StatSVN - Directory [root]

[root]

AISC (16 files, 3904 lines)

AISC_COM (1 files, 16 lines)

AISC (8 files, 2077 lines)

C (15 files, 2740 lines)

AISC_MKPTPS (4 files, 1873 lines)

ALEIO (0 files, 0 lines)

ALIV3 (0 files, 0 lines)

ARBDB (85 files, 45838 lines)

EXAMPLES (0 files, 0 lines)

ARBDB2 (0 files, 0 lines)

ARBDBPP (0 files, 0 lines)

ARBDBS (0 files, 0 lines)

ARBDB_COMPRESS (0 files, 0 lines)

ARB_GDE (16 files, 4067 lines)

AWDEMO (0 files, 0 lines)

AWT (32 files, 12314 lines)

AWTC (6 files, 1048 lines)

AWTI (10 files, 3136 lines)

BERGEY (0 files, 0 lines)

BINDEP (37 files, 171 lines)

BINDINGS (2 files, 267 lines)

PERL (4 files, 1028 lines)

PYTHON (4 files, 147 lines)

BUGEX (1 files, 188 lines)

CAT (0 files, 0 lines)

CHIP (0 files, 0 lines)

CONSENSUS_TREE (16 files, 3495 lines)

CONVERTALN (36 files, 6594 lines)

CORE (50 files, 9413 lines)

DBSERVER (3 files, 563 lines)

DIST (19 files, 7444 lines)

DUMMYINC (0 files, 0 lines)

EDIT (0 files, 0 lines)

EDIT4 (51 files, 28755 lines)

EISPACK (7 files, 29478 lines)

GDE (2 files, 145 lines)

AxML (5 files, 5977 lines)

CLUSTAL (13 files, 4954 lines)

CLUSTALW (33 files, 21348 lines)

CORE (0 files, 0 lines)

FASTDNAML (7 files, 6447 lines)

FASTTREE (3 files, 10348 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, 75634 lines)

extensions (3 files, 72 lines)

mxscarna_src (21 files, 6911 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 (66 files, 71352 lines)

doc (42 files, 21478 lines)

PHYML (22 files, 15180 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, 78797 lines)

PROBCONS (2 files, 31 lines)

probcons (17 files, 6323 lines)

RAxML (31 files, 72525 lines)

RAxML8 (4 files, 581 lines)

SATIVA (4 files, 396 lines)

sativa (3 files, 1494 lines)

epac (8 files, 2380 lines)

ete2 (1 files, 185 lines)

SUPPORT (10 files, 2584 lines)

TREEPUZZLE (6 files, 854 lines)

data (0 files, 0 lines)

doc (3 files, 1653 lines)

src (18 files, 17676 lines)

GDEHELP (11 files, 887 lines)

DATA_FILES (0 files, 0 lines)

FASTA (0 files, 0 lines)

GENBANK (1 files, 1500 lines)

MATRIX (9 files, 258 lines)

HELP_PLAIN (3 files, 135 lines)

HELP_WRITTEN (12 files, 849 lines)

MENUS (22 files, 2290 lines)

PHYLIP (0 files, 0 lines)

GENOM (17 files, 5496 lines)

GENOM_IMPORT (18 files, 2811 lines)

GFX (2 files, 1079 lines)

GL (1 files, 61 lines)

glAW (10 files, 1498 lines)

glpng (4 files, 716 lines)

HEADERLIBS (7 files, 206 lines)

HELP_SOURCE (16 files, 3821 lines)

genhelp (6 files, 200 lines)

oldhelp (0 files, 0 lines)

prompt (0 files, 0 lines)

seer (0 files, 0 lines)

source (10 files, 721 lines)

ISLAND_HOPPING (12 files, 2102 lines)

JAVALIB (0 files, 0 lines)

MERGE (16 files, 5920 lines)

MULTI_PROBE (21 files, 6012 lines)

NALIGNER (26 files, 7916 lines)

NAMES (4 files, 1536 lines)

