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 -----BEGIN PGP SIGNATURE----- iQJDBAEBCgAtFiEEM8soQxPpC9J9y0UjYAMWptwndHYFAmpb7sAPHHBndEBkZWJp YW4ub3JnAAoJEGADFqbcJ3R26PsP/jeoPZyP8UuAYogXK9C87gW72HNNUYGmqTHI 5EHHcy2qmamWD3ryascE09ej5uQFkrSadxUVowl66ZdrSiychP2hx28ajxi+ryuu rNT/4giThi0VicRfayIWwfc/OlR5ElBOWnfOyK46RX/wiZpdOGH4Qtv2n1Ugh+JH Qg17y11sKKf02tXd45GIanv0jXie6DbvtOjRO+rYfazNo78Wifit9PJ7ybuMExEF dlESzk9mYemeEwaV5er07HBIpC5ws+tibQXa+eQU7ozt+Tvr+Nk654XnuKmgDHF9 ZCCEXMd56tNEziAGddCjgBeRnG6K3cypazZ4B4F/zSk8N4zCGC3Av+Eolhhlxsi8 iH/GYIclf4eILO2ZGT1IJl3Wbk95ET5TbB70QfX9Srkb8WB1LIC9f6W2Ro96VDjs 3Fj0+dzY4NSNPERIFeuz7aKs8+/d8ubKCENkcWTqTh9U5Hkf9LI+sSHSzPz301Ox N1p94nsBnc/eLl0utOP4/zeJeJASFCyDu2LcBklDR31GnZzIoDaS13VXm5XJVSHR taMrxUd3FCjaw0dxL9tD3AY4yEc6zG4Zz1qYGcKI1SBnc7zolZRsPDYdkKlgv+sI igU1PtFmck0x2qJ5BqKn79ukJG5/8SBoDZR5gFi5zt9ukASVwZjEzBwv1jVorgK3 jSHVPpLT =DO/G -----END PGP SIGNATURE-----
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); + } + } + }
