Your message dated Thu, 04 Apr 2013 20:18:22 +0100 with message-id <1365103102.6034.6.camel@jacala.jungle.funky-badger.org> and subject line Re: Bug#696387: unblock: debian-med/1.13.2 has caused the Debian Bug report #696387, regarding unblock: debian-med/1.13.2 to be marked as done. This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact owner@bugs.debian.org immediately.) -- 696387: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=696387 Debian Bug Tracking System Contact owner@bugs.debian.org with problems
--- Begin Message ---
- To: Debian Bug Tracking System <submit@bugs.debian.org>
- Subject: unblock: debian-med/1.13.2
- From: Andreas Tille <tille@debian.org>
- Date: Thu, 20 Dec 2012 10:20:16 +0100
- Message-id: <20121220092016.9123.58048.reportbug@mail.an3as.eu>
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 + kingAttachment: debian-med_1.13.2.debdiff.gz
Description: GNU Zip compressed data
--- End Message ---
--- Begin Message ---
- To: Andreas Tille <tille@debian.org>, 696387-done@bugs.debian.org
- Subject: Re: Bug#696387: unblock: debian-med/1.13.2
- From: "Adam D. Barratt" <adam@adam-barratt.org.uk>
- Date: Thu, 04 Apr 2013 20:18:22 +0100
- Message-id: <1365103102.6034.6.camel@jacala.jungle.funky-badger.org>
- In-reply-to: <20121220092016.9123.58048.reportbug@mail.an3as.eu>
- References: <20121220092016.9123.58048.reportbug@mail.an3as.eu>
On Thu, 2012-12-20 at 10:20 +0100, Andreas Tille wrote: > Please unblock package debian-med Done. Regards, Adam
--- End Message ---