Re: [Debian-med-packaging] Problems building latest version of htsjdk
Hi Olivier,
On Tue, Sep 18, 2018 at 09:35:02AM +0200, Olivier Sallou wrote:
> I fixed htsjdk and pushed my updates.
Thanks for your work on this.
> I can upload the package unless you want additional updates.
I'd like to, but I keep on getting errors starting with:
...
Gradle suite > Gradle test > htsjdk.samtools.util.BinaryCodecTest.timeTest STANDARD_OUT
13ms to write
Gradle suite > Gradle test > htsjdk.samtools.util.BlockCompressedInputStreamTest.testCustomInflater[3](htsjdk.samtools.util.BlockCompressedInputStreamTest$$Lambda$80/619950902@383f5ec6, null, 21, htsjdk.samtool
java.net.UnknownHostException: broadinstitute.github.io
at java.base/java.net.AbstractPlainSocketImpl.connect(AbstractPlainSocketImpl.java:221)
at java.base/java.net.Socket.connect(Socket.java:591)
at java.base/java.net.Socket.connect(Socket.java:540)
at java.base/sun.net.NetworkClient.doConnect(NetworkClient.java:182)
at java.base/sun.net.www.http.HttpClient.openServer(HttpClient.java:474)
at java.base/sun.net.www.http.HttpClient.openServer(HttpClient.java:569)
at java.base/sun.net.www.http.HttpClient.<init>(HttpClient.java:242)
at java.base/sun.net.www.http.HttpClient.New(HttpClient.java:341)
at java.base/sun.net.www.http.HttpClient.New(HttpClient.java:362)
at java.base/sun.net.www.protocol.http.HttpURLConnection.getNewHttpClient(HttpURLConnection.java:1242)
at java.base/sun.net.www.protocol.http.HttpURLConnection.plainConnect0(HttpURLConnection.java:1181)
at java.base/sun.net.www.protocol.http.HttpURLConnection.plainConnect(HttpURLConnection.java:1075)
at java.base/sun.net.www.protocol.http.HttpURLConnection.connect(HttpURLConnection.java:1009)
at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1581)
at java.base/sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1509)
at htsjdk.samtools.seekablestream.SeekableHTTPStream.read(SeekableHTTPStream.java:124)
at java.base/java.io.BufferedInputStream.fill(BufferedInputStream.java:252)
at java.base/java.io.BufferedInputStream.read1(BufferedInputStream.java:292)
at java.base/java.io.BufferedInputStream.read(BufferedInputStream.java:351)
at htsjdk.samtools.seekablestream.SeekableBufferedStream.read(SeekableBufferedStream.java:133)
at htsjdk.samtools.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:571)
at htsjdk.samtools.util.BlockCompressedInputStream.readBytes(BlockCompressedInputStream.java:560)
at htsjdk.samtools.util.BlockCompressedInputStream.processNextBlock(BlockCompressedInputStream.java:510)
at htsjdk.samtools.util.BlockCompressedInputStream.nextBlock(BlockCompressedInputStream.java:468)
at htsjdk.samtools.util.BlockCompressedInputStream.readBlock(BlockCompressedInputStream.java:458)
at htsjdk.samtools.util.BlockCompressedInputStream.available(BlockCompressedInputStream.java:196)
at htsjdk.samtools.util.BlockCompressedInputStream.read(BlockCompressedInputStream.java:331)
at java.base/sun.nio.cs.StreamDecoder.readBytes(StreamDecoder.java:284)
at java.base/sun.nio.cs.StreamDecoder.implRead(StreamDecoder.java:326)
at java.base/sun.nio.cs.StreamDecoder.read(StreamDecoder.java:178)
at java.base/java.io.InputStreamReader.read(InputStreamReader.java:185)
at java.base/java.io.BufferedReader.fill(BufferedReader.java:161)
at java.base/java.io.BufferedReader.readLine(BufferedReader.java:326)
at java.base/java.io.BufferedReader.readLine(BufferedReader.java:392)
at htsjdk.samtools.util.BlockCompressedInputStreamTest.testCustomInflater(BlockCompressedInputStreamTest.java:193)
...
ending with
...
<------>at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
<------>at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
<------>at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
<------>at org.gradle.internal.reflect.JavaMethod.invoke(JavaMethod.java:73)
<------>at org.gradle.api.internal.project.taskfactory.StandardTaskAction.doExecute(StandardTaskAction.java:46)
<------>at org.gradle.api.internal.project.taskfactory.StandardTaskAction.execute(StandardTaskAction.java:39)
<------>at org.gradle.api.internal.project.taskfactory.StandardTaskAction.execute(StandardTaskAction.java:26)
<------>at org.gradle.api.internal.AbstractTask$TaskActionWrapper.execute(AbstractTask.java:780)
<------>at org.gradle.api.internal.AbstractTask$TaskActionWrapper.execute(AbstractTask.java:747)
<------>at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter$1.run(ExecuteActionsTaskExecuter.java:121)
<------>at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:336)
<------>at org.gradle.internal.progress.DefaultBuildOperationExecutor$RunnableBuildOperationWorker.execute(DefaultBuildOperationExecutor.java:328)
<------>at org.gradle.internal.progress.DefaultBuildOperationExecutor.execute(DefaultBuildOperationExecutor.java:199)
<------>at org.gradle.internal.progress.DefaultBuildOperationExecutor.run(DefaultBuildOperationExecutor.java:110)
<------>at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeAction(ExecuteActionsTaskExecuter.java:110)
<------>at org.gradle.api.internal.tasks.execution.ExecuteActionsTaskExecuter.executeActions(ExecuteActionsTaskExecuter.java:92)
<------>... 29 more
* Get more help at https://help.gradle.org
BUILD FAILED in 5m 12s
5 actionable tasks: 4 executed, 1 up-to-date
dh_auto_build: gradle --info --console plain --offline --stacktrace --no-daemon --refresh-dependencies --gradle-user-home .gradle -Duser.home=. -Duser.name=debian -Ddebian.package=htsjdk -Dfile.encoding=UTF-8 -
make[1]: *** [debian/rules:19: override_dh_auto_test] Error 25
Feel free to ask me for a complete build log.
> I gonna look at picard-tools
I'm currently building against htsjdk in sid and will upload if it builds fine.
Thanks for your work anyway
Andreas.
--
http://fam-tille.de
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