Lintian Reports

Debian Med Packaging Team

At the time of the last Lintian run, the following possible problems were found in packages maintained by Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.org>, listed by source package. See also the full report, including info, experimental and overridden tags. Also see their QA overview.

abacas (1.3.1-5) §

abacas

adapterremoval (2.3.1-1) §

adapterremoval

aeskulap (0.2.2-beta2+git20190406.ef77f01-1) §

aeskulap

aevol (5.0+ds-1) §

aevol

alien-hunter (1.7-7) §

alien-hunter

ampliconnoise (1.29-8) §

ampliconnoise-dbgsym

arb (6.0.6-4; non-free) §

arb-common

baitfisher (1.2.7+git20180107.e92dbf2+dfsg-1) §

baitfisher

bali-phy (3.4.1+dfsg-2) §

bali-phy-dbgsym

ball (1.4.3~beta1-4) §

ball (1.5.0+git20180813.37fc53c-3)

ballview

libball1.5

libball1.5-dev

libballview1.5

libballview1.5-dev

barrnap (0.9+dfsg-1) §

barrnap

bbmap (38.63+dfsg-1) §

bbmap

bcbio (1.1.5-1) §

bcbio

bcftools (1.9-1) §

bcftools

beads (1.1.18+dfsg-3) §

beads

beast-mcmc (1.10.4+dfsg-1) §

beast-mcmc

libnucleotidelikelihoodcore0-dbgsym

bedops (2.4.35+dfsg-1) §

bedops-dbgsym

bedops (2.4.36+dfsg-2)

bedops

bedops-doc

bedtools (2.27.1+dfsg-4) §

bedtools-test

bedtools (2.28.0+dfsg1-1)

bedtools

bedtools-test

bio-tradis (1.4.1+dfsg-1) §

bio-tradis

biobambam2 (2.0.95-1) §

biobambam2

biobambam2 (2.0.137+dfsg-1)

biobambam2

biococoa (2.2.2-4) §

libbiococoa2-dbgsym (2.2.2-4+b1; main)

biojava-live (1:1.7.1-8) §

libbiojava-java-doc

biojava4-live (4.2.12+dfsg-2) §

biomaj3 (3.1.8-1) §

python3-biomaj3

biomaj3-cli (3.1.10-1) §

python3-biomaj3-cli

biomaj3-daemon (3.0.19-1) §

python3-biomaj3-daemon

biomaj3-download (3.0.21-1) §

python3-biomaj3-download

biomaj3-process (3.0.13-1) §

python3-biomaj3-process

biomaj3-user (3.0.8-1) §

python3-biomaj3-user

biomaj3-zipkin (0.2.2-1) §

bioperl-run (1.7.3-1) §

libbio-perl-run-perl

biosyntax (1.0.0b-1) §

bowtie2 (2.3.5.1-1) §

bowtie2

brig (0.95+dfsg-2) §

brig

camitk (4.1.2-3) §

libcamitk-dev

cct (20170919+dfsg-1) §

cct

cd-hit (4.8.1-2) §

cd-hit

centrifuge (1.0.3-3) §

centrifuge

cfflib (2.0.5-3) §

changeo (0.4.6-1) §

changeo

circos (0.69.9+dfsg-1) §

circos

clearcut (1.0.9-4) §

clearcut-dbgsym

clonalorigin (1.0-3) §

clonalorigin

cnvkit (0.9.6-1) §

cnvkit (0.9.6-1+b1; main)

crac (2.5.2+dfsg-2) §

crac

ctdconverter (2.1-1) §

ctdconverter

ctdopts (1.2-3) §

ctsim (6.0.2-3) §

ctsim-doc

cwltool (1.0.20190915164430+dfsg-1) §

cwltool

cyvcf2 (0.11.5-1) §

python3-cyvcf2

dialign-t (1.0.2-12) §

dialign-tx

dicomscope (3.6.0-20) §

dicomscope

dnaclust (3-7) §

dnaclust

dwgsim (0.1.12-2) §

dwgsim

ecopcr (1.0.1+dfsg-1) §

ecopcr

eigensoft (7.2.1+dfsg-1) §

eigensoft

emboss (6.6.0+dfsg-7) §

emboss (6.6.0+dfsg-7+b1; main)

emboss-doc

emboss-lib (6.6.0+dfsg-7+b1; main)