NAMES_COM (8 files, 298 lines)

NIELS_F77 (0 files, 0 lines)

NTREE (44 files, 19982 lines)

ORS_CGI (0 files, 0 lines)

ORS_COM (0 files, 0 lines)

ORS_SERVER (0 files, 0 lines)

PARSIMONY (19 files, 8911 lines)

PERL2ARB (12 files, 1565 lines)

PERLTOOLS (3 files, 1095 lines)

PERL_SCRIPTS (0 files, 0 lines)

ACI (1 files, 30 lines)

ARBTOOLS (2 files, 661 lines)

DOCUMENTED (0 files, 0 lines)

IFTHELP (4 files, 254 lines)

TESTS (2 files, 78 lines)

BIOPERL (2 files, 119 lines)

GENERAL (1 files, 99 lines)

GENOME (3 files, 452 lines)

IFTHELP (0 files, 0 lines)

MACROS (1 files, 158 lines)

MAUS (0 files, 0 lines)

SAI (2 files, 159 lines)

SPECIES (4 files, 717 lines)

lib (1 files, 80 lines)

test (5 files, 212 lines)

PGT (0 files, 0 lines)

xslt (0 files, 0 lines)

PHYLO (11 files, 2179 lines)

PRIMER_DESIGN (19 files, 2992 lines)

PROBE (25 files, 10636 lines)

PROBE_COM (8 files, 447 lines)

PROBE_DESIGN (11 files, 6593 lines)

PROBE_SERVER (0 files, 0 lines)

PROBE_GROUP (0 files, 0 lines)

PROBE_GROUP_DESIGN (0 files, 0 lines)

TREE_MERGE (0 files, 0 lines)

WORKER (0 files, 0 lines)

PROBE_SET (32 files, 6865 lines)

PROBE_WEB (0 files, 0 lines)

CLIENT (0 files, 0 lines)

SERVER (0 files, 0 lines)

READSEQ (9 files, 5275 lines)

RNA3D (20 files, 4657 lines)

Attic (0 files, 0 lines)

OPENGL (0 files, 0 lines)

data (0 files, 0 lines)

images (0 files, 0 lines)

RNACMA (8 files, 1584 lines)

SECEDIT (28 files, 8538 lines)

SEER (0 files, 0 lines)

SEQ_QUALITY (12 files, 2448 lines)

SERVERCNTRL (4 files, 560 lines)

SH (34 files, 2392 lines)

SL (2 files, 101 lines)

ALILINK (7 files, 2367 lines)

ALIVIEW (4 files, 172 lines)

AP_TREE (8 files, 2372 lines)

ARB_TREE (4 files, 565 lines)

AW_HELIX (4 files, 359 lines)

AW_NAME (5 files, 1074 lines)

CB (7 files, 1127 lines)

CONSENSUS (3 files, 1730 lines)

DB_QUERY (5 files, 3021 lines)

DB_SCANNER (4 files, 801 lines)

DB_UI (5 files, 2063 lines)

FAST_ALIGNER (8 files, 5861 lines)

FILE_BUFFER (0 files, 0 lines)

FILTER (6 files, 901 lines)

FILTSEQEXP (3 files, 652 lines)

GROUP_SEARCH (3 files, 4171 lines)

GUI_ALIVIEW (9 files, 1350 lines)

HELIX (6 files, 822 lines)

INSDEL (3 files, 2421 lines)

ITEMS (10 files, 1735 lines)

ITEM_SHADER (5 files, 2393 lines)

LOCATION (4 files, 611 lines)

MACROS (10 files, 1871 lines)

MATRIX (4 files, 319 lines)

NDS (3 files, 1225 lines)

NEIGHBOURJOIN (5 files, 574 lines)

PRONUC (8 files, 2764 lines)

PTCLEAN (4 files, 262 lines)

PVP (3 files, 566 lines)

QUERY (3 files, 667 lines)

REFENTRIES (4 files, 527 lines)

REGEXPR (4 files, 365 lines)

