[Debian-med-packaging] Bug#796731: freecontact: FTBFS on mips (test suite failure)

[Dejan Latinovic]

Hi,

I had tried to build freecontact locally on two different cavium boards.
On both board build failed with TERM signal error on testing.

It seems that this is the command that  causes TERM signal:
> /build/freecontact-hkgMtc/freecontact-1.0.21/src/.libs/lt-freecontact --parprof=psicov --density=0 -f ./demo_1000.aln --threads 0 --debug


The results of running this command manually:


> time /build/freecontact-hkgMtc/freecontact-1.0.21/src/.libs/lt-freecontact --parprof=psicov --density=0 -f ./demo_1000.aln --threads 0 --debug

> Effective parameters: --apply-gapth=0 --clustpc=62 --cov20=0 --estimate-ivcov=1 --gapth=0.9 --mincontsep=5 --pseudocnt=1 --pscount-weight=0 --rho=-1 --density=0 [shrink_lambda=0.1] --output-format=pfrmat_rr
will use 2 OMP threads
> total weight (variation) of alignment = 561.595172234625
> 
> seq weight loop for 1000 seqs took 0.126313 secs
> will use 2 OMP threads
> calculated column aa frequencies, gap cols = 4
> calculated pair frequency table in 9.83136 secs
> collected apc_mean[MI] = 0.165528914074767
> aa freq sum (cell) = 0.999993945475299, pairfreq sum (cell) = 0.999988196197513
> formed covariance matrix (126/126,4)
> cov matrix Cholesky... not positive definite, dmean dev: 0.0457782
> cov matrix Cholesky... not positive definite, dmean dev: 0.0412004
> cov matrix Cholesky... not positive definite, dmean dev: 0.0370804
> cov matrix Cholesky... not positive definite, dmean dev: 0.0333723
> cov matrix Cholesky... not positive definite, dmean dev: 0.0300351
> cov matrix Cholesky... not positive definite, dmean dev: 0.0270316
> cov matrix Cholesky... not positive definite, dmean dev: 0.0243284
> cov matrix Cholesky... not positive definite, dmean dev: 0.0218956
> cov matrix Cholesky... not positive definite, dmean dev: 0.019706
> cov matrix Cholesky... not positive definite, dmean dev: 0.0177354
> cov matrix Cholesky... not positive definite, dmean dev: 0.0159619
> cov matrix Cholesky... not positive definite, dmean dev: 0.0143657
> cov matrix Cholesky... not positive definite, dmean dev: 0.0129291
> cov matrix Cholesky...
> shrank covariance matrix in 15300.1 secs
> will try rho 0.00178064, exact solution
>  iteration =   1Error: inverse covariance matrix estimation exceeded time limit (1800 sec).
> 
> real	290m35.185s
> user	37m40.530s
> sys	253m0.660s


Regards,
Dejan