emboss-test

jemboss

emboss-explorer (2.2.0-10) §

emboss-explorer

epigrass (2.4.7-2) §

estscan (3.0.3-3) §

estscan

falcon (1.8.8-1) §

falcon

fast5 (0.6.5-3) §

fast5

fasta3 (36.3.8g-1; non-free) §

fasta3

fastlink

fastlink-dbgsym

ffindex (0.9.9.9-3) §

libffindex0

fis-gtm (6.3-007-1) §

fis-gtm-6.3-007 (6.3-007-1+b1; main)

freebayes (1.3.1-1) §

freebayes

freemedforms-project (0.9.4-2) §

freemedforms-libs (0.9.4-2+b2; main)

fsm-lite (1.0-3) §

fw4spl (17.2.0-2) §

fw4spl

g2 (0.72-8) §

libg20 (0.72-8+b1; main)

galileo (0.5.1-6) §

galileo-daemon

gbrowse (2.56+dfsg-4) §

gbrowse

gbrowse-data

gdcm (2.8.9-1~exp1) §

gdcm-doc

gemma (0.98.1+dfsg-1) §

gemma

genometester (4.0+git20180508.a9c14a6+dfsg-1) §

genometester

genometools (1.5.10+ds-3) §

ghmm (0.9~rc3-2) §

ghmm

gnumed-client (1.7.7+dfsg-1) §

gwama (2.2.2+dfsg-2) §

hhsuite (3.2.0-2) §

hhsuite

hmmer2 (2.3.2+dfsg-6) §

libhmmer2-dev

htsjdk (2.18.2+dfsg-2) §

libhtsjdk-java-doc

htslib (1.9-11) §

libhts-dev

hyphy (2.3.14+dfsg-2) §

hyphy-mpi

hyphy-pt

igor (1.3.0+dfsg-1) §

igor

imagej (1.52p-1) §

libij-java-doc

insighttoolkit4 (4.12.2-dfsg1-4) §

libinsighttoolkit4-dev (4.12.2-dfsg1-4+b2; main)

libinsighttoolkit4.12 (4.12.2-dfsg1-4+b2; main)

insighttoolkit4 (4.13.0-dfsg1-2~exp1)

libinsighttoolkit4-dev

libinsighttoolkit4.13

insighttoolkit4 (4.13.2-dfsg1-1~exp)

invesalius (3.1.99992-3) §

invesalius

invesalius (3.1.99993-1)

ipig (0.0.r5-3) §

ipig

ismrmrd (1.4.0-1) §

libismrmrd1.3

iva (1.0.9+ds-6) §

iva (1.0.9+ds-6+b1; main)

jam-lib (0.1.git20180106.740247a+dfsg-1) §

libjam-java-doc

jebl2 (0.1+git20180418.653eb83-1) §

libjebl2-java-doc

jheatchart (0.6-1) §

libjheatchart-java-doc

jmodeltest (2.1.10+dfsg-7) §

jmodeltest

kallisto (0.46.0+dfsg-1) §

kallisto

khmer (2.1.2+dfsg-6) §

kineticstools (0.6.1+git20180425.27a1878-2) §

lagan (2.0-5) §

lamarc (2.1.10.1+dfsg-4) §

lamarc

last-align (984-1) §

last-align

libace-perl (1.92-8) §

libace-perl (1.92-8+b1; main)

libbio-graphics-perl (2.40-3) §

libbio-graphics-perl

libbio-mage-perl (20030502.3-5) §

libbio-mage-perl

libbio-mage-utils-perl (20030502.0-4) §

libbio-mage-utils-perl

libbpp-phyl-omics (2.4.1-1) §

libbpp-phyl-omics3

libcolt-free-java (1.2.0+dfsg-7) §

libcolt-free-java-doc

libdeflate (1.3-3) §

libdeflate0

libgenome (1.3.11+svn20110227.4616-2) §

libgenome-perl (0.06-5) [Uploader] §

libgenome-perl

libgkarrays (2.1.0+dfsg-2) §

libgkarrays1-dbgsym

libgzstream (1.5+dfsg-4) §

libgzstream0-dbgsym

libhac-java (0.20110510-3) §

libhac-java-doc

libhmsbeagle (3.1.2+dfsg-6) §

libhmsbeagle1v5

libjung-free-java (2.0.1+dfsg-1) §

libjung-free-java-doc

liblemon (1.3.1+dfsg-2) §

liblemon-dev

liblemon-utils

libmaus2 (2.0.611-1) §

libmaus2 (2.0.663-1)

