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, 45951 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, 12322 lines)

AWTC (6 files, 1047 lines)

AWTI (10 files, 3135 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, 6596 lines)

CORE (51 files, 9533 lines)

DBSERVER (3 files, 563 lines)

DIST (19 files, 7459 lines)

DUMMYINC (0 files, 0 lines)

EDIT (0 files, 0 lines)

EDIT4 (53 files, 29792 lines)

EISPACK (7 files, 29478 lines)

GDE (2 files, 153 lines)

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)

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, 903 lines)

MENUS (22 files, 2308 lines)

PHYLIP (0 files, 0 lines)

GENOM (17 files, 5500 lines)

GENOM_IMPORT (18 files, 2811 lines)

GFX (2 files, 1079 lines)

GL (1 files, 63 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 (25 files, 2099 lines)

ISLAND_HOPPING (12 files, 2100 lines)

JAVALIB (0 files, 0 lines)

MERGE (16 files, 5931 lines)

MULTI_PROBE (21 files, 6107 lines)

NALIGNER (26 files, 7914 lines)

NAMES (4 files, 1536 lines)

NAMES_COM (8 files, 298 lines)

NIELS_F77 (0 files, 0 lines)

NTREE (44 files, 20113 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, 1584 lines)

PERLTOOLS (3 files, 1085 lines)

PERL_SCRIPTS (0 files, 0 lines)

ACI (1 files, 30 lines)

ARBTOOLS (2 files, 869 lines)

DOCUMENTED (0 files, 0 lines)

IFTHELP (4 files, 254 lines)

TESTS (2 files, 78 lines)

BIOPERL (2 files, 119 lines)

DB (1 files, 665 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 (5 files, 838 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, 10623 lines)

PROBE_COM (8 files, 447 lines)

PROBE_DESIGN (11 files, 6662 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, 5288 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, 8374 lines)

SEER (0 files, 0 lines)

SEQ_QUALITY (12 files, 2285 lines)

SERVERCNTRL (4 files, 599 lines)

SH (37 files, 2719 lines)

SL (2 files, 102 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, 426 lines)

AW_NAME (5 files, 1074 lines)

CB (7 files, 1127 lines)

CONSENSUS (3 files, 1730 lines)

DB_QUERY (5 files, 3041 lines)

DB_SCANNER (4 files, 801 lines)

DB_UI (5 files, 2067 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, 4222 lines)

GUI_ALIVIEW (9 files, 1352 lines)

HELIX (6 files, 824 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, 1964 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, 565 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, 1221 lines)

SEQUENCE (10 files, 1755 lines)

TRANSLATE (4 files, 340 lines)

TREEDISP (10 files, 7583 lines)

TREE_ADMIN (4 files, 344 lines)

TREE_READ (5 files, 1221 lines)

TREE_WRITE (5 files, 616 lines)

XFERGUI (2 files, 1294 lines)

XFERSET (3 files, 2152 lines)

SOURCE_TOOLS (63 files, 10760 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, 2155 lines)

TEMPLATES (49 files, 8460 lines)

TEST (0 files, 0 lines)

TESTAWT (0 files, 0 lines)

TESTVECTORFONT (0 files, 0 lines)

TOOLS (28 files, 12380 lines)

TREEGEN (17 files, 1454 lines)

TREE_COMPRESS (0 files, 0 lines)

TRS (0 files, 0 lines)

UNIT_TESTER (24 files, 6144 lines)

flags (1 files, 2 lines)

run (42 files, 21338 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, 163 lines)

WINDOW (75 files, 26384 lines)

XML (4 files, 499 lines)

XML_IMPORT (0 files, 0 lines)

IMP_TREE (0 files, 0 lines)

bin (2 files, 219 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 (8 files, 522 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 (103 files, 3739 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 (17 files, 839 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 (19 files, 1791 lines)

Author	Changes	Lines of Code	Lines per Change
Totals	1200 (100.0%)	16744 (100.0%)	13.9
westram	1093 (91.1%)	15450 (92.3%)	14.1
oldcode	9 (0.8%)	760 (4.5%)	84.4
epruesse	33 (2.8%)	281 (1.7%)	8.5
boehnel	4 (0.3%)	75 (0.4%)	18.7
yadhu	17 (1.4%)	74 (0.4%)	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 2025-07-19 11:55 Rev.: 19507

* avoid building arb as root:
- may cause test failures (permissions checks apparently succeed unexpectedly when called as root)

9 lines of code changed in 1 file:

Makefile (+9)

westram 2023-11-23 12:44 Rev.: 19492

* mention {{{libgomp1}}} (required by FastTreeMP)

1 lines of code changed in 1 file:

arb_INSTALL.txt (+1)

westram 2023-08-05 13:40 Rev.: 19446

* introduce {{{onlyC_flags}}}
- flags used for C compilation only.
- similar to {{{cxxflags}}} (references added).
- pass down onlyC_flags into AxML, CLUSTAL, CLUSTALW, FASTDNAML, FASTTREE, GL, MrBAYES, PHYLIP, PHYML*, RAxML, SINA(unused), SOURCE_TOOLS, SUPPORT, TOOLS, TREEGEN + TREEPUZZLE.
- set flags to {{{-Werror-implicit-function-declaration}}}
* error is only effective in a small part of these modules.
* TODO: need to activate warnings -> will activate the error as well.

