- fixes compilation error on OSX (with perl 5.16)
thx to matt
11 lines of code changed in 1 file:
* reintegrates 'fix' into 'trunk'
- implements #501
* adds:
- log:branches/fix@11904:11910
108 lines of code changed in 1 file:
* reintegrates 'fix' into 'trunk'
- fixes #499
* adds:
- log:branches/fix@11890:11901
194 lines of code changed in 2 files:
* document implementation of #484
10 lines of code changed in 1 file:
- add missing comment to closing #endif of test-sections
20 lines of code changed in 19 files:
- highlight differences in production code triggered by build-flag 'UNIT_TESTS'
28 lines of code changed in 16 files:
* reintegrates 'cleanup' into 'trunk'
* adds:
- log:branches/cleanup@11876:11885
87 lines of code changed in 24 files:
* 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:
* 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:
* 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:
* code visibility
- made functions static
- moved functions into UNIT_TESTS section
375 lines of code changed in 21 files:
* 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:
- fix #497
6 lines of code changed in 1 file:
* add symbol-export options directly to [cl]flags
8 lines of code changed in 1 file:
- fix NULL ptr conversions
6 lines of code changed in 2 files:
- fix some format strings (detected by 32bit compile)
3 lines of code changed in 3 files:
- 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:
- 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:
- 32bit compilation passes (fixes #494; native compilation)
0 lines of code changed in 1 file:
* 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:
- added libglib2.0-dev
2 lines of code changed in 1 file:
- append 32bit suffix to version info
22 lines of code changed in 1 file:
- fix 32-bit cross-compile (on 64bit system). Fixes #494
- should also fix vv.
9 lines of code changed in 1 file:
don't crash if NDS cannot read a DB string (partial/hotfix for #481)
1 lines of code changed in 1 file:
* reintegrates 'deb' into 'trunk'
- fixes #215
- performs #489
* adds:
- log:branches/deb@11801:11814
87 lines of code changed in 15 files:
fix #315
1 lines of code changed in 1 file:
- fixes #490
10 lines of code changed in 1 file:
* export 'LINUX' and 'REDHAT' to submakefiles
* use ifeq instead of ifdef (completes [11804])
9 lines of code changed in 7 files:
* 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:
- fix SEGV (failed to detect species as 'missing in tree')
4 lines of code changed in 1 file:
* 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:
* merge [11784] from 'macros' into 'trunk'
0 lines of code changed in 2 files:
* reintegrates 'macros' into 'trunk'
- implements #456
* adds:
- log:branches/macros@11761:11777
114 lines of code changed in 23 files:
- temporarily dump all logs (to detect what's so slow on colab)
(reverted by [12410])
2 lines of code changed in 1 file:
* 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:
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:
- rename
90 lines of code changed in 3 files:
* 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:
- added action 'rm' (shows commands to remove any branch/tag)
38 lines of code changed in 1 file:
* reintegrates 'bugrep' into 'trunk'
- implements #391
* adds:
- log:branches/bugrep@11744:11753
204 lines of code changed in 5 files:
* supports optional argument 'from_tarball' (-> skips 'make save')
11 lines of code changed in 1 file:
* add whole 'mafft-###'-directory strictly as in SVN
1 lines of code changed in 1 file:
* remove directories 'binaries' and 'scripts' from SVN and generate them from Makefile
15 lines of code changed in 3 files:
* create parent directories recursive (random failures)
20 lines of code changed in 1 file:
* 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:
- always release source-tarball
9 lines of code changed in 1 file:
- updated changes (reviewed trunk commits: log:trunk@9690:11735?limit=999)
17 lines of code changed in 1 file:
- '\n' works as LF in SRT
1 lines of code changed in 1 file:
- set DEVELOPER=RELEASE in jenkins' config.makefile
[reviewed code-locations where DEVEL_RELEASE is used]
4 lines of code changed in 1 file:
* copy arb_README.txt and arb_install.sh only in one build (ubuntu1004/RELEASE)
5 lines of code changed in 1 file:
* set arb version to 6.0
4 lines of code changed in 2 files:
* need to 'make show_version' (otherwise script sees wrong version id)
3 lines of code changed in 1 file:
* reverts [11717]
* merge [11714] into trunk (accidentally went into 'rc')
65 lines of code changed in 8 files:
* ~~set trunk version to 6.0~~
(reverted by [11718])
4 lines of code changed in 2 files:
- changed version
1 lines of code changed in 1 file:
- describe
- when to update changelog / version
- when to wait for / trigger jenkins jobs
20 lines of code changed in 2 files:
don't jump in tree if displayed_root is NULL (fixes #477)
1 lines of code changed in 1 file: