[med-svn] [Git][med-team/mapdamage][master] 6 commits: New upstream version 2.0.9+dfsg

[Andreas Tille]

Andreas Tille pushed to branch master at Debian Med / mapdamage


Commits:
4ae67b6e by Andreas Tille at 2018-12-08T21:38:12Z
New upstream version 2.0.9+dfsg
- - - - -
a80a5d97 by Andreas Tille at 2018-12-08T21:38:12Z
Update upstream source from tag 'upstream/2.0.9+dfsg'

Update to upstream version '2.0.9+dfsg'
with Debian dir b6a5d94ab06db27eb4838fb7bae3b676cb1aade7
- - - - -
d58d9605 by Andreas Tille at 2018-12-08T21:38:12Z
New upstream version

- - - - -
3c964fc6 by Andreas Tille at 2018-12-08T21:38:50Z
Remove trailing whitespace in debian/changelog

- - - - -
805f45f8 by Andreas Tille at 2018-12-08T21:38:50Z
Remove trailing whitespace in debian/rules

- - - - -
3c484663 by Andreas Tille at 2018-12-08T21:41:57Z
Upload to unstable

- - - - -


4 changed files:

- debian/changelog
- debian/rules
- mapdamage/Rscripts/stats/function.R
- mapdamage/seq.py


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+mapdamage (2.0.9+dfsg-1) unstable; urgency=medium
+
+  * New upstream version
+  * Remove trailing whitespace in debian/changelog
+  * Remove trailing whitespace in debian/rules
+
+ -- Andreas Tille <tille at debian.org>  Sat, 08 Dec 2018 22:38:50 +0100
+
 mapdamage (2.0.8+dfsg-2) unstable; urgency=medium
 
   [ Steffen Moeller ]
@@ -39,7 +47,7 @@ mapdamage (2.0.6+dfsg-2) unstable; urgency=medium
     r-cran-rcppgsl package
   * Edit path to seqtk in composition.py
     Closes: #859090
-  * Fix typo in tests/control 
+  * Fix typo in tests/control
   * Add patch to fix quantile call to remove NA and NaNs
   * Add dependency providing liblapack.so and libblas.so
     Closes: #859091
@@ -47,7 +55,7 @@ mapdamage (2.0.6+dfsg-2) unstable; urgency=medium
   * Add information how to check R libraries and what to do in case of errors
     to README.test
   * Provide tests for examples from documentation
-    Closes: #848326 
+    Closes: #848326
   * Fixed typo in README.test
 
  -- Nadiya Sitdykova <rovenskasa at gmail.com>  Thu, 23 Mar 2017 21:34:41 -0700


=====================================
debian/rules
=====================================
@@ -17,4 +17,4 @@ override_dh_install:
 	dh_install
 	mv `find debian -name rescale_test.py` $(TESTDIR)
 	sed -i 's/^import rescale/from mapdamage &/' $(TESTDIR)/rescale_test.py
-	
+


=====================================
mapdamage/Rscripts/stats/function.R
=====================================
@@ -145,7 +145,7 @@ seqProbVecLambda <- function(lambda,lambda_disp,m,fo_only=NA,re_only=NA){
 
 #The following is an MC simulation code to mimic the 
 #nick frequency part in the model from Philip
-seqProbVecNuWithLengths<- cxxfunction( signature(
+seqProbVecNuWithLengths<- cxxfunction(methods::signature(
                                       I_la="numeric",
                                       I_la_disp="numeric",
                                       I_nu="numeric",
@@ -270,7 +270,7 @@ logLikFunOneBaseSlow <- function(Gen,S,Theta,deltad,deltas,laVec,nuVec,m,lin){
 
 #The same logic as in logLikFunOneBaseSlow except using a compiled code 
 #to do the hard work
-logLikFunOneBaseFast <- cxxfunction(signature(
+logLikFunOneBaseFast <- cxxfunction(methods::signature(
                                       I_Gen="numeric",
                                       I_S="numeric",
                                       I_Theta="numeric",


=====================================
mapdamage/seq.py
=====================================
@@ -63,6 +63,12 @@ def read_fasta_index(filename):
         print_err("Column 2 in FASTA index did not contain a number, found '%s':" % ref[1], filename, line)
         return None
 
+  if not fai:
+    sys.stderr.write("Error: Index for %r does contain any sequences.\n" % (filename,))
+    sys.stderr.write("       Please ensure that FASTA file is valid, and\n")
+    sys.stderr.write("       re-index file using 'samtool faidx'.\n")
+    return None
+
   return fai
 
 



View it on GitLab: https://salsa.debian.org/med-team/mapdamage/compare/8ad2d6e981d61f0a84c0889c57caf2c414d79978...3c484663e67fa5595048daa173d0ec1e88269a11

-- 
View it on GitLab: https://salsa.debian.org/med-team/mapdamage/compare/8ad2d6e981d61f0a84c0889c57caf2c414d79978...3c484663e67fa5595048daa173d0ec1e88269a11
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