March 2014 Commit Log

Number of Commits:
57
Number of Active Developers:
2
westram 2014-03-31 10:17 Rev.: 11914


- fixes compilation error on OSX (with perl 5.16)
thx to matt

11 lines of code changed in 1 file:

westram 2014-03-30 11:04 Rev.: 11911


* reintegrates 'fix' into 'trunk'
- implements #501
* adds:
- log:branches/fix@11904:11910

108 lines of code changed in 1 file:

westram 2014-03-28 11:07 Rev.: 11902


* reintegrates 'fix' into 'trunk'
- fixes #499
* adds:
- log:branches/fix@11890:11901

194 lines of code changed in 2 files:

westram 2014-03-27 16:50 Rev.: 11899


* document implementation of #484

10 lines of code changed in 1 file:

westram 2014-03-25 12:06 Rev.: 11889


- add missing comment to closing #endif of test-sections

20 lines of code changed in 19 files:

westram 2014-03-25 11:53 Rev.: 11888


- highlight differences in production code triggered by build-flag 'UNIT_TESTS'

28 lines of code changed in 16 files:

westram 2014-03-24 21:30 Rev.: 11886


* reintegrates 'cleanup' into 'trunk'
* adds:
- log:branches/cleanup@11876:11885

87 lines of code changed in 24 files:

westram 2014-03-24 18:57 Rev.: 11874


* reintegrates 'customize' into 'trunk'
- implements #484
- clean up worst things in GDE to allow use of custom menu-files
* adds:
- log:branches/customize@11828:11840,11844:11873

975 lines of code changed in 40 files:

westram 2014-03-22 10:34 Rev.: 11844


* merge [11840:11843] from 'customize' into 'trunk'
* adds:
- log:branches/customize@11841:11843
* skipped changes in ARB_GDE
- log:branches/customize/ARB_GDE@11841:11843 ~~(might fail to reintegrate)~~

360 lines of code changed in 22 files:

westram 2014-03-21 18:54 Rev.: 11839


* removed 16k dead code from ARB_GDE (code was only necessary to run GDE-GUI; removed for #79)

14 lines of code changed in 9 files:

westram 2014-03-21 17:35 Rev.: 11838


* code visibility
- made functions static
- moved functions into UNIT_TESTS section

375 lines of code changed in 21 files:

westram 2014-03-21 14:02 Rev.: 11837


* fixed a hack in GDE code (fixes #498)
- due to path change done in [11813], result files of external tools were misinterpreted as ARB-database

8 lines of code changed in 1 file:

westram 2014-03-21 11:47 Rev.: 11836


- fix #497

6 lines of code changed in 1 file:

westram 2014-03-19 19:15 Rev.: 11827


* add symbol-export options directly to [cl]flags

8 lines of code changed in 1 file:

westram 2014-03-19 16:27 Rev.: 11826


- fix NULL ptr conversions

6 lines of code changed in 2 files:

westram 2014-03-19 16:27 Rev.: 11825


- fix some format strings (detected by 32bit compile)

3 lines of code changed in 3 files:

westram 2014-03-19 15:40 Rev.: 11824


- document differences between 32- and 64bit versions of ARB NJ (neighbourjoin)
- difference is somehow related to effect of toggling TEST_FORWARD_ORDER

12 lines of code changed in 1 file:

westram 2014-03-19 15:34 Rev.: 11823


- document differences between 32- and 64bit versions in probe-design unittest-results
- only affects amount of non-group-species estimated for decreased temperature (only last shown position has differences). Assuming this is caused by numeric issues, accepting it.

15 lines of code changed in 1 file:

westram 2014-03-19 14:03 Rev.: 11822


- 32bit compilation passes (fixes #494; native compilation)

0 lines of code changed in 1 file:

westram 2014-03-19 14:00 Rev.: 11821


* prepare !MrBayes-32bit compilation
- pass down ARB_64 into submakefiles
- generate dependencies in !MrBayes Makefile (fixes missing dependency from config.h)
- pass ARB_64 and DARWIN to gcc and use them to define flags in config.h:
* ARB_64 -> SSE_ENABLED + _64BIT
* ARB_DARWIN -> MAC_VERSION (UNIX_VERSION otherwise)
* let 32bit-compile fail for now

205 lines of code changed in 5 files:

westram 2014-03-19 12:39 Rev.: 11820


- added libglib2.0-dev

2 lines of code changed in 1 file:

westram 2014-03-19 12:10 Rev.: 11819


- append 32bit suffix to version info

22 lines of code changed in 1 file:

westram 2014-03-19 09:54 Rev.: 11818


- fix 32-bit cross-compile (on 64bit system). Fixes #494
- should also fix vv.

