dnanexus-rnd / GLnexus

Scalable gVCF merging and joint variant calling for population sequencing projects

Apache License 2.0

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error in make step #182

Closed berry08 closed 4 years ago

berry08 commented 5 years ago

makeError

CZ docker are not available in our server, GLnexus was installed with cmake. Some errors present in the make step: PASS: capnp-evolution-test PASS: src/capnp/compiler/capnp-test.sh FAIL: capnp-test

Testsuite summary for Capn Proto 0.7.0

TOTAL: 3

PASS: 2

SKIP: 0

XFAIL: 0

FAIL: 1

XPASS: 0

ERROR: 0

============================================================================ See ./test-suite.log Please report to capnproto@googlegroups.com

make[6]: [Makefile:3475：test-suite.log] 错误 1 make[5]: [Makefile:3583：check-TESTS] 错误 2 make[4]: [Makefile:3805：check-am] 错误 2 make[3]: [Makefile:3807：check] 错误 2 make[2]: [CMakeFiles/capnp.dir/build.make:113：external/src/capnp-stamp/capnp-build] 错误 2 make[1]: [CMakeFiles/Makefile2:482：CMakeFiles/capnp.dir/all] 错误 2 make: *** [Makefile:141：all] 错误 2

mlin commented 5 years ago

Hi,

Are you able to try the static executable from the releases page? It does not need Docker although it does need a reasonably modern Linux environment. This would avoid the need to compile from scratch.
It looks like the error is in the unit tests of capnproto, a third-party library which GLnexus uses. However, the error messages you shared are not specific as to what went wrong. If you look in the mentioned test-suite.log there might be more information worth asking about either here or on capnproto itself.

xquek commented 5 years ago

I had similar issue with capnproto - https://github.com/capnproto/capnproto/issues/863.

Looks like an issue with the test failing on file systems that do not support sparse files and can be ignored

@berry08 you can consider ignoring it or try compiling it in a machine of a different file system.

berry08 commented 5 years ago

I had similar issue with capnproto - capnproto/capnproto#863.

Looks like an issue with the test failing on file systems that do not support sparse files and can be ignored

@berry08 you can consider ignoring it or try compiling it in a machine of a different file system. I have ignored this library by modifing makefile， but other errors oppears

mlin commented 5 years ago

Hi @berry08 we don't have enough information to help you right now. Please see if there's any useful detail in the aforementioned capnproto test-suite.log file, in particular whether the failing test has to do with exotic filesystem functionality as @xquek suggested, or whether it might be something else.

mlin commented 4 years ago

Closing this issue for now; will still be happy to help given additional info