Your message dated Mon, 12 Nov 2018 16:22:14 +0000
with message-id <e1gmeyc-0008fh...@fasolo.debian.org>
and subject line Bug#913566: fixed in htsjdk 2.16.1+dfsg-2
has caused the Debian Bug report #913566,
regarding htsjdk FTBFS with OpenJDK 11
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.
(NB: If you are a system administrator and have no idea what this
message is talking about, this may indicate a serious mail system
misconfiguration somewhere. Please contact ow...@bugs.debian.org
immediately.)
--
913566: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=913566
Debian Bug Tracking System
Contact ow...@bugs.debian.org with problems
--- Begin Message ---
Source: htsjdk
Version: 2.16.1+dfsg-1
Severity: serious
Tags: ftbfs
https://tests.reproducible-builds.org/debian/rb-pkg/unstable/amd64/htsjdk.html
...
Compiling with JDK Java compiler API.
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceDictionary.java:34:
error: package javax.xml.bind.annotation does not exist
import javax.xml.bind.annotation.XmlElement;
^
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceDictionary.java:35:
error: package javax.xml.bind.annotation does not exist
import javax.xml.bind.annotation.XmlRootElement;
^
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceDictionary.java:36:
error: package javax.xml.bind.annotation does not exist
import javax.xml.bind.annotation.XmlTransient;
^
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceRecord.java:26:
error: package javax.xml.bind.annotation does not exist
import javax.xml.bind.annotation.XmlAttribute;
^
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceRecord.java:27:
error: package javax.xml.bind.annotation does not exist
import javax.xml.bind.annotation.XmlRootElement;
^
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceRecord.java:28:
error: package javax.xml.bind.annotation does not exist
import javax.xml.bind.annotation.XmlValue;
^
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/AbstractSAMHeaderRecord.java:26:
error: package javax.xml.bind.annotation does not exist
import javax.xml.bind.annotation.XmlTransient;
^
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/AbstractSAMHeaderRecord.java:36:
error: cannot find symbol
@XmlTransient /* don't consider this class for XML-serialization */
^
symbol: class XmlTransient
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceRecord.java:41:
error: cannot find symbol
@XmlRootElement(name="Reference")
^
symbol: class XmlRootElement
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceDictionary.java:44:
error: cannot find symbol
@XmlRootElement(name="References")
^
symbol: class XmlRootElement
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceDictionary.java:51:
error: cannot find symbol
@XmlElement(name="Reference")
^
symbol: class XmlElement
location: class SAMSequenceDictionary
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceDictionary.java:63:
error: cannot find symbol
@XmlTransient //we use the field instead of getter/setter
^
symbol: class XmlTransient
location: class SAMSequenceDictionary
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceRecord.java:103:
error: cannot find symbol
@XmlValue
^
symbol: class XmlValue
location: class SAMSequenceRecord
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceRecord.java:117:
error: cannot find symbol
@XmlAttribute(name="length")
^
symbol: class XmlAttribute
location: class SAMSequenceRecord
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceRecord.java:121:
error: cannot find symbol
@XmlAttribute(name="assembly")
^
symbol: class XmlAttribute
location: class SAMSequenceRecord
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceRecord.java:125:
error: cannot find symbol
@XmlAttribute(name="species")
^
symbol: class XmlAttribute
location: class SAMSequenceRecord
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceRecord.java:129:
error: cannot find symbol
@XmlAttribute(name="md5")
^
symbol: class XmlAttribute
location: class SAMSequenceRecord
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/SAMSequenceRecord.java:136:
error: cannot find symbol
@XmlAttribute(name="index")
^
symbol: class XmlAttribute
location: class SAMSequenceRecord
/build/1st/htsjdk-2.16.1+dfsg/src/main/java/htsjdk/samtools/cram/structure/EncodingParams.java:36:
error: package javax.xml.bind does not exist
return id.name() + ":" +
javax.xml.bind.DatatypeConverter.printHexBinary(Arrays.copyOfRange(params, 0,
Math.max(20, params.length)));
^
Note: Some input files use or override a deprecated API.
Note: Recompile with -Xlint:deprecation for details.
Note: Some input files use unchecked or unsafe operations.
Note: Recompile with -Xlint:unchecked for details.
19 errors
--- End Message ---
--- Begin Message ---
Source: htsjdk
Source-Version: 2.16.1+dfsg-2
We believe that the bug you reported is fixed in the latest version of
htsjdk, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to 913...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Olivier Sallou <osal...@debian.org> (supplier of updated htsjdk package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing ftpmas...@ftp-master.debian.org)
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA256
Format: 1.8
Date: Mon, 12 Nov 2018 15:38:32 +0000
Source: htsjdk
Binary: libhtsjdk-java libhtsjdk-java-doc
Architecture: source all
Version: 2.16.1+dfsg-2
Distribution: unstable
Urgency: medium
Maintainer: Debian Med Packaging Team
<debian-med-packag...@lists.alioth.debian.org>
Changed-By: Olivier Sallou <osal...@debian.org>
Description:
libhtsjdk-java - Java API for high-throughput sequencing data (HTS) formats
libhtsjdk-java-doc - Documentation for the java HTSJDK library
Closes: 913566
Changes:
htsjdk (2.16.1+dfsg-2) unstable; urgency=medium
.
* Fix FTBS with OpenJDK 11 (Closes: #913566)
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Files:
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htsjdk_2.16.1+dfsg-2.debian.tar.xz
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htsjdk_2.16.1+dfsg-2_amd64.buildinfo
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libhtsjdk-java-doc_2.16.1+dfsg-2_all.deb
9d19cc45af0bc4f368184c9877d91906 1493482 java optional
libhtsjdk-java_2.16.1+dfsg-2_all.deb
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