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