July 2014 Commit Log

Number of Commits:
46
Number of Active Developers:
2
epruesse 2014-07-31 12:37 Rev.: 12638

add gcc 4.9.1 (merge from debian patches)

1 lines of code changed in 1 file:

westram 2014-07-29 11:47 Rev.: 12605


- restrict save test to DEBUG build

2 lines of code changed in 1 file:

westram 2014-07-29 09:56 Rev.: 12604


- ~~use suggested fix for #582~~

(reverted by [12678])

16 lines of code changed in 1 file:

westram 2014-07-28 20:05 Rev.: 12603


* merge [12602] from 'alilink' into 'trunk'

2 lines of code changed in 2 files:

westram 2014-07-28 18:42 Rev.: 12600


* no longer use aw_popup_exit (causes resource problems)
- either use GBK_terminate or pass back error
* shutdown_macro_recording before exit during startup

19 lines of code changed in 4 files:

westram 2014-07-28 18:39 Rev.: 12599


- update prototypes

0 lines of code changed in 1 file:

epruesse 2014-07-28 15:02 Rev.: 12598

Use arb_socket_open in ARBDB
- DRY: gbcm_get_n_id is gone, gbcm_open_socket reduced to replacing ":"
- gbcm_write_flush simplified
- SIGPIPE handler no longer necessary
- Error messages changed (hopefully nicer now)

34 lines of code changed in 3 files:

westram 2014-07-28 09:48 Rev.: 12593


- update depends for [12591]

0 lines of code changed in 2 files:

epruesse 2014-07-28 02:17 Rev.: 12592

remove more traces of common.a

3 lines of code changed in 5 files:

epruesse 2014-07-28 01:57 Rev.: 12591

AISC now uses arb_open_socket, arb_socket_write and ..._read.
- SIGPIPE is disabled via setsockopt on mac and via MSG_NOSIGNAL
on Linux.
- No more usleep in write loop.
- arb_socket_write returns -1 on failure
(needed change to client.c as aisc_s_write and aisc_c_write
differed in error handling)
- common.[hc] are gone
- fixes build failure in build 797

104 lines of code changed in 10 files:

epruesse 2014-07-27 23:54 Rev.: 12590

- fork() server process instead of using "nc" (would be another build-dep)
- return "" if ENOENT or ECONNREFUSED

90 lines of code changed in 1 file:

westram 2014-07-27 13:29 Rev.: 12588


- disable NDEBUG dumps (ptserver)

10 lines of code changed in 2 files:

epruesse 2014-07-27 13:24 Rev.: 12587

- add arb_open_socket()
- fix bug in arb_shell_expand()

262 lines of code changed in 3 files:

epruesse 2014-07-27 13:14 Rev.: 12586

change error message (this is AISC, not the DB SERVER)

1 lines of code changed in 1 file:

epruesse 2014-07-27 12:59 Rev.: 12585

disable UNIT_TESTER warnings by default

4 lines of code changed in 1 file:

westram 2014-07-24 16:41 Rev.: 12578


depends for [12577]

13 lines of code changed in 1 file:

epruesse 2014-07-24 14:09 Rev.: 12577

add arb_shell_expan(const char*) function to handle path expansion

108 lines of code changed in 2 files:

westram 2014-07-23 14:57 Rev.: 12572


- use seqdata from edit4 screenshot as launch icon (implements #365)

64 lines of code changed in 2 files:

westram 2014-07-23 10:21 Rev.: 12570


- replace 'edit4 launch icon'
- applies to #365 (hoping that the new icon is more intuitive)

117 lines of code changed in 3 files:

westram 2014-07-22 16:19 Rev.: 12566


* merge some changes from 'stable' back into 'trunk'
* adds:
- log:branches/stable@12561:12563
- [http://bugs.arb-home.de/changeset?new=12560%40branches%2Fstable%2Farb_CHANGES.txt&old=12268%40branches%2Frc%2Farb_CHANGES.txt misc changelog updates]

