmasker, [-reputer,-] rmblast, roche454ace2caf, rose, rosetta, sap, seaview, seq-gen, seqan-apps, {+seqtk,+} sequenceconverter.app, {+sga,+} sift, smalt, snap, {+snpeff,+} soapdenovo, spice, splitstree, {+spread-phy,+} sra-sdk, ssaha, strap, tacg, taverna, taxinspector, tetra, tigr-assembler, {+tigr-glimmer-mg,+} tophat, trace2dbest, tracetuner, treebuilder3d, [-treeplot,-] treetime, [-treevolve, trf,-] {+treeview,+} tripal, trnascan-se, twain, ugene, uniprime, vegan, vienna-rna, vmd, wgs-assembler, x-tandem-pipeline, [-zodiac-] {+zalign, zodiac-zeden+}
Description: Debian Med micro-biology packages
This metapackage will install Debian packages related to molecular biology,
structural biology and bioinformatics for use in life sciences.
Package: med-bio-dev
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: bioperl, bioperl-run, biosquid, libace-perl, {+libai-fann-perl,+} libbio-graphics-perl, libbio-mage-perl, libbio-mage-utils-perl, libbio-primerdesigner-perl, libbiococoa-dev, libbiojava-java, {+libbiojava3-java,+} libchado-perl, libffindex0-dev, libgenome-1.3-0-dev, libgo-perl, {+libhmsbeagle-dev,+} libjebl2-java, libncbi6-dev, libpal-java, {+librg-blast-parser-perl,+} librg-reprof-bundle-perl, librostlab-blast-doc, librostlab-blast0-dev, librostlab-doc, librostlab3-dev, {+libsort-key-top-perl,+} libsrf-dev, libstaden-read-dev, libtfbs-perl, libvibrant6-dev, libzerg-perl, libzerg0-dev, mcl, python-biopython, python-cogent, r-bioc-biobase, r-cran-genetics, r-cran-haplo.stats, ruby-bio, seqan-dev
Suggests: bioclipse, biostrings, iranges, [-libajax6-dev,-] {+libbamtools-dev,+} libbio-das-perl, {+libforester-java,+} libgbfp-dev, {+libgenometools0-dev,+} libgff-perl, libmems-1.5-1, [-libnucleus6-dev,-] {+libnhgri-blastall-perl, libopenmm4-dev,+} libqsearch-dev, [-librg-blast-parser-perl,-] {+librcsb-core-wrapper0-dev,+} libsbml5-dev, {+libswarm2-dev, octace-bioinfo,+} octave-bioinfo, [-pysam,-] {+python-biom-format, python-librcsb-core-wrapper,+} python-mmtk, {+python-pysam, r-bioc-biocgenerics,+} r-cran-rocr
Description: Debian Med packages for development of micro-biology applications
This metapackage will install Debian packages which might be helpful
for development of applications for micro-biological research.
Package: med-cloud
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: autodock, clustalw, python-cogent, raster3d
Suggests: bagphenotype, clustalw-mpi, r-other-valdar-bagphenotype.library
Description: Debian Med bioinformatics applications usable in cloud computing
This metapackage will install Debian packages related to molecular biology,
structural biology and bioinformatics for use in life sciences, that do not
depend on graphical toolkits and therefore can fit on system images for use
in cloud computing clusters, where space can be limited.
Package: med-data
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: {+freediams, freemedforms-freedata,+} python-hl7
Suggests: [-drugref.org, freediams-] {+drugref.org+}
Description: Debian Med drug databases
[-There is at least one-]
{+This metapackage will install+} free [-medical-] drug {+databases and related
applications. The+} database [-packaged for Debian
which-] can be [-installed using this metapackage. It is supported-] {+accessed+} by {+any EMR using+}
the
[-GNUmed Electronic Medical Record package.-] {+application.+}
Package: med-dental
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: imagetooth
Suggests: {+entangle,+} openmolar
Description: Debian Med packages related to dental practice
This metapackage contains dependencies for a collection of software
which might be helpful for dentists to manage their practice.
Package: med-epi
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: epigrass, r-cran-diagnosismed, r-cran-epi, r-cran-epibasix, r-cran-epicalc, r-cran-epir, r-cran-epitools
Suggests: netepi-analysis, netepi-collection, r-cran-msm, r-cran-surveillance, [-repast, swarm-] {+repast+}
Description: Debian Med epidemiology related packages
This metapackage will install tools that are useful in epidemiological
research. Several packages making use of the GNU R data language for
statistical investigation. It might be a good idea to read the paper
"A short introduction to R for Epidemiology" at
http://staff.pubhealth.ku.dk/%7Ebxc/Epi/R-intro.pdf
Package: med-imaging
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: aeskulap, amide, {+ants,+} biosig-tools, caret, ctn, ctsim, dcmtk, dicom3tools, dicomnifti, dicomscope, ginkgocadx, gofigure2, gwyddion, imagej, imagevis3d, itksnap, {+king,+} libgdcm-tools, medcon, minc-tools, mriconvert, mricron, mrtrix, nifti-bin, odin, openmeeg-tools, openslide-tools, pixelmed-java, plastimatch, python-dipy, python-mvpa, python-nifti, python-nipy, python-nipype, python-nitime, sigviewer, sofa-apps, tifffile, via-bin, volview, voxbo, xmedcon
Suggests: afni, [-ants,-] bioimagesuite, bioimagexd, blox, brainvisa, {+camitk-imp,+} cdmedicpacs, cellprofiler, cmtk, connectomeviewer, conquest-dicom-server, [-dcm4che,-] {+crea,+} dcm4chee, devide, dicom4j, dicoogle, drjekyll, dti-query, dtitk, ecg2png, eeglab, elastix, fiji, freesurfer, fsl, fslview, gimias, hid, imagemagick, imview, {+incf-nidash-oneclick-clients,+} insightapplications, invesalius, isis, jemris, jist, kradview, [-libvista2,-] {+libdcm4che-java,+} lipsia, maris, mayam, medisnap, mesa-test-tools, {+mia-tools, mialmpick,+} micromanager, mipav, miview, mni-autoreg, mni-colin27-nifti, mni-icbm152-nlin-2009, mni-n3, mrisim, omero, opendicom.net, openelectrophy, opensourcepacs, openwalnut, {+orthanc, paraview,+} piano, pngquant, pymeg, pysurfer, pyxid, slicer, stabilitycalc, stir, tempo, visit, vmtk, xnat
Description: Debian Med imaging packages
This metapackage will install Debian packages which might be useful in
medical image processing.
