Dear release team,
the new upstream version of probcons is a bugfix. Here is the debdiff.
Only the main source file has been changed. The other changes are
accessory, such as increasing the version number or updating README.
The package itself has been slightly modified: the watch file was fixed,
and ${source:Version} was changed to ${binary:Version} for
probcons-extra, in which /usr/share/doc/probcons-extra is a symlink to
/usr/share/doc/probcons. A patch in debian/patches was updated to match
the new Makefile, in which the version number was changed.
Have a nice day,
-- Charles Plessy, Wako, Saitama, Japan
diff -Nru /tmp/WvbmmACHFN/probcons-1.10/debian/changelog
/tmp/nkiW2nYLiX/probcons-1.11/debian/changelog
--- /tmp/WvbmmACHFN/probcons-1.10/debian/changelog 2007-02-22
10:27:18.000000000 +0900
+++ /tmp/nkiW2nYLiX/probcons-1.11/debian/changelog 2007-02-22
10:27:19.000000000 +0900
@@ -1,3 +1,11 @@
+probcons (1.11-1) unstable; urgency=low
+
+ * New upstream release fixing a bug with conflict between --annot and -a
+ options.
+ * Mended the watch file in the source package.
+
+ -- Charles Plessy <[EMAIL PROTECTED]> Wed, 14 Feb 2007 23:15:36 +0900
+
probcons (1.10-1) unstable; urgency=low
* Initial release Closes: #365499
diff -Nru /tmp/WvbmmACHFN/probcons-1.10/debian/control
/tmp/nkiW2nYLiX/probcons-1.11/debian/control
--- /tmp/WvbmmACHFN/probcons-1.10/debian/control 2007-02-22
10:27:18.000000000 +0900
+++ /tmp/nkiW2nYLiX/probcons-1.11/debian/control 2007-02-22
10:27:19.000000000 +0900
@@ -26,7 +26,7 @@
Package: probcons-extra
Architecture: any
-Depends: probcons (= ${source:Version}), ${shlibs:Depends}, ${misc:Depends}
+Depends: probcons (= ${binary:Version}), ${shlibs:Depends}, ${misc:Depends}
Suggests: gnuplot-nox | gnuplot-x11
Priority: extra
Description: Extra programs from the probcons package
diff -Nru
/tmp/WvbmmACHFN/probcons-1.10/debian/patches/10_add-RNA-in-Makefile.dpatch
/tmp/nkiW2nYLiX/probcons-1.11/debian/patches/10_add-RNA-in-Makefile.dpatch
--- /tmp/WvbmmACHFN/probcons-1.10/debian/patches/10_add-RNA-in-Makefile.dpatch
2007-02-22 10:27:18.000000000 +0900
+++ /tmp/nkiW2nYLiX/probcons-1.11/debian/patches/10_add-RNA-in-Makefile.dpatch
2007-02-22 10:27:19.000000000 +0900
@@ -12,8 +12,8 @@
@@ -16,6 +16,7 @@
################################################################################
- OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.10"
-+OTHERFLAGS-RNA = -DNumInsertStates=1 -DVERSION="1.10"
+ OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.11"
++OTHERFLAGS-RNA = -DNumInsertStates=1 -DVERSION="1.11"
# debug mode
#CXXFLAGS = -g -W -Wall -pedantic -DENABLE_CHECKS -fno-inline $(OTHERFLAGS)
diff -Nru /tmp/WvbmmACHFN/probcons-1.10/debian/watch
/tmp/nkiW2nYLiX/probcons-1.11/debian/watch
--- /tmp/WvbmmACHFN/probcons-1.10/debian/watch 2007-02-22 10:27:18.000000000
+0900
+++ /tmp/nkiW2nYLiX/probcons-1.11/debian/watch 2007-02-22 10:27:19.000000000
+0900
@@ -1,2 +1,3 @@
version=3
-http://probcons.stanford.edu/pub/probcons(.*)\.tar\.gz
+http://probcons.stanford.edu/download.html probcons_v(\d+)_(\d+)\.tar\.gz
+
diff -Nru /tmp/WvbmmACHFN/probcons-1.10/Main.cc
/tmp/nkiW2nYLiX/probcons-1.11/Main.cc
--- /tmp/WvbmmACHFN/probcons-1.10/Main.cc 2005-03-22 06:51:24.000000000
+0900
+++ /tmp/nkiW2nYLiX/probcons-1.11/Main.cc 2006-12-01 20:04:37.000000000
+0900
@@ -1023,7 +1023,10 @@
MultiSequence *alignment = ProcessTree (tree, sequences, sparseMatrices,
model);
+ SafeVector<int> oldOrdering;
if (enableAlignOrder){
+ for (int i = 0; i < alignment->GetNumSequences(); i++)
+ oldOrdering.push_back (alignment->GetSequence(i)->GetSortLabel());
alignment->SaveOrdering();
enableAlignOrder = false;
}
@@ -1037,6 +1040,12 @@
cerr << endl;
+ if (oldOrdering.size() > 0){
+ for (int i = 0; i < (int) oldOrdering.size(); i++){
+ alignment->GetSequence(i)->SetSortLabel(oldOrdering[i]);
+ }
+ }
+
// return final alignment
return alignment;
}
@@ -1402,6 +1411,9 @@
for (int i = 0; i < numSeqs; i++) seqs[i] =
alignment->GetSequence(i)->GetDataPtr();
SafeVector<pair<int,int> > active;
active.reserve (numSeqs);
+
+ SafeVector<int> lab;
+ for (int i = 0; i < numSeqs; i++)
lab.push_back(alignment->GetSequence(i)->GetSortLabel());
// for every column
for (int i = 1; i <= alignLength; i++){
@@ -1410,10 +1422,11 @@
active.clear();
for (int j = 0; j < numSeqs; j++){
if (seqs[j][i] != '-'){
- active.push_back (make_pair(j, ++position[j]));
+ active.push_back (make_pair(lab[j], ++position[j]));
}
}
+ sort (active.begin(), active.end());
outfile << setw(4) << ComputeScore (active, sparseMatrices) << endl;
}
diff -Nru /tmp/WvbmmACHFN/probcons-1.10/Makefile
/tmp/nkiW2nYLiX/probcons-1.11/Makefile
--- /tmp/WvbmmACHFN/probcons-1.10/Makefile 2005-04-22 03:54:59.000000000
+0900
+++ /tmp/nkiW2nYLiX/probcons-1.11/Makefile 2006-12-01 20:10:31.000000000
+0900
@@ -15,7 +15,7 @@
# c) RELEASE mode
################################################################################
-OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.10"
+OTHERFLAGS = -DNumInsertStates=2 -DVERSION="1.11"
# debug mode
#CXXFLAGS = -g -W -Wall -pedantic -DENABLE_CHECKS -fno-inline $(OTHERFLAGS)
diff -Nru /tmp/WvbmmACHFN/probcons-1.10/README
/tmp/nkiW2nYLiX/probcons-1.11/README
--- /tmp/WvbmmACHFN/probcons-1.10/README 2005-03-17 03:55:40.000000000
+0900
+++ /tmp/nkiW2nYLiX/probcons-1.11/README 2006-12-01 20:09:50.000000000
+0900
@@ -105,3 +105,6 @@
-- Reduced memory consumption by
-- not storing posterior matrix transposes
-- restricting consistency-derived posterior matrices to original
posterior matrix
+
+1.11, 12/1/2006 (Chuong Do)
+ -- Fixed bug with conflict between --annot and -a options
\ Pas de fin de ligne à la fin du fichier.
--
Charles Plessy
http://charles.plessy.org
Wako, Saitama, Japan
--
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