libmaus2-2

libmaus2-dev

libmems (1.6.0+4725-8) §

libmems-dev (1.6.0+4725-8+b1; main)

libmialm (1.0.9-2) §

libminc (2.4.03-2) §

libmuscle (3.7+4565-6) §

libmuscle1

libncl (2.1.21+git20190531.feceb81-1) §

libncl-dev

ncl-tools

liboptions-java (0.0.20120113-3) §

liboptions-java-doc

libpal-java (1.5.1+dfsg-5) §

libpal-java-doc

librandom123 (1.09+dfsg-2) §

librcsb-core-wrapper (1.005-6) §

libsbml (5.16.0+dfsg-2) §

libsbml (5.17.2+dfsg-3)

libsbml5-java

libsis-base-java (18.09~pre1+git20180827.fe4953e+dfsg-1) §

libsis-base-java

libsis-base-jni

libsis-jhdf5-java (14.12.6-2) §

libsmithwaterman (0.0+git20160702.2610e25-7) §

libsmithwaterman-dev

libtecla (1.6.3-2.1) §

libtfbs-perl (0.7.1-2) §

libtfbs-perl (0.7.1-2+b1; main)

libvcflib (1.0.0~rc2+dfsg-2) §

libvcflib-tools-dbgsym

libvcflib (1.0.0+dfsg-2)

libvcflib-tools

libvistaio (1.2.19-2) §

lucy (1.20-1) §

lucy

maude (2.7-2) §

mauve-aligner (2.4.0+4736-2) §

mauve-aligner

mcl (1:14-137+ds-4) §

mcl

melting (4.3.1+dfsg-3) §

metaphlan2 (2.7.8-1) §

metaphlan2

metastudent (2.0.1-7) §

metastudent-data (2.0.1-4) §

mgltools-bhtree (1.5.7-3; non-free) §

mgltools-bhtree

mgltools-cadd (1.5.7-4; non-free) §

mgltools-cadd

mgltools-cmolkit (1.5.7~rc1+cvs.20140424-2; non-free) §

mgltools-cmolkit

mgltools-dejavu (1.5.7-3; non-free) §

mgltools-dejavu

mgltools-geomutils (1.5.7-3; non-free) §

mgltools-geomutils

mgltools-gle (1.5.7-3; non-free) §

mgltools-gle

mgltools-mglutil (1.5.7-4; non-free) §

mgltools-mglutil

mgltools-molkit (1.5.7-3; non-free) §

mgltools-molkit

mgltools-networkeditor (1.5.7-4; non-free) §

mgltools-networkeditor

mgltools-opengltk (1.5.7-3; non-free) §

mgltools-opengltk

mgltools-pmv (1.5.7-3; non-free) §

mgltools-pmv

mgltools-pyautodock (1.5.7-3; non-free) §

mgltools-pyautodock

mgltools-pybabel (1.5.7-3; non-free) §

mgltools-pybabel

mgltools-pyglf (1.5.7-3; non-free) §

mgltools-pyglf

mgltools-scenario2 (1.5.7-2; non-free) §

mgltools-scenario2

mgltools-sff (1.5.7-3; non-free) §

mgltools-sff

mgltools-support (1.5.7-3; non-free) §

mgltools-support

mgltools-symserv (1.5.7-2; non-free) §

mgltools-symserv

mgltools-utpackages (1.5.7-3; non-free) §

mgltools-utpackages

mgltools-viewerframework (1.5.7-3; non-free) §

mgltools-vision (1.5.7+dfsg-2; non-free) §

mgltools-vision

mgltools-visionlibraries (1.5.7-2; non-free) §

mgltools-visionlibraries

mgltools-volume (1.5.7-3; non-free) §

mgltools-volume

mgltools-webservices (1.5.7-3; non-free) §

mgltools-webservices

mia (2.4.6-4) §

mialmpick (0.2.14-2) §

miaviewit (1.0.5-2) §

libmiaviewit-dev

microbegps (1.0.0-5) §

microbegps

microbiomeutil (20101212+dfsg1-2) §

chimeraslayer

nast-ier

wigeon

minc-tools (2.3.00+dfsg-3) §

minc-tools (2.3.00+dfsg-3+b1; main)

mira (4.9.6-4) §

mobyle (1.5.5+dfsg-6) §

mobyle

mobyle-utils

mobyle-utils-dbgsym

mobyle-programs (5.1.2-3) §

mobyle-programs

mrbayes (3.2.6+dfsg-2) §

mrbayes-doc

mrs (6.0.5+dfsg-7) §

mrs-dbgsym (6.0.5+dfsg-7+b2; main)

