Error building jar for Hail 0.2.11

#1

Hi!
I’m trying to build Hail 0.2 with the following command:

./gradlew -Dspark.version=2.2.1 -Dspark.version=2.2.1 -Dpy4j.version=0.10.4 -Dbreeze.version=0.13.1 shadowJar

And get the error:

compileJava UP-TO-DATE
:generateBuildInfo
:nativeLib
g++ -march=sandybridge -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Werror -Wextra -fPIC -ggdb -fno-strict-aliasing -I…/resources/include -I/usr/lib/jvm/java-8-openjdk-amd64/include -I/usr/lib/jvm/java-8-openjdk-amd64/include/linux testutils/unit-tests.cpp -MG -M -MF build/testutils/unit-tests.d -MT build/testutils/unit-tests.o
g++ -march=sandybridge -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Werror -Wextra -fPIC -ggdb -fno-strict-aliasing -I…/resources/include -I/usr/lib/jvm/java-8-openjdk-amd64/include -I/usr/lib/jvm/java-8-openjdk-amd64/include/linux test.cpp -MG -M -MF build/test.d -MT build/test.o
g++ -march=sandybridge -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Werror -Wextra -fPIC -ggdb -fno-strict-aliasing -I…/resources/include -I/usr/lib/jvm/java-8-openjdk-amd64/include -I/usr/lib/jvm/java-8-openjdk-amd64/include/linux ibs.cpp -MG -M -MF build/ibs.d -MT build/ibs.o
g++ -march=sandybridge -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Werror -Wextra -fPIC -ggdb -fno-strict-aliasing -I…/resources/include -I/usr/lib/jvm/java-8-openjdk-amd64/include -I/usr/lib/jvm/java-8-openjdk-amd64/include/linux davies.cpp -MG -M -MF build/davies.d -MT build/davies.o
g++ -march=sandybridge -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Werror -Wextra -fPIC -ggdb -fno-strict-aliasing -I…/resources/include -I/usr/lib/jvm/java-8-openjdk-amd64/include -I/usr/lib/jvm/java-8-openjdk-amd64/include/linux cache-tests.cpp -MG -M -MF build/cache-tests.d -MT build/cache-tests.o
g++ -march=sandybridge -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Werror -Wextra -fPIC -ggdb -fno-strict-aliasing -I…/resources/include -I/usr/lib/jvm/java-8-openjdk-amd64/include -I/usr/lib/jvm/java-8-openjdk-amd64/include/linux Upcalls.cpp -MG -M -MF build/Upcalls.d -MT build/Upcalls.o
g++ -march=sandybridge -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Werror -Wextra -fPIC -ggdb -fno-strict-aliasing -I…/resources/include -I/usr/lib/jvm/java-8-openjdk-amd64/include -I/usr/lib/jvm/java-8-openjdk-amd64/include/linux Region_test.cpp -MG -M -MF build/Region_test.d -MT build/Region_test.o
g++ -march=sandybridge -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Werror -Wextra -fPIC -ggdb -fno-strict-aliasing -I…/resources/include -I/usr/lib/jvm/java-8-openjdk-amd64/include -I/usr/lib/jvm/java-8-openjdk-amd64/include/linux Region.cpp -MG -M -MF build/Region.d -MT build/Region.o
g++ -march=sandybridge -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Werror -Wextra -fPIC -ggdb -fno-strict-aliasing -I…/resources/include -I/usr/lib/jvm/java-8-openjdk-amd64/include -I/usr/lib/jvm/java-8-openjdk-amd64/include/linux PartitionIterators.cpp -MG -M -MF build/PartitionIterators.d -MT build/PartitionIterators.o
g++ -march=sandybridge -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Werror -Wextra -fPIC -ggdb -fno-strict-aliasing -I…/resources/include -I/usr/lib/jvm/java-8-openjdk-amd64/include -I/usr/lib/jvm/java-8-openjdk-amd64/include/linux ObjectArray.cpp -MG -M -MF build/ObjectArray.d -MT build/ObjectArray.o
g++ -march=sandybridge -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Werror -Wextra -fPIC -ggdb -fno-strict-aliasing -I…/resources/include -I/usr/lib/jvm/java-8-openjdk-amd64/include -I/usr/lib/jvm/java-8-openjdk-amd64/include/linux NativeStatus.cpp -MG -M -MF build/NativeStatus.d -MT build/NativeStatus.o
g++ -march=sandybridge -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Werror -Wextra -fPIC -ggdb -fno-strict-aliasing -I…/resources/include -I/usr/lib/jvm/java-8-openjdk-amd64/include -I/usr/lib/jvm/java-8-openjdk-amd64/include/linux NativePtr.cpp -MG -M -MF build/NativePtr.d -MT build/NativePtr.o
g++ -march=sandybridge -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Werror -Wextra -fPIC -ggdb -fno-strict-aliasing -I…/resources/include -I/usr/lib/jvm/java-8-openjdk-amd64/include -I/usr/lib/jvm/java-8-openjdk-amd64/include/linux NativeModule.cpp -MG -M -MF build/NativeModule.d -MT build/NativeModule.o
g++ -march=sandybridge -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Werror -Wextra -fPIC -ggdb -fno-strict-aliasing -I…/resources/include -I/usr/lib/jvm/java-8-openjdk-amd64/include -I/usr/lib/jvm/java-8-openjdk-amd64/include/linux NativeLongFunc.cpp -MG -M -MF build/NativeLongFunc.d -MT build/NativeLongFunc.o