3 lines of code changed in 1 file:

Makefile (+3 -1)

westram 2023-07-13 17:44 Rev.: 19435

* fix NDEBUG builds for gcc 10.1 - 10.5
- allow to use 10.4 + 10.5
- expect 18 vectorizations starting with gcc 10.1
- suppress bogus warning
- similar to [19434]

1 lines of code changed in 1 file:

Makefile (+1 -1)

westram 2023-07-11 10:52 Rev.: 19428

* add dependencies to {{{make}}} + {{{time}}}.
* call {{{apt-get}}} using {{{sudo}}} => support for limited sudo access.

4 lines of code changed in 1 file:

arb_UBUNTU.txt (+4 -2)

westram 2023-06-15 15:31 Rev.: 19393

* reintegrates 'ali' into 'trunk'
- refactored misused enum
- support for helix pairs:
* drop non-standard defs
* add more user defs
- change defaults
- add several predefined configs (esp. for IUPAC ambiguity codes)
* adds: log:branches/ali@19376:19392

3 lines of code changed in 1 file:

arb_CHANGES.txt (+3)

westram 2023-06-03 13:36 Rev.: 19376

* reintegrates 'ali' into 'trunk'
- completes #854
* adds: log:branches/ali@19363:19375

1 lines of code changed in 1 file:

arb_CHANGES.txt (+1)

westram 2022-11-13 16:47 Rev.: 19339

* reintegrates 'refactor' into 'trunk'
- eliminates old interface of {{{GBS_strstruct}}}
- add a few new unittests (editor-config string + some PT-SERVER-functions)
* adds: log:branches/refactor@19300:19338

1 lines of code changed in 1 file:

Makefile (+1 -1)

westram 2022-10-27 14:59 Rev.: 19285

* again update prerequisites: use libxerces-c-dev
* also use changed prerequisites in {{{arb_INSTALL.txt}}}

3 lines of code changed in 1 file:

arb_INSTALL.txt (+3 -2)

westram 2022-09-07 16:01 Rev.: 19266

* replace {{{realpath}}} locally in install script
- cannot use {{{arb_path.sh}}} here, because it's not yet installed.

42 lines of code changed in 1 file:

arb_install.sh (+42 -6)

westram 2022-09-03 19:23 Rev.: 19260

* cosmetic changes to text output.

5 lines of code changed in 1 file:

arb_install.sh (+5 -5)

westram 2022-09-03 19:22 Rev.: 19259

* backup {{{arb_tcp.dat}}} only when
- {{{arb_tcp.dat}}} exists and
- no backup was done today.

7 lines of code changed in 1 file:

arb_install.sh (+7 -3)

westram 2022-09-03 19:21 Rev.: 19258

* add "I don't want to edit anything" option

13 lines of code changed in 1 file:

arb_install.sh (+13 -8)

westram 2022-09-03 19:19 Rev.: 19257

* install sina together with arb, when a fat tarball is detected.

55 lines of code changed in 1 file:

arb_install.sh (+55)

westram 2022-09-03 19:17 Rev.: 19256

* use absolute name of entered installation path.
* detect arb- and sina-tarballs
- use absolute names of these tarballs
- eliminate weird {{{arb.tgz}}} symlinking.
* show arb-version url (in wiki) when no tarball found.

59 lines of code changed in 1 file:

arb_install.sh (+59 -36)

westram 2022-09-03 19:15 Rev.: 19255

* separator only inserts single empty line.
* insert single empty lines using separator.

17 lines of code changed in 1 file:

arb_install.sh (+17 -19)

westram 2022-09-03 19:13 Rev.: 19254

* print questions and important lines as {{{bold}}} and/or {{{underlined}}}.

30 lines of code changed in 1 file:

arb_install.sh (+30 -26)

westram 2022-09-03 19:10 Rev.: 19253

* indent case sections.

109 lines of code changed in 1 file:

arb_install.sh (+109 -103)

westram 2022-09-03 19:08 Rev.: 19252

* add section headers for readability.
* do not repeatedly print instructions when user enters wrong answer.

31 lines of code changed in 1 file:

arb_install.sh (+31 -13)

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

72 lines of code changed in 5 files:

.gitignore (+1 -1), Makefile (+35 -5), arb_CHANGES.txt (+3), arb_INSTALL.txt (+30 -7), config.makefile.template (+3)

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)

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Most Recent Commits