mypy (0.720-3) §

mypy

nanopolish (0.11.1-1) §

nanopolish

ncbi-blast+ (2.8.1-1) §

ncbi-blast+ (2.9.0-1)

ncbi-blast+

ncbi-blast+-legacy

ncbi-entrez-direct (10.9.20190219+ds-1) §

ncbi-entrez-direct (10.9.20190219+ds-1+b10; main)

ncbi-tools6 (6.1.20170106-6) §

ncbi-tools6 (6.1.20170106+dfsg1-7)

libncbi6

libvibrant6-dev

ngs-sdk (2.9.3-1) §

libngs-sdk2-dbgsym

njplot (2.4-8) §

njplot-dbgsym

nutsqlite (2.0.6-1) §

nutsqlite

obitools (1.2.12+dfsg-2) §

obitools (1.2.13+dfsg-1)

obitools

odil (0.10.0-3) §

odil (0.10.0-7)

opencfu (3.9.0-3) §

opencfu

openslide (3.4.1+dfsg-4) §

libopenslide-dev

opensurgsim (0.7.0-8) §

libopensurgsim

orthanc (1.5.7+dfsg-2) §

orthanc

orthanc-dicomweb (1.0+dfsg-1) §

orthanc-dicomweb

orthanc-mysql (2.0-2) §

orthanc-mysql

orthanc-postgresql (3.2-1) §

orthanc-postgresql

orthanc-webviewer (2.5-1) §

orthanc-webviewer

orthanc-wsi (0.6-2) §

orthanc-wsi

paml (4.9i+dfsg-1) §

paml

paraclu (9-2) §

paraclu

pbalign (0.3.2-1) §

pbbam (0.23.0+dfsg-1) §

pbbamtools (0.23.0+dfsg-1+b1; main)

pbbarcode (0.8.0-5) §

pbbarcode

pbdagcon (0.3+git20161121.0000000+ds-1.1) §

pbdagcon

pbgenomicconsensus (2.3.2-5) §

pbgenomicconsensus

pbh5tools (0.8.0+git20170929.58d54ff+dfsg-1) §

pbseqlib (5.3.1+dfsg-2.1) §

libblasr (5.3.1+dfsg-2.1+b1; main)

libpbdata (5.3.1+dfsg-2.1+b1; main)

libpbihdf (5.3.1+dfsg-2.1+b1; main)

pbsuite (15.8.24+dfsg-3) §

pdb2pqr (2.1.1+dfsg-5) §

pdb2pqr-doc

phast (1.5+dfsg-1) §

phast

phipack (0.0.20160614-3) §

phipack

phybin (0.3-3) §

phybin

phylip (1:3.697+dfsg-1) §

phylip

phyml (3:3.3.20180621-2) §

phyml-dbgsym

phyml (3:3.3.20190321-2)

phyml

phyx (1.0+ds-1) §

phyx

picard-tools (2.18.25+dfsg-2) §

libpicard-java-doc

pirs (2.0.2+dfsg-8) §

pirs

pirs-dbgsym

pixelmed (20150917+git20151209.36f3174+dfsg-2) §

libpixelmed-java-doc

pixelmed-apps

pixelmed-www

pixelmed-codec (20170512-2) §

libpixelmed-codec-java

populations (1.2.33+svn0120106+dfsg-2) §

prokka (1.13.7+dfsg-1) §

proteinortho (5.16.b+dfsg-1) §

proteinortho-dbgsym

proteinortho (6.0.6+dfsg-1)

proteinortho

psortb (3.0.6+dfsg-1) §

psortb (3.0.6+dfsg-1+b1; main)

pybel (0.13.1-1) §

python3-pybel

pymia (0.1.9-2) §

python-biom-format (2.1.7+dfsg-3) §

python3-biom-format

python-bx (0.8.2-1) §

python-bx (0.8.4-2)

