Your message dated Sat, 12 Sep 2026 08:05:41 +0000
with message-id <[email protected]>
and subject line Released in 13.7
has caused the Debian Bug report #1142377,
regarding trixie-pu: package milib/2.2.0+dfsg-1+deb13u1
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.
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--
1142377: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=1142377
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: release.debian.org
Severity: normal
Tags: trixie
X-Debbugs-Cc: [email protected]
Control: affects -1 + src:milib
User: [email protected]
Usertags: pu
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Dear Release Team,
I would like to propose an upload to stable for milib.
[ Reason ]
There is a FTBFS bug #1139472 in src:milib, due to an exception that is newly
thrown by a class in libjackson2-databind-java, version 2.14.0. This latter
package has been introduced in unstable and then in stable-p-u and
oldstable-p-u, hence a FTBFS in unstable, stable and oldstable.
The proposed upload fixes this build failure, with the same patch that has been
successfully fixing it in unstable and testing for three weeks.
[ Impact ]
If the update is not approved, the package will go on FTBFS-ing in stable and
the program could crash if the newly raised IOException of jackson-databind is
indeed thrown at runtime.
[ Tests ]
The build-time tests run successfully in unstable, stable and oldstable, and
the package has been in testing for three weeks.
[ Risks ]
Honestly, code is trivial as we are just catching one more exception in the
code, nothing else changed.
[ Checklist ]
[X] *all* changes are documented in the d/changelog
[X] I reviewed all changes and I approve them
[X] attach debdiff against the package in stable
[X] the issue is verified as fixed in unstable
[ Changes ]
The change is the application of a patch, which is exactly the one I applied
in unstable in version 2.2.0+dfsg-2.
[ Other info ]
There is a companion bug for the fix in oldstable.
Thanks a lot for your consideration,
- --
Pierre
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diff -Nru milib-2.2.0+dfsg/debian/changelog milib-2.2.0+dfsg/debian/changelog
--- milib-2.2.0+dfsg/debian/changelog 2022-12-30 14:38:35.000000000 +0100
+++ milib-2.2.0+dfsg/debian/changelog 2026-07-17 15:02:41.000000000 +0200
@@ -1,3 +1,9 @@
+milib (2.2.0+dfsg-1+deb13u1) trixie; urgency=medium
+
+ * Patching code to catch IOException (Closes: #1139472)
+
+ -- Pierre Gruet <[email protected]> Fri, 17 Jul 2026 15:02:41 +0200
+
milib (2.2.0+dfsg-1) unstable; urgency=medium
* New upstream version 2.2.0+dfsg
diff -Nru milib-2.2.0+dfsg/debian/patches/series
milib-2.2.0+dfsg/debian/patches/series
--- milib-2.2.0+dfsg/debian/patches/series 2022-11-14 21:52:46.000000000
+0100
+++ milib-2.2.0+dfsg/debian/patches/series 2026-07-17 15:02:41.000000000
+0200
@@ -2,3 +2,4 @@
guava_interface.patch
deactivate_test_reading_build_properties.patch
flaky_test.patch
+uncaught_IOException.patch
diff -Nru milib-2.2.0+dfsg/debian/patches/uncaught_IOException.patch
milib-2.2.0+dfsg/debian/patches/uncaught_IOException.patch
--- milib-2.2.0+dfsg/debian/patches/uncaught_IOException.patch 1970-01-01
01:00:00.000000000 +0100
+++ milib-2.2.0+dfsg/debian/patches/uncaught_IOException.patch 2026-07-17
15:01:02.000000000 +0200
@@ -0,0 +1,84 @@
+Description: catching IOException newly thrown by
+ com.fasterxml.jackson.databind.ObjectMapper
+Author: Pierre Gruet <[email protected]>
+Bug-Debian: https://bugs.debian.org/1139472
+Forwarded: no
+Last-Update: 2026-06-28
+
+--- a/src/main/java/com/milaboratory/util/ReportUtil.java
++++ b/src/main/java/com/milaboratory/util/ReportUtil.java
+@@ -89,6 +89,8 @@
+ return content.getBytes(StandardCharsets.UTF_8);
+ } catch (JsonProcessingException e) {
+ throw new RuntimeException(e);
++ } catch (IOException e) {
++ throw new RuntimeException(e);
+ }
+ }
+
+--- a/src/main/java/com/milaboratory/util/GlobalObjectMappers.java
++++ b/src/main/java/com/milaboratory/util/GlobalObjectMappers.java
+@@ -42,7 +42,12 @@
+ private static ObjectMapper PRETTY = null;
+
+ public static String toOneLine(Object object) throws
JsonProcessingException {
+- String str =
GlobalObjectMappers.getOneLine().writeValueAsString(object);
++ String str;
++ try {
++ str = GlobalObjectMappers.getOneLine().writeValueAsString(object);
++ } catch (IOException e) {
++ throw new RuntimeException(e);
++ }
+
+ if (str.contains("\n"))
+ throw new RuntimeException("Internal error.");
+---
a/src/main/java/com/milaboratory/core/alignment/kaligner2/KAlignerParameters2.java
++++
b/src/main/java/com/milaboratory/core/alignment/kaligner2/KAlignerParameters2.java
+@@ -21,6 +21,8 @@
+ import com.milaboratory.core.sequence.NucleotideSequence;
+ import com.milaboratory.util.GlobalObjectMappers;
+
++import java.io.IOException;
++
+ /**
+ * @author Dmitry Bolotin
+ * @author Stanislav Poslavsky
+@@ -712,6 +714,8 @@
+ return "KAlignerParameters" +
GlobalObjectMappers.getPretty().writeValueAsString(this);
+ } catch (JsonProcessingException e) {
+ return "Error...";
++ } catch (IOException e) {
++ throw new RuntimeException(e);
+ }
+ }
+ }
+---
a/src/main/java/com/milaboratory/core/alignment/AffineGapAlignmentScoring.java
++++
b/src/main/java/com/milaboratory/core/alignment/AffineGapAlignmentScoring.java
+@@ -24,6 +24,7 @@
+ import com.milaboratory.core.sequence.Sequence;
+ import com.milaboratory.util.GlobalObjectMappers;
+
++import java.io.IOException;
+ import java.io.ObjectStreamException;
+
+ /**
+@@ -155,6 +156,8 @@
+ return GlobalObjectMappers.getPretty().writeValueAsString(this);
+ } catch (JsonProcessingException e) {
+ throw new RuntimeException(e);
++ } catch (IOException e) {
++ throw new RuntimeException(e);
+ }
+ }
+
+---
a/src/main/java/com/milaboratory/core/alignment/kaligner1/KAlignerParameters.java
++++
b/src/main/java/com/milaboratory/core/alignment/kaligner1/KAlignerParameters.java
+@@ -630,6 +630,8 @@
+ return "KAlignerParameters" +
GlobalObjectMappers.getPretty().writeValueAsString(this);
+ } catch (JsonProcessingException e) {
+ return "Error...";
++ } catch (IOException e) {
++ throw new RuntimeException(e);
+ }
+ }
+ }
--- End Message ---
--- Begin Message ---
Version: 13.7
This update was released as part of 13.7.
--- End Message ---