.
It installs several packages supporting DICOM (Digital Imaging and
Communications in Medicine) which is the de-facto standard for medical
image management. The standard defines data structures and services for
the exchange of medical images and related information. The latest release
has been published in 2008 and consists of 18 parts.
.
For more information, you can visit the NEMA homepage
http://medical.nema.org/ .
.
The status of the official DICOM base standard plus all the
supplements and correction items are summarized at David Clunie's webpage:
http://www.dclunie.com/dicom-status/status.html
where you'll find direct links to the most recent yearly edition
ftp://medical.nema.org/medical/dicom/2008/ .
Package: med-imaging-dev
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: cimg-dev, ctn-dev, gmic, {+libactiviz.net-cil,+} libbiosig-dev, libcv-dev, libgdcm2-dev, libgdf-dev, libgiftiio-dev, libigstk4-dev, libinsighttoolkit3-dev, libmdc2-dev, libminc-dev, libnifti-dev, {+libopenigtlink1-dev,+} libopenmeeg-dev, libopenslide-dev, [-libteem1-dev,-] libvia-dev, libvolpack1-dev, {+libvtk5-dev,+} libvxl1-dev, odin, python-cfflib, python-dicom, python-dipy, python-gdcm, python-mvpa, python-nibabel, python-nipy, python-nipype, python-nitime, python-pyxnat
Suggests: emokit, igstk-examples, insighttoolkit3-examples, [-libactiviz.net5.6-cil,-] libbio-formats-java, [-libctkcore0-dev,-] {+libcamitk3-dev, libctk-dev,+} libeegdev-dev, {+libmia-2.0-dev,+} libmni-perllib-perl, libnifti-doc, libopenslide-java, [-libvista2-dev,-] {+libteem1-dev, libvistaio-dev,+} libvtk5.4, libxdffileio-dev, {+octave-dicom, python-casmoothing,+} python-libavg, python-openslide
Description: Debian Med packages for medical image development
This metapackage will install Debian packages which might be useful
for developing applications for medical image processing.
Package: med-oncology
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: dicompyler
Suggests: planunc, uw-prism
Description: Debian Med packages for oncology
This metapackage will install tools that are useful for radiation
oncology.
Package: med-pharmacy
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: chemtool
Suggests: raccoon
Description: Debian Med packages for pharmaceutical research
This metapackage contains dependencies for a
collection of software and documentation which is useful for
pharmaceutical research.
Package: med-physics
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: octave, paw, paw++, r-base
Suggests: biosig, gate, openvibe, paw-demos
Description: Debian Med packages for medical physicists
This metapackage contains dependencies for a
collection of software and documentation which is useful for
medical physicists in radiation oncology, diagnostics imaging
and related fields.
Package: med-practice
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: clinica, {+freediams, freemedforms-emr,+} ginkgocadx, gnumed-client, gnumed-server, libchipcard-tools, r-cran-medadherence
Suggests: clearhealth, elementalclinic, elexis, {+entangle,+} freeb, [-freediams,-] freeicd, freemed, [-freemedforms,-] freeshim, libctapimkt0, medintux, mirrormed, mirth, openemr, openpms, openrep, proteus, qrisk2, remitt, resmedicinae, sqlclinic, thera-pi, tinyheb
Description: Debian Med packages for practice management
This metapackage contains dependencies for a collection of software
which might be helpful for practitioners to manage their practice.
Package: med-psychology
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: praat, psignifit, psychopy, python-pyepl, r-cran-foreign, r-cran-psy
Suggests: miscpsycho, psignifit3, psych, psychometric, psychotree, psyphy, science-psychophysics, visionegg
Description: Debian Med packages for psychology
This metapackage contains dependencies for a collection of software
which might be helpful for psychological research.
Package: med-rehabilitation
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: sitplus
Suggests: aghermann
Description: Debian Med packages for rehabilitation technologies
This metapackage will install tools that are useful for
rehabilitation and therapy.
Package: med-statistics
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: r-bioc-edger, r-bioc-limma, {+r-bioc-qvalue,+} r-cran-pvclust, [-r-cran-qvalue,-] r-cran-randomforest
Suggests: r-cran-beeswarm, science-statistics
Description: Debian Med statistics
This metapackage will install packages which are helpful to do statistics
with a special focus on tasks in medical care.