ROOTED_TREE (0 files, 0 lines)

SAICALC (5 files, 3200 lines)

SEQIO (5 files, 1219 lines)

SEQUENCE (10 files, 1755 lines)

TRANSLATE (4 files, 340 lines)

TREEDISP (10 files, 7515 lines)

TREE_ADMIN (4 files, 346 lines)

TREE_READ (5 files, 1232 lines)

TREE_WRITE (5 files, 616 lines)

XFERGUI (2 files, 1294 lines)

XFERSET (3 files, 2152 lines)

SOURCE_TOOLS (63 files, 10742 lines)

COMPILE_COMPAT (4 files, 131 lines)

docs (1 files, 79 lines)

refactor (2 files, 32 lines)

release (2 files, 407 lines)

STAT (9 files, 2156 lines)

TEMPLATES (48 files, 8383 lines)

TEST (0 files, 0 lines)

TESTAWT (0 files, 0 lines)

TESTVECTORFONT (0 files, 0 lines)

TOOLS (28 files, 12388 lines)

TREEGEN (17 files, 1454 lines)

TREE_COMPRESS (0 files, 0 lines)

TRS (0 files, 0 lines)

UNIT_TESTER (24 files, 6113 lines)

flags (1 files, 2 lines)

run (42 files, 21335 lines)

consense (0 files, 0 lines)

1 (7 files, 475 lines)

2 (5 files, 894 lines)

3 (4 files, 1543 lines)

4 (3 files, 146 lines)

6 (1 files, 49 lines)

diff (4 files, 72 lines)

display (25 files, 17249 lines)

distance (5 files, 151 lines)

fakehome (0 files, 0 lines)

general (6 files, 90 lines)

help (3 files, 933 lines)

homefake (0 files, 0 lines)

.arb_prop (1 files, 1 lines)

impexp (39 files, 4469 lines)

pars (22 files, 828 lines)

pvp (4 files, 63 lines)

tools (23 files, 475 lines)

trees (1 files, 27 lines)

xsub (4 files, 511 lines)

sockets (0 files, 0 lines)

valgrind (2 files, 179 lines)

WETC (3 files, 115 lines)

WINDOW (75 files, 26347 lines)

XML (4 files, 499 lines)

XML_IMPORT (0 files, 0 lines)

IMP_TREE (0 files, 0 lines)

bin (2 files, 217 lines)

doc (1 files, 85 lines)

etc (6 files, 5366 lines)

fig2dev (0 files, 0 lines)

dev (0 files, 0 lines)

lib (8 files, 12081 lines)

BUGS (2 files, 69 lines)

addlibs (1 files, 14 lines)

arb_default (7 files, 694 lines)

desktop (4 files, 21 lines)

dtd (2 files, 92 lines)

export (14 files, 130 lines)

gde (2 files, 28 lines)

icons (0 files, 0 lines)

import (9 files, 680 lines)

nonformats (7 files, 783 lines)

inputMasks (9 files, 343 lines)

macros (5 files, 240 lines)

.checks (3 files, 675 lines)

ARB (0 files, 0 lines)

SEQ_DATA (1 files, 111 lines)

motifHack (3 files, 322 lines)

pixmaps (0 files, 0 lines)

nas (3 files, 18 lines)

pictures (102 files, 3716 lines)

PARS (0 files, 0 lines)

awt (19 files, 599 lines)

awtc (2 files, 47 lines)

consensus (2 files, 368 lines)

cpro (2 files, 72 lines)

demo (0 files, 0 lines)

edit4 (16 files, 819 lines)

etc (0 files, 0 lines)

faligner (3 files, 139 lines)

findcorr (0 files, 0 lines)

merge (12 files, 473 lines)

pars (3 files, 184 lines)

phylo (3 files, 67 lines)

query (5 files, 133 lines)

seer (0 files, 0 lines)

unused (0 files, 0 lines)

demo (0 files, 0 lines)

findcorr (0 files, 0 lines)

