StatSVN - Directory GDE/

[root]/GDE

AxML (5 files, 5978 lines)

CLUSTAL (13 files, 4953 lines)

CLUSTALW (33 files, 21375 lines)

CORE (0 files, 0 lines)

FASTDNAML (7 files, 6446 lines)

FASTTREE (3 files, 10353 lines)

HGL_SRC (0 files, 0 lines)

LOOPTOOL (0 files, 0 lines)

MAFFT (1 files, 55 lines)

mafft-7.053-without-extensions (0 files, 0 lines)

core (0 files, 0 lines)

scripts (0 files, 0 lines)

mafft-7.055-with-extensions (4 files, 309 lines)

core (90 files, 75652 lines)

extensions (3 files, 73 lines)

mxscarna_src (21 files, 6918 lines)

probconsRNA (20 files, 7594 lines)

vienna (6 files, 11842 lines)

MOLPHY (0 files, 0 lines)

doc (0 files, 0 lines)

utl (0 files, 0 lines)

MUSCLE (2 files, 45 lines)

src (190 files, 34747 lines)

unused (3 files, 548 lines)

MrBAYES (1 files, 45 lines)

mrbayes_3.2.1 (31 files, 114641 lines)

PHYLIP (60 files, 70322 lines)

doc (42 files, 21478 lines)

PHYML (22 files, 15006 lines)

PHYML20130708 (2 files, 64 lines)

phyml (18 files, 22761 lines)

bin (0 files, 0 lines)

doc (17 files, 24532 lines)

examples (5 files, 1255 lines)

lg4x (5 files, 142 lines)

src (68 files, 78802 lines)

PROBCONS (2 files, 31 lines)

probcons (17 files, 6323 lines)

RAxML (31 files, 72542 lines)

RAxML8 (4 files, 588 lines)

SATIVA (4 files, 397 lines)

sativa (3 files, 1494 lines)

epac (8 files, 2380 lines)

ete2 (1 files, 185 lines)

SINA (1 files, 83 lines)

builddir (0 files, 0 lines)

src (1 files, 1022 lines)

SUPPORT (10 files, 2522 lines)

TREEPUZZLE (6 files, 854 lines)

data (0 files, 0 lines)

doc (3 files, 1653 lines)

src (18 files, 17634 lines)

Author	Changes	Lines of Code	Lines per Change
Totals	65 (100.0%)	364 (100.0%)	5.6
westram	50 (76.9%)	287 (78.8%)	5.7
oldcode	1 (1.5%)	49 (13.5%)	49.0
epruesse	3 (4.6%)	13 (3.6%)	4.3
aboeckma	7 (10.8%)	7 (1.9%)	1.0
jobb	1 (1.5%)	4 (1.1%)	4.0
yadhu	1 (1.5%)	3 (0.8%)	3.0
artemov	2 (3.1%)	1 (0.3%)	0.5

Most Recent Commits

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

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

7 lines of code changed in 1 file:

GDE: Makefile (+7 -14)

westram 2023-08-05 14:22 Rev.: 19455

* keep {{{-W -Wall}}} everywhere in GDE => activates -Werror-implicit-function-declaration.
- Note: (re)build of GDE tools fails.

1 lines of code changed in 1 file:

GDE: Makefile (+1 -1)

westram 2023-08-05 13:46 Rev.: 19447

* suppression of warnings for source-subtrees:
- comment + warn when suppressed (currently suppressed in GDE)

8 lines of code changed in 1 file:

GDE: Makefile (+8 -2)

westram 2022-09-01 16:19 Rev.: 19245

* reintegrates 'sina' into 'trunk'
- build/deliver sina together with arb
* adds: log:branches/sina@18984:19043,19046:19069,19072:19244

10 lines of code changed in 1 file:

GDE: Makefile (+10 -1)

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

* eliminate trailing whitespace from Makefiles.

3 lines of code changed in 1 file:

GDE: Makefile (+3 -3)

westram 2019-08-16 12:58 Rev.: 18012

* fix cflags substitutions done for GDE:
- include trailing space
- using sth like {{{-fopt-info-vec-optimized}}} resulted in {{{-optimized}}} => compile failed e.g. for PHYLIP

5 lines of code changed in 1 file:

GDE: Makefile (+5 -5)

westram 2017-08-09 14:59 Rev.: 16223

* reintegrates 'cover' into 'trunk'
- fixes compilation with COVERAGE
* ARB perl module failed to load (since [13739])
* linking executables broken (apparently since [14038])
* adds: log:branches/cover@16213:16222

4 lines of code changed in 1 file:

GDE: Makefile (+4)

epruesse 2017-03-22 21:19 Rev.: 15656

Allow skipping individual tool builds

Tools built and distributed with ARB can be skipped if their folder name
is found within ARB_BUILD_SKIP_PKGS.