Package: med-tools
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: edfbrowser, hunspell-de-med, pcalendar, pondus, quitcount, wgerman-medical, workrave
Suggests: cl-pubmed, cycle, {+entangle,+} hunspell-en-med, mencal, mssstest, python-clips
Description: Debian Med several tools
This metapackage will install tools for several purposes in health care.
Currently it contains some simple programs for Personal Health.
Package: med-typesetting
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: {+king,+} texlive-latex-extra, texlive-science
Suggests: {+biber,+} bibus, jabref-plugin-oo, kbibtex, referencer
Description: Debian Med support for typesetting and publishing
This metapackage will install Debian packages that might be helpful
for typesetting and publishing in medical care and structural
biology.
diff -Nru debian-med-1.11/debian/changelog debian-med-1.13.2/debian/changelog
--- debian-med-1.11/debian/changelog 2012-04-17 10:04:12.000000000 +0200
+++ debian-med-1.13.2/debian/changelog 2012-12-20 09:30:16.000000000 +0100
@@ -1,3 +1,45 @@
+debian-med (1.13.2) unstable; urgency=low
+
+ * Build-Depends: blends-dev (>= 0.6.16.2)
+ * Added dependency in imaging-dev: libopenigtlink1-dev
+
+ -- Andreas Tille <tille@debian.org> Thu, 20 Dec 2012 09:13:33 +0100
+
+debian-med (1.13.1) unstable; urgency=low
+
+ * Revert name change from med-pharmacy -> med-pharma
+ Closes: #694424
+
+ -- Andreas Tille <tille@debian.org> Tue, 27 Nov 2012 17:37:26 +0100
+
+debian-med (1.13) unstable; urgency=low
+
+ * med-rehabilitation: sitplus is back to testing - regenerate dependencies
+ * Some new prospective packages in tasks
+
+ -- Andreas Tille <tille@debian.org> Wed, 07 Nov 2012 11:39:29 +0100
+
+debian-med (1.12) unstable; urgency=low
+
+ * debian/control:
+ Usual changes of dependency based on the resolving of new packages
+ in Debian as specified in the tasks files
+ * config/control: Enhanced readability and spelling of long description
+ * Added dependencies due to packages progressing to testing after last upload
+ Bio: r-cran-genabel, gentle, dssp, neobio, fasttree
+ Bio-dev: libbiojava3-java, libai-fann-perl, librg-blast-parser-perl,
+ libsort-key-top-perl, libhmsbeagle-dev
+ Imaging: ants, king
+ Practice: freediams, freemedforms-freedata, freemedforms-emr
+ * Removed dependencies due to packages removed from testing
+ Bio: gassst (removed in #689957)
+ Rehabilitation: sitplus (lacking build-depends in testing, see #680798)
+ * Renamed metapackages: med-pharmacy -> med-pharma
+ * Add debian/med-*.lintian-overrides to prevent false positives about
+ homepage links
+
+ -- Andreas Tille <tille@debian.org> Mon, 05 Nov 2012 15:52:59 +0100
+
debian-med (1.11) unstable; urgency=low
* debian/control(.stub):
diff -Nru debian-med-1.11/debian/control debian-med-1.13.2/debian/control
--- debian-med-1.11/debian/control 2012-04-17 10:05:13.000000000 +0200
+++ debian-med-1.13.2/debian/control 2012-12-20 09:30:51.000000000 +0100
@@ -5,7 +5,7 @@
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
DM-Upload-Allowed: yes
Uploaders: Andreas Tille <tille@debian.org>
-Build-Depends-Indep: blends-dev (>= 0.6.15)
+Build-Depends-Indep: blends-dev (>= 0.6.16.2)
Standards-Version: 3.9.3
Vcs-Browser: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/
Vcs-Svn: svn://svn.debian.org/blends/projects/med/trunk/debian-med/
@@ -26,42 +26,39 @@
Replaces: med-common
Provides: med-common
Description: Debian Med general config package
- This package provides the basic infrastructure of all med-* packages and is
- needed by them.
+ This package provides the basic infrastructure of all metapackages assembled
+ by the Debian Med team.
.
- This package provides some files which are common to all med-* packages.
- Moreover it introduces a method to handle system users in a group
- med using debconf.
- .
- Other packages in Debian Med Project are:
- .
- * med-bio biological research
- * med-bio-dev developing applications in biological research
- * med-cloud command line biol. applications for cloud computing
- * med-data drug databases
- * med-dental helping tools for dentists
- * med-epi epidemiology
- * med-imaging image processing
- * med-imaging-dev developing applications for image processing
- * med-pharmacy pharmaceutical research
- * med-physics radiation oncology, diagnostic imaging, related fields
- * med-practice general practitioners
- * med-psychology psychological research
- * med-statistics miscellaneous tools medical for statistics
- * med-tools contains miscellaneous tools
- * med-typesetting depends from useful tools for typesetting
- .
- Note: All these packages are so called metapackages. This means they are not
- executable programs, but only links to other packages. This way you will
- conveniently get all the non-commercial medical software which is available
- for Debian GNU/Linux.
-
+ This metapackage provides common features shared between the different
+ metapackages of the project. Moreover it introduces a method to handle a
+ 'med' system users group using debconf.
