Recent changes to bugs

inconsistency in parameter and manual description

Marcelo S Zanetti — Thu, 24 Jul 2014 19:09:03 -0000

Report by cymon:

https://sourceforge.net/p/codonphyml/discussion/users/thread/e9ffefdf/#7eba

#5 BLASLAPACK DEPENDENCY ON DEBIAN BINARIES

Marcelo S Zanetti — Thu, 24 Jul 2014 18:05:32 -0000

John Denton also wrote this: "Would it be possible to get a version of the Windows executable of codonPhyML with the code SSE optimized? The version currently on the website does not appear to have any code optimization."

#4 Best between NNI and SPR is still broken

Marcelo S Zanetti — Thu, 24 Jul 2014 18:03:57 -0000

status: accepted --> closed

#4 Best between NNI and SPR is still broken

Marcelo S Zanetti — Thu, 24 Jul 2014 18:03:45 -0000

Commented out two sanity checks in file utilities.c, within function "Best_Of_NNI_And_SPR". It is similar to the numerical issues we had during execution, while restoring NNI and SPR moves. The error comes from that fact that the original likelihood is slightly different from the number obtained after restoring a move. Must be a numerical issue due to large tree sizes, with long sequences.

#6 Compiling error in models.c PADEAPPROX

Marcelo S Zanetti — Thu, 24 Jul 2014 17:58:28 -0000

status: open --> closed

#6 Compiling error in models.c PADEAPPROX

Marcelo S Zanetti — Thu, 24 Jul 2014 17:58:16 -0000

Changed "int info;" to "int info=0;" Must be caused by an extremely strict compiler check.

Compiling error in models.c PADEAPPROX

Marcelo S Zanetti — Wed, 30 Oct 2013 17:13:01 -0000

Reported by Salvador:

This time I got this error message which I guess it is a bug on the code.

models.c: In function ‘PadeApprox’:
models.c:4378:49: error: ‘info’ undeclared (first use in this function)
models.c:4378:49: note: each undeclared identifier is reported only once for each function it appears in

Compiling error in models.c PADEAPPROX

Marcelo S Zanetti — Wed, 30 Oct 2013 17:13:01 -0000

Ticket 6 has been modified: Compiling error in models.c PADEAPPROX
Edited By: Marcelo S Zanetti (mszanetti)
Status updated: u'open' => u'closed'

BLASLAPACK DEPENDENCY ON DEBIAN BINARIES

Marcelo S Zanetti — Tue, 27 Aug 2013 09:13:20 -0000

can we remove the dependency on debian implementation of BLAS/LAPACK and make it more general, allowing direct use in RedHat for example?

(question by Cymon)

Best between NNI and SPR is still broken

Marcelo S Zanetti — Wed, 19 Jun 2013 10:10:45 -0000

codonphyml-omp -i cymon.phy -d codon -m MG -g THBAPPC -t e -s BEST -f optimize -w g --wclasses 6

. (179696 sec) [ -300178.5019] [ts/tv ratio ][3.14 ]
. (179696 sec) [ -300178.5019] [dn/ds ratio ]
. (179696 sec) [ -300178.5019] [Alpha and Beta ][0.68 1.86 ]
. (179696 sec) [ -300178.5019] [CF3x4 freqs. ]
. (179741 sec) [ -300178.5019] [Topology ]
. (180547 sec) [ -300178.5014] [Topology ]
. (181803 sec) [ -300178.5014] [ts/tv ratio ][3.14 ]
. (181803 sec) [ -300178.5014] [dn/ds ratio ]
. (181803 sec) [ -300178.5014] [Alpha and Beta ][0.68 1.86 ]
. (181803 sec) [ -300178.5014] [CF3x4 freqs. ]

. Checking for NNIs, optimizing five branches...

. best_lnL = -300178.496325, c_lnL = -300178.501354
. Err in file utilities.c at line 11530

Testing with -s NNI and -s SPR works fine ... the problem is the -s BEST