debian/NEWS.Debian

+bio-tradis (1.3.3+dfsg-3) unstable; urgency=medium
+
+The package r-bioc-edger was removed from Debian since it was severely
+outdated.  An upgrade is not possible since recent version of BioConductor
+Edger can not be distributed by Debian since it is using non-distributable
+code locfit.
+
+Thus you need to manually install Edger in your R environment.
+
+ -- Andreas Tille <tille@debian.org>  Mon, 12 Feb 2018 15:05:27 +0100
+

debian/README.Debian

@@ -6,3 +6,11 @@ it has to be excluded from the package source.  You can find the
 documentation here:
 
     https://github.com/sanger-pathogens/Bio-Tradis/blob/master/BioTraDISTutorial.pdf
+
+
+Please note: You need to manually install BioConductor Edger which can
+not be distributed by Debian in recent version since it is using
+non-distributable code locfit.  So the way outdated r-bioc-edger package
+was removed from Debian.
+
+ -- Andreas Tille <tille@debian.org>  Mon, 12 Feb 2018 15:05:27 +0100

debian/changelog

+bio-tradis (1.3.3+dfsg-3) unstable; urgency=medium
+
+  * Standards-Version: 4.1.3
+  * Downgrade r-bioc-edger from Depends to Suggests since the package
+    was removed from Debian but people might consider local installations
+    Closes: #890096
+  * debhelper 11
+
+ -- Andreas Tille <tille@debian.org>  Mon, 12 Feb 2018 15:13:51 +0100
+
 bio-tradis (1.3.3+dfsg-2) unstable; urgency=medium
 
   * Team upload.

debian/compat

-10
+11

debian/control

@@ -4,12 +4,12 @@ Uploaders: Andreas Tille <tille@debian.org>
 Section: perl
 Testsuite: autopkgtest-pkg-perl
 Priority: optional
-Build-Depends: debhelper (>= 10),
+Build-Depends: debhelper (>= 11~),
                libtrycatch-perl,
                libtest-most-perl,
                libtest-files-perl,
                libbio-perl-perl
-Standards-Version: 4.0.0
+Standards-Version: 4.1.3
 Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/bio-tradis.git
 Vcs-Git: https://anonscm.debian.org/git/debian-med/bio-tradis.git
 Homepage: https://github.com/sanger-pathogens/Bio-Tradis
@@ -22,10 +22,10 @@ Depends: ${perl:Depends},
          samtools,
          tabix,
          r-base-core,
-         r-bioc-edger,
          r-cran-getopt,
          r-cran-mass
-Suggests: artemis
+Suggests: artemis,
+          r-bioc-edger,
 Description: analyse the output from TraDIS analyses of genomic sequences
  Bio-Tradis contains a set of tools to analyse the output from
  TraDIS analyses.
@@ -33,3 +33,7 @@ Description: analyse the output from TraDIS analyses of genomic sequences
  The Bio-Tradis analysis pipeline is implemented as an extensible Perl
  library which can either be used as is, or as a basis for the
  development of more advanced analysis tools.
+ .
+ Please note: You need to manually install BioConductor Edger which can
+ not be distributed by Debian in recent version since it is using
+ non-distributable code locfit.