+ .
+ The Debian Med Project include metapackages for different tasks, which are:
+ * applications for microbiological research and support for development of
+ biological applications
+ * cloud computing in microbiological research
+ * drug databases
+ * dental surgery practice
+ * epidemiology and medical statistics
+ * image processing and support for imaging application development
+ * pharmacological research
+ * radiation oncology, diagnostic imaging and related fields
+ * medical practice
+ * psychological research and practice
+ * rehabilitation
+ * typesetting and publishing
+ * miscellaneous tools
+ .
+ Each task is represented by a metapackage. Metapackages do not contain
+ executable programs, but rather dependencies from other packages. This way
+ you will conveniently get all free medical software which is available for
+ Debian by simply installing the relevant metapackage
Package: med-bio
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: abacas, acedb-other, acedb-other-belvu, acedb-other-dotter, adun.app, alien-hunter, altree, amap-align, ampliconnoise, autodock, autodock-vina, autogrid, ballview, bedtools, biomaj, blast2, bowtie, bowtie2, boxshade, bwa, cd-hit, clonalframe, clustalo, clustalw, clustalx, dialign, dialign-tx, disulfinder, dotur, embassy-domainatrix, embassy-domalign, embassy-domsearch, emboss, exonerate, fastdnaml, fastlink, fastx-toolkit, ffindex, figtree, filo, gamgi, garlic, gassst, gbrowse, gdpc, gff2aplot, gff2ps, ghemical, glam2, grinder, gromacs, hhsuite, hmmer, infernal, jalview, jellyfish, jmol, kalign, last-align, librg-utils-perl, loki, mafft, maq, maqview, massxpert, melting, mipe, mira-assembler, mlv-smile, mothur, mrbayes, mummer, muscle, mustang, ncbi-blast+, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, ncoils, njplot, perlprimer, phyml, picard-tools, plasmidomics, plink, poa, populations, primer3, probalign, probcons, proda, profnet-bval, profnet-chop, profnet-con,
profnet-isis, profnet-md, profnet-norsnet, profnet-prof, profnet-snapfun, profphd, profphd-net, profphd-utils, proftmb, pymol, pynast, python-cogent, qiime, r-bioc-cummerbund, r-bioc-hilbertvis, r-cran-qtl, r-other-bio3d, r-other-mott-happy, rasmol, raster3d, raxml, readseq, reprof, rnahybrid, samtools, sibsim4, sigma-align, sim4, squizz, ssake, staden-io-lib-utils, t-coffee, tabix, theseus, tigr-glimmer, tm-align, transtermhp, tree-puzzle | tree-ppuzzle, treeviewx, vcftools, velvet, wise
-Suggests: abyss, act, agdbnet, amos-assembler, amoscmp, anfo, apollo, arachne, arb, artemis, asap, augustus, autodocktools, axparafit, axpcoords, bagphenotype, bambus, beads, beast-mcmc, big-blast, bio-mauve, blimps-utils, blixem, btk-core, cactus, caftools, cain, cap3, cdna-db, chado, cinema, circos, clonalorigin, clustalw-mpi, cluster3, cmap, coalesce, codonw, compclust, contralign, coot, copycat, crossbow, cufflinks, cytoscape, das-proserver, dazzle, decipher, e-hive, ecell, eigensoft, elph, embassy-phylip, emboss-explorer, emboss-kaptain, ensembl, est-db, estferret, estscan, exalt, excavator, fas, fasta, fasttree, figaro, finex, fluctuate, forester, forge, galaxy, gbioseq, gbrowse-syn, genemark, genesplicer, genetrack, genezilla, genographer, gentle, glimmerhmm, gmap, gmv, grogui, haploview, hawkeye, hexamer, hilbertvisgui, igv, jbrowse, jigsaw, jstreeview, jtreeview, kempbasu, lagan, lamarc, logomat-m, lucy, mage2tab, maker2, martj, maude, mauvealigner, maxd, melting-gu
i, meme, mesquite, metarep, microbiomeutil, migrate, minimus, mirbase, mobyle, molekel, molphy, mozilla-biofox, msatfinder, mugsy, mummergpu, murasaki, mview, neobio, ngila, obo-edit, oligoarrayaux, omegamap, operondb, pal2nal, paml, partigene, patman, pcma, pdb2pqr, pfaat, pftools, phagefinder, phpphylotree, phy-spread, phylip, phylographer, phylowin, plato, prank, proalign, profit, prot4est, pyrophosphate-tools, python-orange, python-rdkit, python-reaper, qtlcart, r-ape, r-other-genabel, r-other-valdar-bagphenotype.library, raccoon, ray-denovoassembler, rbs-finder, rdp-classifier, recombine, repeatfinder, repeatmasker, reputer, rmblast, roche454ace2caf, rose, rosetta, sap, seaview, seq-gen, seqan-apps, sequenceconverter.app, sift, smalt, snap, soapdenovo, spice, splitstree, sra-sdk, ssaha, strap, tacg, taverna, taxinspector, tetra, tigr-assembler, tophat, trace2dbest, tracetuner, treebuilder3d, treeplot, treetime, treevolve, trf, tripal, trnascan-se, twain, ugene, uniprime