window (1 files, 24 lines)

pixmaps (84 files, 3509 lines)

edit (20 files, 602 lines)

unused (0 files, 0 lines)

icons (7 files, 273 lines)

unused (0 files, 0 lines)

merge (1 files, 48 lines)

pgt (0 files, 0 lines)

print (6 files, 239 lines)

unused (0 files, 0 lines)

seer (0 files, 0 lines)

unused (0 files, 0 lines)

protein_2nd_structure (0 files, 0 lines)

rna3d (5 files, 4617 lines)

images (17 files, 0 lines)

sellists (9 files, 100 lines)

submit (3 files, 1061 lines)

ptpan (0 files, 0 lines)

util (18 files, 1629 lines)

Author	Changes	Lines of Code	Lines per Change
Totals	1176 (100.0%)	16278 (100.0%)	13.8
westram	1069 (90.9%)	14984 (92.1%)	14.0
oldcode	9 (0.8%)	760 (4.7%)	84.4
epruesse	33 (2.8%)	281 (1.7%)	8.5
boehnel	4 (0.3%)	75 (0.5%)	18.7
yadhu	17 (1.4%)	74 (0.5%)	4.3
meierh	12 (1.0%)	24 (0.1%)	2.0
richter	4 (0.3%)	19 (0.1%)	4.7
baderk	17 (1.4%)	18 (0.1%)	1.0
spanfeln	1 (0.1%)	11 (0.1%)	11.0
foerster	2 (0.2%)	11 (0.1%)	5.5
arb_build	1 (0.1%)	8 (0.0%)	8.0
aboeckma	2 (0.2%)	5 (0.0%)	2.5
jobb	1 (0.1%)	4 (0.0%)	4.0
artemov	2 (0.2%)	2 (0.0%)	1.0
littschw	1 (0.1%)	1 (0.0%)	1.0
lai	1 (0.1%)	1 (0.0%)	1.0

Most Recent Commits

westram 2022-07-21 14:01 Rev.: 19167

* reintegrates 'split' into 'trunk'
* adds: log:branches/split@19102:19166

1 lines of code changed in 1 file:

arb_CHANGES.txt (+1)

westram 2022-06-25 09:50 Rev.: 19076

* set default values early:
- SANITIZE (avoids warning about undefined variable).
- IGNORE_LEAKS

10 lines of code changed in 1 file:

Makefile (+10 -14)

westram 2022-06-22 10:44 Rev.: 19074

* partial merge from 'sina' into 'trunk'
* adds: log:branches/sina@19070:19071

48 lines of code changed in 1 file:

Makefile (+48 -1)

westram 2022-06-17 13:29 Rev.: 19060

* align version numbers (cosmetic).

11 lines of code changed in 1 file:

Makefile (+11 -11)

westram 2022-06-17 13:28 Rev.: 19059

* accept gcc 10.x-series (1-3)

1 lines of code changed in 1 file:

Makefile (+1)

westram 2022-06-17 11:56 Rev.: 19056

* accept gcc 9.5.0
- vectorizations fail as with 9.4.0

1 lines of code changed in 1 file:

Makefile (+1 -1)

westram 2022-06-17 11:41 Rev.: 19055

* accept gcc 9.4.0
* loop vectorizations failing with gcc 9.1 - 9.3 also fail with 9.4.

1 lines of code changed in 1 file:

Makefile (+1 -1)

westram 2022-06-17 11:39 Rev.: 19054

* accept gcc 8.5.0

1 lines of code changed in 1 file:

Makefile (+1 -1)

westram 2022-05-20 09:39 Rev.: 19043

* only check for {{{makedepend}}} when dependencies are updated (not required for plain build).
* update requirements
- makedepend not required for compile (only for develop).
- opengl.