9 lines of code changed in 1 file:

epruesse 2014-03-18 21:58 Rev.: 11817

don't crash if NDS cannot read a DB string (partial/hotfix for #481)

1 lines of code changed in 1 file:

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


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

87 lines of code changed in 15 files:

epruesse 2014-03-18 20:33 Rev.: 11812

fix #315

1 lines of code changed in 1 file:

westram 2014-03-18 18:15 Rev.: 11810


- fixes #490

10 lines of code changed in 1 file:

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


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

9 lines of code changed in 7 files:

westram 2014-03-18 16:11 Rev.: 11804


* Makefile
- set defaults for undefined config.makefile-variables
- use ifeq instead of ifdef (fixes 'ifdef USE_CLANG' which did the wrong thing; reactivates -O99 linker flag for gcc-compilation)

31 lines of code changed in 1 file:

westram 2014-03-18 11:58 Rev.: 11800


- fix SEGV (failed to detect species as 'missing in tree')

4 lines of code changed in 1 file:

westram 2014-03-18 10:58 Rev.: 11798


* reintegrates 'macros' into 'trunk'
- fixes #485
- implements #455
- allow reverse sorting of species entries (DB-order)
* adds:
- log:branches/macros@11780:11783,11785:11797

432 lines of code changed in 22 files:

westram 2014-03-13 11:11 Rev.: 11785


* merge [11784] from 'macros' into 'trunk'

0 lines of code changed in 2 files:

westram 2014-03-12 12:19 Rev.: 11778


* reintegrates 'macros' into 'trunk'
- implements #456
* adds:
- log:branches/macros@11761:11777

114 lines of code changed in 23 files:

westram 2014-03-11 17:03 Rev.: 11774


- temporarily dump all logs (to detect what's so slow on colab)

(reverted by [12410])

2 lines of code changed in 1 file:

westram 2014-03-11 15:43 Rev.: 11773


* work around situations where ARB_PROP is undefined (can't create session log -> skip it; fixes #482)
* avoid warning ("rm: cannot remove `/home/ralf/.arb_prop/logs/20140311_143417.16245/crashed': No such file or directory")

55 lines of code changed in 1 file:

epruesse 2014-03-08 16:58 Rev.: 11760

do not write to stderr in SIGPIPE handler (fixes #476)

stderr is typically a pipe itself. If it is closed before the program
terminates, writing to it from the SIGPIPE handler will cause another
SIGPIPE to be raised, resulting in an infinite loop.

5 lines of code changed in 1 file:

westram 2014-03-08 14:46 Rev.: 11759


- rename

90 lines of code changed in 3 files:

westram 2014-03-08 14:36 Rev.: 11758


* show duration of the 3 slowest units (help to detect why unittest are sometimes so incredibly slow on colab)
* pretty print duration

34 lines of code changed in 1 file:

westram 2014-03-08 14:21 Rev.: 11757


- added action 'rm' (shows commands to remove any branch/tag)

38 lines of code changed in 1 file:

westram 2014-03-08 12:06 Rev.: 11754


* reintegrates 'bugrep' into 'trunk'
- implements #391
* adds:
- log:branches/bugrep@11744:11753

204 lines of code changed in 5 files:

westram 2014-03-04 21:20 Rev.: 11743


* supports optional argument 'from_tarball' (-> skips 'make save')

11 lines of code changed in 1 file:

westram 2014-03-04 20:46 Rev.: 11741


* add whole 'mafft-###'-directory strictly as in SVN

1 lines of code changed in 1 file:

westram 2014-03-04 20:15 Rev.: 11740


* remove directories 'binaries' and 'scripts' from SVN and generate them from Makefile

15 lines of code changed in 3 files:

westram 2014-03-04 20:15 Rev.: 11739


* create parent directories recursive (random failures)

20 lines of code changed in 1 file:

westram 2014-03-04 18:00 Rev.: 11738


* fix build from tarball
- fix name of tag-#define expected in svn_revision.h
- xpm-converter creates target directories on-the-fly

25 lines of code changed in 5 files:

westram 2014-03-04 16:27 Rev.: 11737


- always release source-tarball

9 lines of code changed in 1 file:

westram 2014-03-04 14:23 Rev.: 11736


- updated changes (reviewed trunk commits: log:trunk@9690:11735?limit=999)

17 lines of code changed in 1 file:

westram 2014-03-04 13:15 Rev.: 11735


- '\n' works as LF in SRT

1 lines of code changed in 1 file:

westram 2014-03-03 16:49 Rev.: 11734


- set DEVELOPER=RELEASE in jenkins' config.makefile
[reviewed code-locations where DEVEL_RELEASE is used]

4 lines of code changed in 1 file:

westram 2014-03-01 16:59 Rev.: 11724


* copy arb_README.txt and arb_install.sh only in one build (ubuntu1004/RELEASE)

5 lines of code changed in 1 file:

westram 2014-03-01 16:41 Rev.: 11723


* set arb version to 6.0

4 lines of code changed in 2 files:

westram 2014-03-01 16:39 Rev.: 11722


* need to 'make show_version' (otherwise script sees wrong version id)

3 lines of code changed in 1 file:

westram 2014-03-01 15:58 Rev.: 11718


* reverts [11717]
* merge [11714] into trunk (accidentally went into 'rc')

65 lines of code changed in 8 files:

westram 2014-03-01 15:38 Rev.: 11717


* ~~set trunk version to 6.0~~

(reverted by [11718])

4 lines of code changed in 2 files:

westram 2014-03-01 13:00 Rev.: 11710


- changed version

1 lines of code changed in 1 file:

westram 2014-03-01 12:59 Rev.: 11709


- describe
- when to update changelog / version
- when to wait for / trigger jenkins jobs

20 lines of code changed in 2 files:

epruesse 2014-03-01 01:26 Rev.: 11706

don't jump in tree if displayed_root is NULL (fixes #477)

1 lines of code changed in 1 file:

February 2014 »

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