, vegan, vienna-rna, vmd, wgs-assembler, x-tandem-pipeline, zodiac
+Recommends: abacas, acedb-other, acedb-other-belvu, acedb-other-dotter, adun.app, alien-hunter, altree, amap-align, ampliconnoise, autodock, autodock-vina, autogrid, ballview, bedtools, biomaj, blast2, bowtie, bowtie2, boxshade, bwa, cd-hit, clonalframe, clustalo, clustalw, clustalx, dialign, dialign-tx, disulfinder, dotur, dssp, embassy-domainatrix, embassy-domalign, embassy-domsearch, emboss, exonerate, fastdnaml, fastlink, fasttree, fastx-toolkit, ffindex, figtree, filo, gamgi, garlic, gbrowse, gdpc, gentle, gff2aplot, gff2ps, ghemical, glam2, grinder, gromacs, hhsuite, hmmer, infernal, jalview, jellyfish, jmol, kalign, last-align, librg-utils-perl, loki, mafft, maq, maqview, massxpert, melting, mipe, mira-assembler, mlv-smile, mothur, mrbayes, mummer, muscle, mustang, ncbi-blast+, ncbi-epcr, ncbi-tools-bin, ncbi-tools-x11, ncoils, neobio, njplot, perlprimer, phyml, picard-tools, plasmidomics, plink, poa, populations, primer3, probalign, probcons, proda, profnet-bval, pro
fnet-chop, profnet-con, profnet-isis, profnet-md, profnet-norsnet, profnet-prof, profnet-snapfun, profphd, profphd-net, profphd-utils, proftmb, pymol, pynast, python-cogent, qiime, r-bioc-cummerbund, r-bioc-hilbertvis, r-cran-genabel, r-cran-qtl, r-other-bio3d, r-other-mott-happy, rasmol, raster3d, raxml, readseq, reprof, rnahybrid, samtools, sibsim4, sigma-align, sim4, squizz, sra-toolkit, ssake, staden-io-lib-utils, t-coffee, tabix, theseus, tigr-glimmer, tm-align, transtermhp, tree-puzzle | tree-ppuzzle, treeviewx, vcftools, velvet, wise
+Suggests: abyss, act, amos-assembler, amoscmp, anfo, apollo, arachne, arb, artemis, asap, augustus, autodocktools, axparafit, axpcoords, bagphenotype, bambus, bamtools, beads, beast-mcmc, big-blast, bigsdb, blimps-utils, blixem, btk-core, cactus, caftools, cain, cap3, cdbfasta, cdna-db, cinema, circos, clonalorigin, clustalw-mpi, cluster3, cmap, coalesce, codonw, compclust, concavity, conservation-code, contralign, coot, copycat, crossbow, cufflinks, cytoscape, das-proserver, dazzle, decipher, e-hive, ecell, edtsurf, eigensoft, elph, embassy-phylip, emboss-explorer, ensembl, est-db, estferret, estscan, exalt, excavator, fas, fasta, fastqc, figaro, finex, fluctuate, forester, forge, galaxy, gassst, gbioseq, gbrowse-syn, genemark, genesplicer, genetrack, genezilla, genographer, genometools, glimmerhmm, gmap, gmv, grogui, haploview, hawkeye, hexamer, hilbertvisgui, hmmer2, igv, jbrowse, jigsaw, jstreeview, kempbasu, lagan, lamarc, logol-bin, logomat-m, ltrsift, lucy, macs, mage
2tab, maker2, martj, maude, mauvealigner, maxd, melting-gui, meme, mesquite, metarep, microbiomeutil, migrate, minimus, mirbase, mobyle, molekel, mosaik-aligner, mozilla-biofox, mpsqed, msatfinder, mugsy, mummergpu, murasaki, mview, ncbi-seg, ngila, norsnet, norsp, nw-align, oases, obo-edit, oligoarrayaux, omegamap, operondb, pal2nal, paml, partigene, patman, patristic, pcma, pdb2pqr, pfaat, pftools, phagefinder, phpphylotree, phy-spread, phylip, phylographer, phyloviz-core, phylowin, plato, prank, predictnls, predictprotein, proalign, profbval, profisis, profit, prot4est, pscan-tfbs, psipred, pyrophosphate-tools, python-orange, python-rdkit, python-reaper, qtlcart, r-ape, r-other-valdar-bagphenotype.library, raccoon, ray-denovoassembler, rbs-finder, rdp-classifier, recombine, repeatmasker, rmblast, roche454ace2caf, rose, rosetta, sap, seaview, seq-gen, seqan-apps, seqtk, sequenceconverter.app, sga, sift, smalt, snap, snpeff, soapdenovo, spice, splitstree, spread-phy, sra-sd
k, ssaha, strap, tacg, taverna, taxinspector, tetra, tigr-assembler, tigr-glimmer-mg, tophat, trace2dbest, tracetuner, treebuilder3d, treetime, treeview, tripal, trnascan-se, twain, ugene, uniprime, vegan, vienna-rna, vmd, wgs-assembler, x-tandem-pipeline, zalign, zodiac-zeden
Description: Debian Med micro-biology packages
This metapackage will install Debian packages related to molecular biology,
structural biology and bioinformatics for use in life sciences.