g++ -march=sandybridge -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Werror -Wextra -fPIC -ggdb -fno-strict-aliasing -I…/resources/include -I/usr/lib/jvm/java-8-openjdk-amd64/include -I/usr/lib/jvm/java-8-openjdk-amd64/include/linux NativeCodeSuite.cpp -MG -M -MF build/NativeCodeSuite.d -MT build/NativeCodeSuite.o
g++ -march=sandybridge -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Werror -Wextra -fPIC -ggdb -fno-strict-aliasing -I…/resources/include -I/usr/lib/jvm/java-8-openjdk-amd64/include -I/usr/lib/jvm/java-8-openjdk-amd64/include/linux NativeBoot.cpp -MG -M -MF build/NativeBoot.d -MT build/NativeBoot.o
g++ -march=sandybridge -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Werror -Wextra -fPIC -ggdb -fno-strict-aliasing -I…/resources/include -I/usr/lib/jvm/java-8-openjdk-amd64/include -I/usr/lib/jvm/java-8-openjdk-amd64/include/linux Logging.cpp -MG -M -MF build/Logging.d -MT build/Logging.o
g++ -march=sandybridge -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Werror -Wextra -fPIC -ggdb -fno-strict-aliasing -I…/resources/include -I/usr/lib/jvm/java-8-openjdk-amd64/include -I/usr/lib/jvm/java-8-openjdk-amd64/include/linux Encoder.cpp -MG -M -MF build/Encoder.d -MT build/Encoder.o
g++ -march=sandybridge -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Werror -Wextra -fPIC -ggdb -fno-strict-aliasing -I…/resources/include -I/usr/lib/jvm/java-8-openjdk-amd64/include -I/usr/lib/jvm/java-8-openjdk-amd64/include/linux Decoder.cpp -MG -M -MF build/Decoder.d -MT build/Decoder.o
g++ -march=sandybridge -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Werror -Wextra -fPIC -ggdb -fno-strict-aliasing -I…/resources/include -I/usr/lib/jvm/java-8-openjdk-amd64/include -I/usr/lib/jvm/java-8-openjdk-amd64/include/linux ApproximateQuantiles_test.cpp -MG -M -MF build/ApproximateQuantiles_test.d -MT build/ApproximateQuantiles_test.o
g++ -o build/NativeBoot.o -march=sandybridge -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Werror -Wextra -fPIC -ggdb -fno-strict-aliasing -I…/resources/include -I/usr/lib/jvm/java-8-openjdk-amd64/include -I/usr/lib/jvm/java-8-openjdk-amd64/include/linux -MD -MF build/NativeBoot.d -MT build/NativeBoot.o -c NativeBoot.cpp
g++ -fvisibility=default -rdynamic -shared -march=sandybridge -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Werror -Wextra -fPIC -ggdb -fno-strict-aliasing -I…/resources/include -I/usr/lib/jvm/java-8-openjdk-amd64/include -I/usr/lib/jvm/java-8-openjdk-amd64/include/linux build/NativeBoot.o -o lib/linux-x86-64/libboot.so
g++ -o build/davies.o -march=sandybridge -O3 -std=c++14 -Ilibsimdpp-2.1 -Wall -Werror -Wextra -fPIC -ggdb -fno-strict-aliasing -I…/resources/include -I/usr/lib/jvm/java-8-openjdk-amd64/include -I/usr/lib/jvm/java-8-openjdk-amd64/include/linux -MD -MF build/davies.d -MT build/davies.o -c davies.cpp
davies.cpp: In member function ‘real DaviesAlgo::qf(real*, real*, int*, int, real, real, int, real, real*, int*)’:
davies.cpp:241:8: error: variable ‘qfval’ might be clobbered by ‘longjmp’ or ‘vfork’ [-Werror=clobbered]
real qfval;
^
cc1plus: all warnings being treated as errors
make: *** [build/davies.o] Error 1
Makefile:63: recipe for target ‘build/davies.o’ failed
:nativeLib FAILED

FAILURE: Build failed with an exception.

What went wrong:
Execution failed for task ':nativeLib'.

Process 'command 'make'' finished with non-zero exit value 2

Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output.

BUILD FAILED

Am I doing something wrong, or is it not supported for Spark 2.2.1?
Thanks in advance!

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#2

What version of g++ do you have?

We’ve seen something like this before, I don’t exactly remember how it was fixed.

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#3

I use g++ 4.9.4.
Thanks again!

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#4

@danking you’ve looked into this, right? Wasn’t this problem related to https://github.com/hail-is/hail/pull/5354?

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#5

remove -Wextra from line 125 of src/main/c/Makefile, or upgrade to a more recent version of gcc. For example, GCC 8.3.0 does not report this.

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#6

Ok thanks so much!

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