[Debian-med-packaging] Bug#1142378: bookworm-pu: package milib/2.2.0+dfsg-1+deb12u1
Pierre Gruet
pgt at debian.org
Sat Jul 18 22:23:38 BST 2026
Package: release.debian.org
Severity: normal
Tags: bookworm
X-Debbugs-Cc: milib at packages.debian.org
Control: affects -1 + src:milib
User: release.debian.org at packages.debian.org
Usertags: pu
-----BEGIN PGP SIGNED MESSAGE-----
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Dear Release Team,
I would like to propose an upload to oldstable 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 oldstable
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 oldstable
[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 stable.
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 15:04:38.000000000 +0200
@@ -1,3 +1,9 @@
+milib (2.2.0+dfsg-1+deb12u1) bookworm; urgency=medium
+
+ * Patching code to catch IOException (Closes: #1139472)
+
+ -- Pierre Gruet <pgt at debian.org> Fri, 17 Jul 2026 15:04:38 +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 15:04:16.000000000 +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 <pgt at debian.org>
+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);
+ }
+ }
+ }
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