@@ -69,8 +66,8 @@
Package: med-bio-dev
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: bioperl, bioperl-run, biosquid, libace-perl, libbio-graphics-perl, libbio-mage-perl, libbio-mage-utils-perl, libbio-primerdesigner-perl, libbiococoa-dev, libbiojava-java, libchado-perl, libffindex0-dev, libgenome-1.3-0-dev, libgo-perl, libjebl2-java, libncbi6-dev, libpal-java, librg-reprof-bundle-perl, librostlab-blast-doc, librostlab-blast0-dev, librostlab-doc, librostlab3-dev, libsrf-dev, libstaden-read-dev, libtfbs-perl, libvibrant6-dev, libzerg-perl, libzerg0-dev, mcl, python-biopython, python-cogent, r-bioc-biobase, r-cran-genetics, r-cran-haplo.stats, ruby-bio, seqan-dev
-Suggests: bioclipse, biostrings, iranges, libajax6-dev, libbio-das-perl, libgbfp-dev, libgff-perl, libmems-1.5-1, libnucleus6-dev, libqsearch-dev, librg-blast-parser-perl, libsbml5-dev, octave-bioinfo, pysam, python-mmtk, r-cran-rocr
+Recommends: bioperl, bioperl-run, biosquid, libace-perl, libai-fann-perl, libbio-graphics-perl, libbio-mage-perl, libbio-mage-utils-perl, libbio-primerdesigner-perl, libbiococoa-dev, libbiojava-java, libbiojava3-java, libchado-perl, libffindex0-dev, libgenome-1.3-0-dev, libgo-perl, libhmsbeagle-dev, libjebl2-java, libncbi6-dev, libpal-java, librg-blast-parser-perl, librg-reprof-bundle-perl, librostlab-blast-doc, librostlab-blast0-dev, librostlab-doc, librostlab3-dev, libsort-key-top-perl, libsrf-dev, libstaden-read-dev, libtfbs-perl, libvibrant6-dev, libzerg-perl, libzerg0-dev, mcl, python-biopython, python-cogent, r-bioc-biobase, r-cran-genetics, r-cran-haplo.stats, ruby-bio, seqan-dev
+Suggests: bioclipse, biostrings, iranges, libbamtools-dev, libbio-das-perl, libforester-java, libgbfp-dev, libgenometools0-dev, libgff-perl, libmems-1.5-1, libnhgri-blastall-perl, libopenmm4-dev, libqsearch-dev, librcsb-core-wrapper0-dev, libsbml5-dev, libswarm2-dev, octace-bioinfo, octave-bioinfo, python-biom-format, python-librcsb-core-wrapper, python-mmtk, python-pysam, r-bioc-biocgenerics, r-cran-rocr
Description: Debian Med packages for development of micro-biology applications
This metapackage will install Debian packages which might be helpful
for development of applications for micro-biological research.
@@ -89,18 +86,18 @@
Package: med-data
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: python-hl7
-Suggests: drugref.org, freediams
+Recommends: freediams, freemedforms-freedata, python-hl7
+Suggests: drugref.org
Description: Debian Med drug databases
- There is at least one free medical drug database packaged for Debian
- which can be installed using this metapackage. It is supported by the
- GNUmed Electronic Medical Record package.
+ This metapackage will install free drug databases and related
+ applications. The database can be accessed by any EMR using
+ the application.
Package: med-dental
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: imagetooth
-Suggests: openmolar
+Suggests: entangle, openmolar
Description: Debian Med packages related to dental practice
This metapackage contains dependencies for a collection of software
which might be helpful for dentists to manage their practice.
@@ -109,7 +106,7 @@
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: epigrass, r-cran-diagnosismed, r-cran-epi, r-cran-epibasix, r-cran-epicalc, r-cran-epir, r-cran-epitools
-Suggests: netepi-analysis, netepi-collection, r-cran-msm, r-cran-surveillance, repast, swarm
+Suggests: netepi-analysis, netepi-collection, r-cran-msm, r-cran-surveillance, repast
Description: Debian Med epidemiology related packages
This metapackage will install tools that are useful in epidemiological
research. Several packages making use of the GNU R data language for
@@ -120,8 +117,8 @@
Package: med-imaging
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: aeskulap, amide, biosig-tools, caret, ctn, ctsim, dcmtk, dicom3tools, dicomnifti, dicomscope, ginkgocadx, gofigure2, gwyddion, imagej, imagevis3d, itksnap, libgdcm-tools, medcon, minc-tools, mriconvert, mricron, mrtrix, nifti-bin, odin, openmeeg-tools, openslide-tools, pixelmed-java, plastimatch, python-dipy, python-mvpa, python-nifti, python-nipy, python-nipype, python-nitime, sigviewer, sofa-apps, tifffile, via-bin, volview, voxbo, xmedcon