16 lines of code changed in 3 files:

Makefile (+6 -5), arb_INSTALL.txt (+6 -4), arb_UBUNTU.txt (+4 -13)

westram 2022-05-18 13:59 Rev.: 19033

* set optimization level to 1 (instead of 0)
- otherwise sanitizer reports bogus buffer-overflows.
- bug had been introduced by r18890
* comment (buffer-overflows occurred in static variable 'glservercntrl' - weird)

4 lines of code changed in 1 file:

Makefile (+4)

westram 2022-04-06 14:34 Rev.: 18983

* updated openGL requirements (for openSuSE leap 15.3).

4 lines of code changed in 1 file:

arb_INSTALL.txt (+4 -2)

westram 2022-04-06 14:33 Rev.: 18982

* fix for sun/rpc moved from glib->libtirpc (e.g. openSuSE leap 15.3 + Fedora 28)

18 lines of code changed in 2 files:

Makefile (+16 -2), arb_INSTALL.txt (+2 -1)

westram 2022-04-06 14:29 Rev.: 18981

* export/use {{{ARB_CORE_LIBS}}} (instead of using {{{ARB_GLIB_LIBS}}} directly).

3 lines of code changed in 1 file:

Makefile (+3 -1)

westram 2022-03-04 16:08 Rev.: 18960

* updated

5 lines of code changed in 1 file:

arb_CHANGES.txt (+5)

westram 2022-03-04 12:26 Rev.: 18959

* reintegrates 'progress' into 'trunk'
- implements #789
* adds: log:branches/progress@18885:18958

6 lines of code changed in 1 file:

Makefile (+6 -10)

westram 2022-02-07 17:32 Rev.: 18925

* add excerpting targets {{{TARFILE}}} + {{{TARFILE_QUICK}}}
- use them from build scripts.

9 lines of code changed in 1 file:

Makefile (+9 -2)

westram 2022-02-07 17:28 Rev.: 18924

* move main targets to bottom.
* separate sections + reorder.

26 lines of code changed in 1 file:

Makefile (+26 -16)

westram 2022-02-07 17:25 Rev.: 18923

* move cloc section.
* use system-cloc.

20 lines of code changed in 1 file:

Makefile (+20 -20)

westram 2022-02-07 17:22 Rev.: 18922

* 'tarfile_quick' now depends on 'all'
* fix build scripts:
- 'build' was executed twice.
- 'clean'+'tarfile_quick' -> 'tarfile'.

1 lines of code changed in 1 file:

Makefile (+1 -1)

westram 2022-02-07 17:20 Rev.: 18921

* remove obsolete targets
- 'release_quick' (relict from old release strategy).
- 'build_CTARGET' and 'reset_committed_build' + related code.

0 lines of code changed in 1 file:

Makefile (-15)

westram 2022-02-07 16:11 Rev.: 18920

* targets 'all' + 'rebuild' failed to report error since r18917
- fixed by adding 'false' to failing else branch
* remove recursive target 'logwrap_target'
- caused to many extra error lines **after** excerpt - renders the whole idea useless.
* instead
- add separate extracting targets for 'all' + 'rebuild' (ALL + REBUILD)
- store needed code in variables to DRY it
* reduce size of excerpt by 2 lines (which get printed after excerpt in case of failure). change header line.
* add decription for targets ALL + REBUILD

18 lines of code changed in 1 file:

Makefile (+18 -25)

westram 2022-02-07 16:01 Rev.: 18919

* fix indentation.
* do not print date on separator when showing help.

38 lines of code changed in 1 file:

Makefile (+38 -37)

westram 2022-02-04 17:51 Rev.: 18917

* add target 'logwrap_target' (allows to wrap any target).
- wrap targets 'all' + 'rebuild'.
* document possibility for silent builds.
* pass name of logfile to script + refer to log in header.
* reserve space for header line.

25 lines of code changed in 1 file:

Makefile (+25 -10)

westram 2022-02-03 12:48 Rev.: 18916

* filter error-messages from failed {{{make all}}} and dump at bottom
* log of last build remains in {{{build.log}}}

17 lines of code changed in 2 files:

.gitignore (+3 -2), Makefile (+14 -1)

westram 2022-02-01 17:03 Rev.: 18912

* target 'patch' always patches versus svn.