4 lines of code changed in 1 file:

GDE: Makefile (+4)

westram 2016-12-30 13:17 Rev.: 15483

* partial merge from 'warnings' into 'trunk'
- no spam from GDE (filter compiler warnings, do not request vectorizer info)
- remove leftover occurrences of {{{grep -P}}} (harmless for OSX; only used for targets 'tags' and 'ut')
* adds: log:branches/warnings@15469:15470,15472,15474:15475,15479:15480

8 lines of code changed in 1 file:

GDE: Makefile (+8 -1)

westram 2015-04-10 14:13 Rev.: 13704

* add config-managers to all GDE windows
- automatically handles any 'arg' defined in .menu files (if argtype != 'filename')
- changed layout (of all 3 gde .figs) to allow to place button for config-manager
- added warnings to gde_menus.hlp (which changes affect configs)

6 lines of code changed in 1 file:

GDE: README (+6 -1)

westram 2014-10-17 12:59 Rev.: 13069

* reintegrates 'sativa' into 'trunk'
- adds experimental version of SATIVA
* adds:
- log:branches/sativa@12886:13068

1 lines of code changed in 1 file:

GDE: Makefile (+1)

westram 2014-08-04 14:45 Rev.: 12661

* fixes target 'depends' (broken by [12659])

15 lines of code changed in 1 file:

GDE: Makefile (+15 -11)

epruesse 2014-08-03 10:15 Rev.: 12659

merge Debian patch disabling tools for which Debian packages exist on
DEBIAN=1 build

7 lines of code changed in 1 file:

GDE: Makefile (+7 -7)

epruesse 2014-07-15 17:25 Rev.: 12508

initial add of RAxML 8

2 lines of code changed in 1 file:

GDE: Makefile (+2)

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

3 lines of code changed in 1 file:

GDE: Makefile (+3 -3)

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: Makefile (+1 -1)

westram 2014-01-10 15:01 Rev.: 11461

* get rid of boring warnings in PROBCONS, MrBAYES and FASTTREE

5 lines of code changed in 1 file:

GDE: Makefile (+5)

westram 2013-08-23 13:30 Rev.: 10479

* async GDE build
- pass down make flags (esp. -j) into subdirectories
- enclose subbuilds in $(SEP) as in main ARB Makefile (showing enter/exit timestamp for each subdir)
- mafft: build/clean core+extensions async
- mrbayes:
* define proper rules to make target 'mb' work with -j (no idea why that is needed)
* do not clear MAKEFLAGS in caller Makefile
- speedup for 'build' (on 8 cores)
* after GDE clean: 60s -> 30s
* after MrBAYES clean: 44s -> 17s

7 lines of code changed in 1 file:

GDE: Makefile (+7 -4)

aboeckma 2013-08-15 12:48 Rev.: 10456

Added rudimentary fasttree menu (need to know which options to use)

1 lines of code changed in 1 file:

GDE: Makefile (+1)

aboeckma 2013-08-07 14:47 Rev.: 10416

Added mr bayes (no menu yet)

1 lines of code changed in 1 file:

GDE: Makefile (+1)

aboeckma 2013-08-06 11:41 Rev.: 10408

Moved PROBCONS to NO_DEPENDS section.

1 lines of code changed in 1 file:

GDE: Makefile (+1 -1)

aboeckma 2013-08-02 11:15 Rev.: 10406

svn ignore probcons files

1 lines of code changed in 1 file:

GDE: Makefile (+1)

aboeckma 2013-08-01 15:18 Rev.: 10393

build muscle as part of gde

1 lines of code changed in 1 file:

GDE: Makefile (+1)

westram 2013-07-23 17:53 Rev.: 10347

* moved MAFFT to dependency-free GDE targets (fixes target 'depends')

1 lines of code changed in 1 file:

GDE: Makefile (+1 -1)

aboeckma 2013-07-23 14:04 Rev.: 10343

Added mafft

1 lines of code changed in 1 file:

