Re: [Debian-med-packaging] Problems building latest version of htsjdk
On 09/18/2018 11:41 AM, Andreas Tille wrote:
> 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:
you have errors after doing some modifications, or from the code I pushed?
Error is linked to a network pb, not finding host broadinstitute.github.io
I may have built with network enabled (which should be disabled for
debian anyway)
>
> ...
> 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.
>
>
--
Olivier Sallou
Univ Rennes, Inria, CNRS, IRISA
Irisa, Campus de Beaulieu
F-35042 RENNES - FRANCE
Tel: 02.99.84.71.95
gpg key id: 4096R/326D8438 (keyring.debian.org)
Key fingerprint = 5FB4 6F83 D3B9 5204 6335 D26D 78DC 68DB 326D 8438
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