1 lines of code changed in 1 file:

Makefile (+1 -1)

westram 2022-02-01 16:48 Rev.: 18911

* partial merge from 'stable' into 'trunk'
* adds: [18908/branches/stable]

4 lines of code changed in 1 file:

arb_CHANGES.txt (+4)

westram 2022-01-29 15:33 Rev.: 18907

* partial merge from 'stable' into 'trunk'
* adds: log:branches/stable@18903:18906

1 lines of code changed in 1 file:

Makefile (+1 -1)

westram 2021-12-20 18:44 Rev.: 18883

* reintegrates 'nds' into 'trunk'
- fixes #841
* adds: log:branches/nds@18843:18882

9 lines of code changed in 1 file:

arb_CHANGES.txt (+9 -2)

westram 2021-12-19 19:14 Rev.: 18875

* ARB_GDE depends on 'menus' (fix failing 'rebuild'; broken by [18866])

1 lines of code changed in 1 file:

Makefile (+1 -1)

westram 2021-11-14 13:18 Rev.: 18842

* allow conditional build of OPENMP version of {{{FastTree}}}
- tweak preprocessor: allow to {{{#define}}} via CLI.
- globally define whether OPENMP shall be used
* export to submakefiles.
* disable under OSX
- capability to build OPENMP binary depends on compiler
- LLVM/Clang 3.7 required
- forward {{{USE_OPENMP}}} into preprocessor.
- in fasttree.menu: when not defined {{{USE_OPENMP}}} -> skip MP option from GUI + hardcode binary.
- conditionally build OPENMP binary depending on {{{USE_OPENMP}}}.

7 lines of code changed in 1 file:

Makefile (+7)

westram 2021-11-10 15:36 Rev.: 18839

* upgrade {{{FastTree}}} to version 2.1.11
- cleanup: define flags and use make variables.
- specify fasttree version in help.
- update changelog.

4 lines of code changed in 1 file:

arb_CHANGES.txt (+4 -1)

westram 2021-10-10 09:33 Rev.: 18781

* reintegrates 'help' into 'trunk'
- relocate help sources
* adds: log:branches/help@18763:18780

0 lines of code changed in 1 file:

arb_OS_X.txt (-1)

westram 2021-09-17 13:44 Rev.: 18735

* fix another obsolete URL

1 lines of code changed in 1 file:

arb_README.txt (+1 -1)

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

* eliminate trailing whitespace from Makefiles.

1 lines of code changed in 1 file:

Makefile (+1 -1)

westram 2021-09-04 10:31 Rev.: 18703

* link to ancient changes

4 lines of code changed in 1 file:

arb_CHANGES.txt (+4)

westram 2021-09-02 18:28 Rev.: 18702

* full update from child 'stable' into 'trunk'
* adds: log:branches/stable@18696:18701

2 lines of code changed in 2 files:

README (+1 -20), arb_README.txt (+1 -1)

westram 2021-09-02 17:50 Rev.: 18700

* again add section for 'changes for next release'.

3 lines of code changed in 1 file:

arb_CHANGES.txt (+3)

westram 2021-09-02 16:46 Rev.: 18698

* again update arb_README.

16 lines of code changed in 1 file:

arb_README.txt (+16 -20)

westram 2021-09-02 09:46 Rev.: 18697

* full update from child 'stable' into 'trunk'
- merge changes done to arb-7.0 release candidate
* adds: log:branches/stable@18690:18695

148 lines of code changed in 5 files:

arb_CHANGES.txt (+1 -1), arb_INSTALL.txt (+11 -4), arb_LICENSE.txt (+20 -22), arb_README.txt (+12 -28), arb_install.sh (+104 -73)

westram 2021-08-26 18:03 Rev.: 18687

* whitespace

1 lines of code changed in 1 file:

arb_CHANGES.txt (+1 -1)

(1002 more)

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Most Recent Commits