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SystemsGenetics / KINC

Knowledge Independent Network Construction
MIT License
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undocumented amx `NA` threshold #141

Closed JohnHadish closed 4 years ago

JohnHadish commented 4 years ago

When running cond-test an error will be thrown if the number of NAs in the amx file exceed some unknown threshold. The error appears if ~20% or more of the rows in a column are NA

Documentation on how many NA are acceptible should be added, and a corresponding error message should be added that provides user with why the run has failed.

Current error when unknown NA threshold is reached:

srun: error: sn7: task 14: Aborted
gsl: init_source.c:29: ERROR: matrix dimension n1 must be positive integer
Default GSL error handler invoked.
[sn7:129328] *** Process received signal ***
[sn7:129328] Signal: Aborted (6)
[sn7:129328] Signal code:  (-6)
[sn7:129328] [ 0] /lib64/libpthread.so.0(+0xf5e0)[0x2afc2c91a5e0]
[sn7:129328] [ 1] /lib64/libc.so.6(gsignal+0x37)[0x2afc2d6251f7]
[sn7:129328] [ 2] /lib64/libc.so.6(abort+0x148)[0x2afc2d6268e8]
[sn7:129328] [ 3] /lib64/libgsl.so.0(+0x784dd)[0x2afc21ff64dd]
[sn7:129328] [ 4] /lib64/libgsl.so.0(gsl_matrix_alloc+0xb5)[0x2afc220335e5]
[sn7:129328] [ 5] /data/ficklin/software/KINC-3.4.1/bin/kinc[0x44701a]
[sn7:129328] [ 6] /data/ficklin/software/KINC-3.4.1/bin/kinc[0x447cee]
[sn7:129328] [ 7] /data/ficklin/software/ACE-3.2.0/lib/libacecore.so.3(_ZN3Ace8Analytic9SerialRun7addWorkEOSt10unique_ptrI22EAbstractAnalyticBlockSt14default_deleteIS3_EE+0x24)[0x2afc21d49894]
[sn7:129328] [ 8] /data/ficklin/software/ACE-3.2.0/lib/libacecore.so.3(_ZN3Ace8Analytic8MPISlave7processERK10QByteArray+0x4c)[0x2afc21d4ef0c]
[sn7:129328] [ 9] /data/ficklin/software/ACE-3.2.0/lib/libacecore.so.3(_ZN3Ace8Analytic8MPISlave12dataReceivedERK10QByteArrayi+0x2b)[0x2afc21d4f0cb]
[sn7:129328] [10] /data/ficklin/software/qt-5.10.1/5.10.1/gcc_64/lib/libQt5Core.so.5(_ZN11QMetaObject8activateEP7QObjectiiPPv+0x986)[0x2afc2c1c1556]
[sn7:129328] [11] /data/ficklin/software/ACE-3.2.0/lib/libacecore.so.3(_ZN3Ace4QMPI12dataReceivedERK10QByteArrayi+0x33)[0x2afc21d5fa23]
[sn7:129328] [12] /data/ficklin/software/ACE-3.2.0/lib/libacecore.so.3(_ZN3Ace4QMPI5probeEP19ompi_communicator_ti+0x120)[0x2afc21d31130]
[sn7:129328] [13] /data/ficklin/software/ACE-3.2.0/lib/libacecore.so.3(_ZN3Ace4QMPI10timerEventEP11QTimerEvent+0x2d)[0x2afc21d315fd]
[sn7:129328] [14] /data/ficklin/software/qt-5.10.1/5.10.1/gcc_64/lib/libQt5Core.so.5(_ZN7QObject5eventEP6QEvent+0x7b)[0x2afc2c1c213b]
[sn7:129328] [15] /data/ficklin/software/qt-5.10.1/5.10.1/gcc_64/lib/libQt5Core.so.5(_ZN16QCoreApplication6notifyEP7QObjectP6QEvent+0x3a)[0x2afc2c195eca]
[sn7:129328] [16] /data/ficklin/software/ACE-3.2.0/lib/libacecli.so.3(_ZN12EApplication6notifyEP7QObjectP6QEvent+0x11)[0x2afc2b51f9f1]
[sn7:129328] [17] /data/ficklin/software/qt-5.10.1/5.10.1/gcc_64/lib/libQt5Core.so.5(_ZN16QCoreApplication15notifyInternal2EP7QObjectP6QEvent+0x108)[0x2afc2c196028]
[sn7:129328] [18] /data/ficklin/software/qt-5.10.1/5.10.1/gcc_64/lib/libQt5Core.so.5(_ZN14QTimerInfoList14activateTimersEv+0x46e)[0x2afc2c1e968e]
[sn7:129328] [19] /data/ficklin/software/qt-5.10.1/5.10.1/gcc_64/lib/libQt5Core.so.5(+0x2d2ea9)[0x2afc2c1e9ea9]
[sn7:129328] [20] /opt/apps/anaconda3/20.02.0/lib/libglib-2.0.so.0(g_main_context_dispatch+0x2cb)[0x2afc21bbdd1b]
[sn7:129328] [21] /opt/apps/anaconda3/20.02.0/lib/libglib-2.0.so.0(+0x52f61)[0x2afc21bbdf61]
[sn7:129328] [22] /opt/apps/anaconda3/20.02.0/lib/libglib-2.0.so.0(g_main_context_iteration+0x2e)[0x2afc21bbdfee]
[sn7:129328] [23] /data/ficklin/software/qt-5.10.1/5.10.1/gcc_64/lib/libQt5Core.so.5(_ZN20QEventDispatcherGlib13processEventsE6QFlagsIN10QEventLoop17ProcessEventsFlagEE+0x5f)[0x2afc2c1ea1af]
[sn7:129328] [24] /data/ficklin/software/qt-5.10.1/5.10.1/gcc_64/lib/libQt5Core.so.5(_ZN10QEventLoop4execE6QFlagsINS_17ProcessEventsFlagEE+0xea)[0x2afc2c19489a]
[sn7:129328] [25] /data/ficklin/software/qt-5.10.1/5.10.1/gcc_64/lib/libQt5Core.so.5(_ZN16QCoreApplication4execEv+0x84)[0x2afc2c19d424]
[sn7:129328] [26] /data/ficklin/software/ACE-3.2.0/lib/libacecli.so.3(_ZN12EApplication4execEv+0x520)[0x2afc2b5214b0]
[sn7:129328] [27] /data/ficklin/software/KINC-3.4.1/bin/kinc[0x40c81d]
[sn7:129328] [28] /lib64/libc.so.6(__libc_start_main+0xf5)[0x2afc2d611c05]
[sn7:129328] [29] /data/ficklin/software/KINC-3.4.1/bin/kinc[0x40cdac]
[sn7:129328] *** End of error message ***
spficklin commented 4 years ago

I just did a quick look at this. This error occurs in the hypergeometric test. According to our discussion the column is quantitative. So, why is it trying to do the hypergeometric test rather than regression?

spficklin commented 4 years ago

Fixed by merged PR