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dnanexus-rnd / GLnexus

Scalable gVCF merging and joint variant calling for population sequencing projects
Apache License 2.0
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Docker build failed #214

Open ghost opened 4 years ago

ghost commented 4 years ago

Hello, with the last version from github

FAIL: capnp-test
PASS: capnp-evolution-test
PASS: src/capnp/compiler/capnp-test.sh
============================================================================
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
============================================================================
Makefile:3474: recipe for target 'test-suite.log' failed
make[6]: *** [test-suite.log] Error 1
Makefile:3580: recipe for target 'check-TESTS' failed
make[5]: *** [check-TESTS] Error 2
Makefile:3804: recipe for target 'check-am' failed
make[4]: *** [check-am] Error 2
make[3]: *** [check] Error 2
Makefile:3807: recipe for target 'check' failed
make[2]: *** [external/src/capnp-stamp/capnp-build] Error 2
CMakeFiles/capnp.dir/build.make:111: recipe for target 'external/src/capnp-stamp/capnp-build' failed
make[1]: *** [CMakeFiles/capnp.dir/all] Error 2
CMakeFiles/Makefile2:515: recipe for target 'CMakeFiles/capnp.dir/all' failed
make: *** [all] Error 2
Makefile:140: recipe for target 'all' failed
The command '/bin/sh -c cmake -DCMAKE_BUILD_TYPE=$build_type . && make -j4' returned a non-zero code: 2
mlin commented 4 years ago

Can you search the directory tree for the mentioned "test-suite.log" file and see if there's a more-specific diagnostic message in there?

ghost commented 4 years ago

No I can't because the said log file is nowhere to be found. I have looked into all the produced directories.

ghost commented 4 years ago

It is successfully installed on another machine with the exact same OS as far as I can tell. So for me the problem is "solved" in the sense I have a running install. I guess we can keep the issue open in case someone else has troubles.

If you have ideas of what I could look at to solve the issue you can let me know.

mlin commented 4 years ago

The error appears to be in the unit tests for capnproto, one of GLnexus' dependent libraries. Probably the log file is being lost when the docker container exits. If you're comfortable fiddling with docker, you could enter an interactive shell at the equivalent point of docker build to reproduce the error and find the log file -- a bit of a gnarly process admittedly.

There has been one similar error reported in the past (#182) which possibly had something to do with the host having an unusual file system, which doesn't support some exotic operations that the capnproto unit tests use and are available in the typical ext3/ext4 setup. Does that possibly apply here?

ghost commented 4 years ago

I am not comfortable with docker at all, I hate that thing.

However, the drive I was trying to install GLnexus on is in ext4. So nothing unusual a priori. Here is the output of df -T 

/dev/sdb1      ext4     3845577736 2607905060 1042305460  72% /media/urbe/MyADrive