Version in base suite: 2.2.0+dfsg-1 Base version: milib_2.2.0+dfsg-1 Target version: milib_2.2.0+dfsg-1+deb13u1 Base file: /srv/ftp-master.debian.org/ftp/pool/main/m/milib/milib_2.2.0+dfsg-1.dsc Target file: /srv/ftp-master.debian.org/policy/pool/main/m/milib/milib_2.2.0+dfsg-1+deb13u1.dsc changelog | 6 ++ patches/series | 1 patches/uncaught_IOException.patch | 84 +++++++++++++++++++++++++++++++++++++ 3 files changed, 91 insertions(+) dpkg-source: warning: cannot verify inline signature for /srv/release.debian.org/tmp/tmpsft1w5db/milib_2.2.0+dfsg-1.dsc: no acceptable signature found dpkg-source: warning: cannot verify inline signature for /srv/release.debian.org/tmp/tmpsft1w5db/milib_2.2.0+dfsg-1+deb13u1.dsc: no acceptable signature found 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 13:38:35.000000000 +0000 +++ milib-2.2.0+dfsg/debian/changelog 2026-07-17 13:02:41.000000000 +0000 @@ -1,3 +1,9 @@ +milib (2.2.0+dfsg-1+deb13u1) trixie; urgency=medium + + * Patching code to catch IOException (Closes: #1139472) + + -- Pierre Gruet 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 20:52:46.000000000 +0000 +++ milib-2.2.0+dfsg/debian/patches/series 2026-07-17 13:02:41.000000000 +0000 @@ -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 00:00:00.000000000 +0000 +++ milib-2.2.0+dfsg/debian/patches/uncaught_IOException.patch 2026-07-17 13:01:02.000000000 +0000 @@ -0,0 +1,84 @@ +Description: catching IOException newly thrown by + com.fasterxml.jackson.databind.ObjectMapper +Author: Pierre Gruet +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); + } + } + }