-Suggests: afni, ants, bioimagesuite, bioimagexd, blox, brainvisa, cdmedicpacs, cellprofiler, cmtk, connectomeviewer, conquest-dicom-server, dcm4che, dcm4chee, devide, dicom4j, dicoogle, drjekyll, dti-query, dtitk, ecg2png, eeglab, elastix, fiji, freesurfer, fsl, fslview, gimias, hid, imagemagick, imview, insightapplications, invesalius, isis, jemris, jist, kradview, libvista2, lipsia, maris, mayam, medisnap, mesa-test-tools, micromanager, mipav, miview, mni-autoreg, mni-colin27-nifti, mni-icbm152-nlin-2009, mni-n3, mrisim, omero, opendicom.net, openelectrophy, opensourcepacs, openwalnut, piano, pngquant, pymeg, pysurfer, pyxid, slicer, stabilitycalc, stir, tempo, visit, vmtk, xnat
+Recommends: aeskulap, amide, ants, biosig-tools, caret, ctn, ctsim, dcmtk, dicom3tools, dicomnifti, dicomscope, ginkgocadx, gofigure2, gwyddion, imagej, imagevis3d, itksnap, king, libgdcm-tools, medcon, minc-tools, mriconvert, mricron, mrtrix, nifti-bin, odin, openmeeg-tools, openslide-tools, pixelmed-java, plastimatch, python-dipy, python-mvpa, python-nifti, python-nipy, python-nipype, python-nitime, sigviewer, sofa-apps, tifffile, via-bin, volview, voxbo, xmedcon
+Suggests: afni, bioimagesuite, bioimagexd, blox, brainvisa, camitk-imp, cdmedicpacs, cellprofiler, cmtk, connectomeviewer, conquest-dicom-server, crea, dcm4chee, devide, dicom4j, dicoogle, drjekyll, dti-query, dtitk, ecg2png, eeglab, elastix, fiji, freesurfer, fsl, fslview, gimias, hid, imagemagick, imview, incf-nidash-oneclick-clients, insightapplications, invesalius, isis, jemris, jist, kradview, libdcm4che-java, lipsia, maris, mayam, medisnap, mesa-test-tools, mia-tools, mialmpick, micromanager, mipav, miview, mni-autoreg, mni-colin27-nifti, mni-icbm152-nlin-2009, mni-n3, mrisim, omero, opendicom.net, openelectrophy, opensourcepacs, openwalnut, orthanc, paraview, piano, pngquant, pymeg, pysurfer, pyxid, slicer, stabilitycalc, stir, tempo, visit, vmtk, xnat
Description: Debian Med imaging packages
This metapackage will install Debian packages which might be useful in
medical image processing.
@@ -144,8 +141,8 @@
Package: med-imaging-dev
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: cimg-dev, ctn-dev, gmic, libbiosig-dev, libcv-dev, libgdcm2-dev, libgdf-dev, libgiftiio-dev, libigstk4-dev, libinsighttoolkit3-dev, libmdc2-dev, libminc-dev, libnifti-dev, libopenmeeg-dev, libopenslide-dev, libteem1-dev, libvia-dev, libvolpack1-dev, libvxl1-dev, odin, python-cfflib, python-dicom, python-dipy, python-gdcm, python-mvpa, python-nibabel, python-nipy, python-nipype, python-nitime, python-pyxnat
-Suggests: emokit, igstk-examples, insighttoolkit3-examples, libactiviz.net5.6-cil, libbio-formats-java, libctkcore0-dev, libeegdev-dev, libmni-perllib-perl, libnifti-doc, libopenslide-java, libvista2-dev, libvtk5.4, libxdffileio-dev, python-libavg, python-openslide
+Recommends: cimg-dev, ctn-dev, gmic, libactiviz.net-cil, libbiosig-dev, libcv-dev, libgdcm2-dev, libgdf-dev, libgiftiio-dev, libigstk4-dev, libinsighttoolkit3-dev, libmdc2-dev, libminc-dev, libnifti-dev, libopenigtlink1-dev, libopenmeeg-dev, libopenslide-dev, libvia-dev, libvolpack1-dev, libvtk5-dev, libvxl1-dev, odin, python-cfflib, python-dicom, python-dipy, python-gdcm, python-mvpa, python-nibabel, python-nipy, python-nipype, python-nitime, python-pyxnat
+Suggests: emokit, igstk-examples, insighttoolkit3-examples, libbio-formats-java, libcamitk3-dev, libctk-dev, libeegdev-dev, libmia-2.0-dev, libmni-perllib-perl, libnifti-doc, libopenslide-java, libteem1-dev, libvistaio-dev, libvtk5.4, libxdffileio-dev, octave-dicom, python-casmoothing, python-libavg, python-openslide
Description: Debian Med packages for medical image development
This metapackage will install Debian packages which might be useful
for developing applications for medical image processing.
@@ -183,8 +180,8 @@
Package: med-practice
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: clinica, ginkgocadx, gnumed-client, gnumed-server, libchipcard-tools, r-cran-medadherence
-Suggests: clearhealth, elementalclinic, elexis, freeb, freediams, freeicd, freemed, freemedforms, freeshim, libctapimkt0, medintux, mirrormed, mirth, openemr, openpms, openrep, proteus, qrisk2, remitt, resmedicinae, sqlclinic, thera-pi, tinyheb
+Recommends: clinica, freediams, freemedforms-emr, ginkgocadx, gnumed-client, gnumed-server, libchipcard-tools, r-cran-medadherence
+Suggests: clearhealth, elementalclinic, elexis, entangle, freeb, freeicd, freemed, freeshim, libctapimkt0, medintux, mirrormed, mirth, openemr, openpms, openrep, proteus, qrisk2, remitt, resmedicinae, sqlclinic, thera-pi, tinyheb
Description: Debian Med packages for practice management
This metapackage contains dependencies for a collection of software
which might be helpful for practitioners to manage their practice.