GDE: Makefile (+1)

westram 2013-07-19 17:53 Rev.: 10312

- allow subdirs w/o dependencies in GDE

11 lines of code changed in 1 file:

GDE: Makefile (+11 -8)

aboeckma 2013-07-19 15:02 Rev.: 10307

added most recent version of phyml

1 lines of code changed in 1 file:

GDE: Makefile (+1)

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

- effect of [9574] (comments only)

1 lines of code changed in 1 file:

GDE: Makefile (+1 -1)

westram 2013-02-13 13:23 Rev.: 9574

- show from where dependencies are updated

1 lines of code changed in 1 file:

GDE: Makefile (+1 -1)

westram 2012-04-21 12:38 Rev.: 8641

* fixed warnings
- possible uninitialized variables
- DEBUG-mode variables
- ISLAND_HOPPING/Makefile: disabled warnings (i wont touch that module, except for removal)

1 lines of code changed in 1 file:

GDE: Makefile (+1 -1)

westram 2011-11-10 11:30 Rev.: 8205

merge from stable_5.0 [8203]
* removed molphy (protml)

0 lines of code changed in 1 file:

GDE: Makefile (-3)

westram 2011-04-16 14:35 Rev.: 7428

* 'make clean up' generated wrong dependencies (merged from dev [7427])

5 lines of code changed in 1 file:

GDE: Makefile (+5 -2)

westram 2011-02-09 10:23 Rev.: 7131

- removed leftover doc-refs to xview

0 lines of code changed in 1 file:

GDE: Makefile (-10)

westram 2010-09-09 22:40 Rev.: 6816

* unit-test improvements (merged [6757] [6758] [6759] [6760] [6761] [6762] [6764] [6791] [6795] [6798] [6799] [6800] [6801] [6802] [6809] [6810])
* moved file compare to test_unit.h
* fake report for skipped tests
* added templates for char compare
* perform minihexdump
* flush output
* added
- {{{TEST_ASSERT_FILES_EQUAL__BROKEN}}}
- {{{TEST_ASSERT_ZERO_OR_SHOW_ERRNO}}}
* create a fake.patch if there are no changes
* all code affecting assertions in UNIT_TESTS-mode went to test_global.h
- overwrites arb_assert()
* undefine UNIT_TESTS for GDE submakefiles (foreign code there)
* arb_test::FlushedOutput::errorf raises assertion itself
* test against I/O errors
* moved test code
- into class StaticCode: class w/o functionality, only holds global static code.
- assertfailmsg -> GlobalTestData
* refactored message printing
* unit-tester switches to run directory itself
- eliminates path hack for valgrind
* control leak-check by variable
* added global test-environment (does nothing yet)

9 lines of code changed in 1 file:

GDE: Makefile (+9 -5)

westram 2009-04-29 13:20 Rev.: 5872

* Changed variable transfer to sub-makefiles
- most variables are now exported via environment (using SOURCE_TOOLS/export2sub or AISC/export2sub)
- only variables that contain different values for different sub-makefile-calls are passed by cl (e.g. cflags, MAIN)
- changed flavour of exported variables (recursively expanded -> simply expanded variables). Please use VAR := VALUE in Makefiles (not VAR = VALUE). See http://www.gnu.org/software/make/manual/html_node/Flavors.html#Flavors for details
* removed/fixed all undefined variables in Makefiles (using 'make --warn-undefined-variables')
* changed names of compile-logs generated in GDE subdir
* added target 'xmlin' (broken, print warning)

2 lines of code changed in 1 file:

GDE: Makefile (+2 -22)

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

1 lines of code changed in 1 file:

GDE: Makefile (+1 -1)

westram 2008-03-11 20:10 Rev.: 5226

- removed CORE (last part using xview)

10 lines of code changed in 1 file:

GDE: Makefile (+10 -19)

westram 2008-03-03 18:42 Rev.: 5192

- renamed MODULE defines (_ARB -> IN_ARB)

1 lines of code changed in 1 file:

GDE: Makefile (+1 -1)

westram 2008-03-02 17:09 Rev.: 5180

- fixed warning suppression for GDE subdirs

30 lines of code changed in 1 file:

GDE: Makefile (+30 -15)

westram 2008-03-01 12:13 Rev.: 5167

- removed marker line from 'clean'

0 lines of code changed in 1 file:

GDE: Makefile (-1)

(24 more)

Directory GDE/

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