python3-bx

python-bz2file (0.98-2) §

python-clips (1.0.7.348+clips-4) §

python-cogent (1.9-14) §

python-easydev (0.9.37-1) §

python-easydev

python3-easydev

python-gffutils (0.9-1) §

python3-gffutils

python-pbcommand (1.1.1-1) §

python-pbcore (1.6.5+dfsg-1) §

python-pybedtools (0.8.0-2) §

pybedtools-bin

python3-pybedtools

python-pyfaidx (0.5.5.2-2) §

python-pyfaidx-examples

python-pyvcf (0.6.8+git20170215.476169c-2) §

pyvcf

python-ruffus (2.8.1-4) §

python-ruffus

python-screed (1.0-3) §

python3-screed

python-skbio (0.5.5-2) §

python-skbio-doc

qcumber (1.0.14+dfsg-1) §

qcumber

qiime (1.9.1+dfsg-3) §

qiime-dbgsym

radiant (2.7.1+dfsg-1) §

radiant

rapmap (0.14.1+dfsg-2) §

rapmap

raxml (8.2.12+dfsg-1) §

raxml

raxml-dbgsym

ray (2.3.1-6) §

ray

rdp-alignment (1.2.0-5) §

rdp-alignment

rdp-classifier (2.10.2-4) §

rdp-classifier

rdp-classifier-doc

reapr (1.0.18+dfsg-4) §

reapr

relion (1.4+dfsg-4) §

reprof (1.0.1-6) §

roary (3.12.0+dfsg-3) §

roary

rsem (1.3.2+dfsg-2) §

rsem

rtax (0.984-6) §

rtax

runcircos-gui (0.0+git20180828.97703b9-1) §

runcircos-gui

sambamba (0.6.7-2) §

samtools (1.9-5) §

samtools

scoary (1.6.16-2) §

scoary

scythe (0.994+git20141017.20d3cff-1) §

seer (1.1.4-2) §

seer (1.1.4-2+b2; main)

seqan (1.4.2+dfsg-3) §

seqan-dev

seqan2 (2.4.0+dfsg-11) §

libseqan2-dev

seqmagick (0.7.0-1) §

seqmagick

sga (0.10.15-4) §

sga

sga-dbgsym

sift (4.0.3b-6; non-free) §

sift

sitplus (1.0.3-5.1) §

smalr (1.1+dfsg-2) §

smalr

snakemake (5.6.0-2) §

snakemake

snap (2013-11-29-9) §

snap

soapsnp (1.03-3) §

soapsnp

sofa-framework (1.0~beta4-12) §

solvate (1.0-2; non-free) §

spread-phy (1.0.7+dfsg-2) §

squizz (0.99d+dfsg-2) §

squizz

sra-sdk (2.9.3+dfsg-1) §

sra-toolkit (2.9.3+dfsg-1+b1; main)

stacks (2.41+dfsg-1) §

stacks

staden (2.0.0+b11-4) §

staden

staden-io-lib (1.14.11-6) §

libstaden-read-dev

staden-io-lib-examples

staden-io-lib-utils

sumaclust (1.0.31-2) §

sumaclust-dbgsym

sumatra (1.0.31-2) §

sumatra-dbgsym

swarm-cluster (2.2.2+dfsg-2) §

swarm

sweed (3.2.1+dfsg-1) §

swissknife (1.75-1) §

libswiss-perl

theseus (3.3.0-8) §

theseus

tifffile (20181128-2) §

tifffile

tnseq-transit (2.5.2-1) §

tnseq-transit

toil (3.20.0-1) §

toil

tophat (2.1.1+dfsg1-2) §

tophat (2.1.1+dfsg1-2+b1; main)

toppred (1.10-7) §

toppred

trace2dbest (3.0.1-1) §

trace2dbest

tracetuner (3.0.6~beta+dfsg-2) §

tracetuner

transrate-tools (1.0.0-2) §

transrate-tools-dbgsym

tree-puzzle (5.2-11) §

trinityrnaseq (2.6.6+dfsg-6) §

trinityrnaseq

trinityrnaseq-dbgsym

trinityrnaseq-examples

trnascan-se (2.0.3-1; non-free) §

trnascan-se

tvc (5.0.3+git20151221.80e144e+dfsg-2) §

tvc

uc-echo (1.12-12) §

uc-echo

ugene (1.31.1+dfsg-1; non-free) §

ugene

unanimity (3.3.0+dfsg-2.1) §

velvetoptimiser (2.2.6-2) §

velvetoptimiser

virulencefinder (2.0.3+git20190809.dde157a-1) §

virulencefinder

volpack (1.0b3-7) §

libvolpack1-dev

vsearch (2.13.6-1) §

vsearch (2.13.6-1+b1; main)

wise (2.4.1-21) §

wise-data

xmedcon (0.16.1+dfsg-1) §

libmdc-dev

medcon

xmedcon