@@ -210,7 +207,7 @@
Package: med-statistics
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: r-bioc-edger, r-bioc-limma, r-cran-pvclust, r-cran-qvalue, r-cran-randomforest
+Recommends: r-bioc-edger, r-bioc-limma, r-bioc-qvalue, r-cran-pvclust, r-cran-randomforest
Suggests: r-cran-beeswarm, science-statistics
Description: Debian Med statistics
This metapackage will install packages which are helpful to do statistics
@@ -220,7 +217,7 @@
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
Recommends: edfbrowser, hunspell-de-med, pcalendar, pondus, quitcount, wgerman-medical, workrave
-Suggests: cl-pubmed, cycle, hunspell-en-med, mencal, mssstest, python-clips
+Suggests: cl-pubmed, cycle, entangle, hunspell-en-med, mencal, mssstest, python-clips
Description: Debian Med several tools
This metapackage will install tools for several purposes in health care.
Currently it contains some simple programs for Personal Health.
@@ -228,8 +225,8 @@
Package: med-typesetting
Architecture: all
Depends: med-tasks (= ${binary:Version}), med-config (= ${binary:Version})
-Recommends: texlive-latex-extra, texlive-science
-Suggests: bibus, jabref-plugin-oo, kbibtex, referencer
+Recommends: king, texlive-latex-extra, texlive-science
+Suggests: biber, bibus, jabref-plugin-oo, kbibtex, referencer
Description: Debian Med support for typesetting and publishing
This metapackage will install Debian packages that might be helpful
for typesetting and publishing in medical care and structural
diff -Nru debian-med-1.11/debian/control.stub debian-med-1.13.2/debian/control.stub
--- debian-med-1.11/debian/control.stub 2012-04-05 08:30:36.000000000 +0200
+++ debian-med-1.13.2/debian/control.stub 2012-12-20 09:30:36.000000000 +0100
@@ -4,7 +4,7 @@
Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>
DM-Upload-Allowed: yes
Uploaders: Andreas Tille <tille@debian.org>
-Build-Depends-Indep: blends-dev (>= 0.6.15)
+Build-Depends-Indep: blends-dev (>= 0.6.16.2)
Standards-Version: 3.9.3
Vcs-Browser: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/
Vcs-Svn: svn://svn.debian.org/blends/projects/med/trunk/debian-med/
diff -Nru debian-med-1.11/debian-med-tasks.desc debian-med-1.13.2/debian-med-tasks.desc --- debian-med-1.11/debian-med-tasks.desc 2012-04-17 10:05:09.000000000 +0200 +++ debian-med-1.13.2/debian-med-tasks.desc 2012-12-20 09:30:47.000000000 +0100 @@ -19,6 +19,7 @@ loki plink r-cran-qtl + r-cran-genabel amap-align boxshade fastx-toolkit @@ -32,7 +33,9 @@ bwa mummer blast2 + ncbi-blast+ mafft + sra-toolkit t-coffee kalign hmmer @@ -98,12 +101,12 @@ samtools bedtools filo - gassst r-bioc-hilbertvis r-other-mott-happy mira-assembler alien-hunter ncoils + gentle picard-tools acedb-other-dotter acedb-other-belvu @@ -112,6 +115,7 @@ mrbayes squizz clonalframe + dssp jellyfish ballview pynast @@ -126,7 +130,8 @@ proftmb hhsuite ffindex - ncbi-blast+ + neobio + fasttree abacas profnet-bval profnet-chop @@ -164,7 +169,9 @@ python-cogent ruby-bio libbiojava-java + libbiojava3-java libgenome-1.3-0-dev + libai-fann-perl libbio-mage-perl libtfbs-perl libgo-perl @@ -190,6 +197,9 @@ librostlab-doc librostlab-blast0-dev librostlab-blast-doc + librg-blast-parser-perl + libsort-key-top-perl + libhmsbeagle-dev Task: med-bio-ngs Section: debian-med @@ -264,13 +274,15 @@ Task: med-data Section: debian-med Description: Debian Med drug databases - There is at least one free medical drug database packaged for Debian - which can be installed using this metapackage. It is supported by the - GNUmed Electronic Medical Record package. + This metapackage will install free drug databases and related + applications. The database can be accessed by any EMR using + the application. Relevance: 10 Key: med-data Packages: list + freediams + freemedforms-freedata python-hl7 Task: med-dental @@ -360,6 +372,7 @@ mricron voxbo mrtrix + ants itksnap mriconvert sigviewer @@ -367,6 +380,7 @@ openmeeg-tools plastimatch biosig-tools + king python-nitime python-dipy @@ -383,6 +397,7 @@ cimg-dev libminc-dev libmdc2-dev + libvtk5-dev libnifti-dev libigstk4-dev libinsighttoolkit3-dev @@ -397,9 +412,10 @@ odin libcv-dev libvxl1-dev - libteem1-dev gmic libgiftiio-dev + libactiviz.net-cil + libopenigtlink1-dev python-dicom libopenmeeg-dev python-nibabel @@ -462,6 +478,8 @@ gnumed-server libchipcard-tools ginkgocadx + freediams + freemedforms-emr r-cran-medadherence clinica @@ -503,7 +521,7 @@ Packages: list r-bioc-edger r-bioc-limma - r-cran-qvalue + r-bioc-qvalue r-cran-randomforest r-cran-pvclust @@ -536,4 +554,5 @@ Packages: list texlive-science texlive-latex-extra + king
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Description: GNU Zip compressed data