23 lines of code changed in 2 files:

westram 2014-07-22 11:32 Rev.: 12553


- fixes #486

5 lines of code changed in 1 file:

epruesse 2014-07-18 13:50 Rev.: 12533

fix AVX version not built due to "USE_GCC_46_OR_HIGHER" not exported

2 lines of code changed in 2 files:

epruesse 2014-07-18 11:43 Rev.: 12532

remove double press-any-key

0 lines of code changed in 1 file:

westram 2014-07-17 16:34 Rev.: 12531


* print to file
- always save in HOME
- write full path to console

10 lines of code changed in 1 file:

westram 2014-07-17 16:15 Rev.: 12530


- several renames
- dump used filename for ascii files

13 lines of code changed in 2 files:

westram 2014-07-17 11:52 Rev.: 12527


use readonly svn url

2 lines of code changed in 2 files:

westram 2014-07-17 10:25 Rev.: 12526


- remove broken help

0 lines of code changed in 1 file:

epruesse 2014-07-16 22:26 Rev.: 12525

- add help for raxml8
- import normal tree also in quick mode
- check against too many/few sequences for model

21 lines of code changed in 2 files:

epruesse 2014-07-16 12:55 Rev.: 12523

fix missing LD_LIBRARY_PATH setup

23 lines of code changed in 1 file:

westram 2014-07-16 08:21 Rev.: 12518


* arb_srclst
- remove 'tar.gz' (cannot match)
- remove explicit expressions for some .tgz (now all packed)
- skip 'TAGS.*'
- trace to STDERR + trace extension matching

16 lines of code changed in 1 file:

epruesse 2014-07-16 01:36 Rev.: 12517

first working version of RAxML8 integration

170 lines of code changed in 3 files:

epruesse 2014-07-16 00:24 Rev.: 12516

srclist doesn't like extensions containing '.' ...

1 lines of code changed in 1 file:

epruesse 2014-07-15 23:21 Rev.: 12515

I really wonder why only it's only one target (ubuntu 10.04) that
is picky about arb_srclist.pl not knowing how to handle some files.

1 lines of code changed in 1 file:

epruesse 2014-07-15 22:43 Rev.: 12514

- fix test case failing because of added menu item
(not sure about verifying the number of menu items in cxx unit tests...)
- fix arb_srclist.pl not knowning what to do with arb_raxml8
- some fixes to script (not yet working)

126 lines of code changed in 5 files:

epruesse 2014-07-15 21:24 Rev.: 12513

only build AVX version of RAxML if GCC >= 4.6.0

17 lines of code changed in 2 files:

epruesse 2014-07-15 19:45 Rev.: 12512

try arb_sed instead of sed (uses gsed on osx)

1 lines of code changed in 1 file:

epruesse 2014-07-15 19:42 Rev.: 12511

add GDE/RAxML8/builddir to directories not included in src tarball

1 lines of code changed in 1 file:

epruesse 2014-07-15 19:41 Rev.: 12510

use suffix stamp for stamp files (ignored by arb_srclst.pl)

5 lines of code changed in 1 file:

epruesse 2014-07-15 19:24 Rev.: 12509

fix OSX sed needs '' after -i

3 lines of code changed in 1 file:

epruesse 2014-07-15 16:25 Rev.: 12508

initial add of RAxML 8

182 lines of code changed in 5 files:

westram 2014-07-09 14:33 Rev.: 12497


* automatically correct output-filename-extension to .txt or .ps

45 lines of code changed in 1 file:

westram 2014-07-09 14:10 Rev.: 12496


- fix a2ps segfault (#573)

1 lines of code changed in 1 file:

westram 2014-07-08 11:47 Rev.: 12491


update

5 lines of code changed in 1 file:

westram 2014-07-08 11:23 Rev.: 12490


- treat dots as 'X' when combining ancestor sequences in ARB_PARSIMONY (protein sequences)
- previously dots where treated as gaps
- dna/rna combine always treated dots as 'N'
- thx to Yan Shi for tracking down that misbehavior
- fixes #144

5 lines of code changed in 1 file:

westram 2014-07-08 10:08 Rev.: 12489


- fixes #572

7 lines of code changed in 1 file:

westram 2014-07-07 12:19 Rev.: 12488


* fix #571
- only trigger branchlength calculation after commands in MOVE- or NNI-modes

5 lines of code changed in 1 file:

June 2014 »

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