Directory GDE/PHYML/

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westram 2023-08-11 13:40 Rev.: 19480

* reintegrates 'gde' into 'trunk'
* adds: log:branches/gde@19460:19479

86 lines of code changed in 15 files:

• GDE/PHYML: eigen.c (+1 -2), free.c (-35), free.h (-3), lk.c (+1 -4), lk.h (+1 -1), main.c (+3 -5), models.c (+8 -16), models.h (-1), optimiz.c (+7 -106), optimiz.h (-2), options.c (+24 -12), simu.c (+19 -27), simu.h (+2 -2), utilities.c (+16 -39), utilities.h (+4 -5)

westram 2023-08-05 13:40 Rev.: 19446

* introduce {{{onlyC_flags}}}
- flags used for C compilation only.
- similar to {{{cxxflags}}} (references added).
- pass down onlyC_flags into AxML, CLUSTAL, CLUSTALW, FASTDNAML, FASTTREE, GL, MrBAYES, PHYLIP, PHYML*, RAxML, SINA(unused), SOURCE_TOOLS, SUPPORT, TOOLS, TREEGEN + TREEPUZZLE.
- set flags to {{{-Werror-implicit-function-declaration}}}
* error is only effective in a small part of these modules.
* TODO: need to activate warnings -> will activate the error as well.

1 lines of code changed in 1 file:

• GDE/PHYML: Makefile (+1 -1)

westram 2021-09-15 13:48 Rev.: 18729

* eliminate trailing whitespace from Makefiles.

1 lines of code changed in 1 file:

• GDE/PHYML: Makefile (+1 -1)

westram 2014-03-18 21:45 Rev.: 11815

* reintegrates 'deb' into 'trunk'
- fixes #215
- performs #489
* adds:
- log:branches/deb@11801:11814

1 lines of code changed in 1 file:

• GDE/PHYML: Makefile (+1 -1)

westram 2014-03-18 16:21 Rev.: 11805

* export 'LINUX' and 'REDHAT' to submakefiles
* use ifeq instead of ifdef (completes [11804])

1 lines of code changed in 1 file:

• GDE/PHYML: Makefile (+1 -1)

westram 2013-10-29 13:23 Rev.: 10955

- renamed
* ACC -> A_CC
* CPP -> A_CXX (misleading atm, since it contains c++flags)

1 lines of code changed in 1 file:

• GDE/PHYML: Makefile (+1 -1)

westram 2013-02-13 13:24 Rev.: 9575

- effect of [9574] (comments only)

1 lines of code changed in 1 file:

• GDE/PHYML: Makefile (+1 -1)

westram 2011-11-28 14:41 Rev.: 8240

- patch for ubuntu 11.10 oneiric / gcc 4.6.1 (thx to Kai)
* dont link PHYML statically
* dont strip symbols
* prefix linker flags passed via compiler with -Wl,

0 lines of code changed in 1 file:

• GDE/PHYML: Makefile (-2)

westram 2009-04-19 19:36 Rev.: 5829

* included some patches for OSX (thx to Matt Cottrell)
* added global switch LINK_STATIC
* added script which checks for tools needed to compile ARB
* typo CCPLIB->CPPLIB

7 lines of code changed in 1 file:

• GDE/PHYML: Makefile (+7 -1)

westram 2007-05-30 15:34 Rev.: 4634

- proper clean (avoid errors if already cleaned)

1 lines of code changed in 1 file:

• GDE/PHYML: Makefile (+1 -1)

westram 2006-10-27 12:07 Rev.: 4209

- removed several dead or generated files

0 lines of code changed in 1 file:

• GDE/PHYML: phyml.dsp (del)

westram 2006-06-23 14:57 Rev.: 4076

- PHYML userdoc

503 lines of code changed in 1 file:

• GDE/PHYML: usersguide_phyliplike.html (new 503)

westram 2006-06-23 13:36 Rev.: 4073

- phyml 2.4.5

14673 lines of code changed in 22 files:

• GDE/PHYML: Makefile (new 115), Makefile.org (new 61), bionj.c (new 434), bionj.h (new 41), eigen.c (new 790), eigen.h (new 35), free.c (new 429), free.h (new 38), lk.c (new 1404), lk.h (new 45), main.c (new 284), models.c (new 1719), models.h (new 41), optimiz.c (new 1655), optimiz.h (new 116), options.c (new 1591), options.h (new 24), phyml.dsp (new), simu.c (new 439), simu.h (new 26), utilities.c (new 4835), utilities.h (new 551)