Directory [root]

Directory Created:
2000-11-23 10:41
Total Files:
17
Deleted Files:
22
Lines of Code:
7957

[root]
    directory in repo AISC (16 files, 3904 lines)
    directory in repo AISC_COM (1 files, 16 lines)
        directory in repo AISC (8 files, 2077 lines)
        directory in repo C (15 files, 2740 lines)
    directory in repo AISC_MKPTPS (4 files, 1873 lines)
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    directory in repo ARB_GDE (16 files, 4067 lines)
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    directory in repo CONSENSUS_TREE (16 files, 3495 lines)
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    directory in repo CORE (51 files, 9505 lines)
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    directory in repo EDIT4 (53 files, 29792 lines)
    directory in repo EISPACK (7 files, 29478 lines)
    directory in repo GDE (2 files, 153 lines)
        directory in repo AxML (5 files, 5978 lines)
        directory in repo CLUSTAL (13 files, 4953 lines)
        directory in repo CLUSTALW (33 files, 21375 lines)
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        directory in repo FASTDNAML (7 files, 6446 lines)
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                directory in repo core (90 files, 75652 lines)
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            directory in repo src (190 files, 34747 lines)
                directory in repo unused (3 files, 548 lines)
        directory in repo MrBAYES (1 files, 45 lines)
            directory in repo mrbayes_3.2.1 (31 files, 114641 lines)
        directory in repo PHYLIP (60 files, 70322 lines)
            directory in repo doc (42 files, 21478 lines)
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                directory in repo doc (17 files, 24532 lines)
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            directory in repo builddir (0 files, 0 lines)
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        directory in repo LOCATION (4 files, 611 lines)
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        directory in repo MATRIX (4 files, 319 lines)
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        directory in repo PRONUC (8 files, 2764 lines)
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        directory in repo QUERY (3 files, 667 lines)
        directory in repo REFENTRIES (4 files, 527 lines)
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        directory in repo TREE_ADMIN (4 files, 344 lines)
        directory in repo TREE_READ (5 files, 1221 lines)
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        directory in repo XFERGUI (2 files, 1294 lines)
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    directory in repo SOURCE_TOOLS (63 files, 10758 lines)
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        directory in repo docs (1 files, 79 lines)
        directory in repo refactor (2 files, 32 lines)
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    directory in repo UNIT_TESTER (24 files, 6144 lines)
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    directory in repo lib (8 files, 12081 lines)
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        directory in repo addlibs (1 files, 14 lines)
        directory in repo arb_default (7 files, 694 lines)
        directory in repo desktop (4 files, 21 lines)
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            directory in repo pars (3 files, 184 lines)
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Lines of Code

Lines of Code

Developers

Author Changes Lines of Code Lines per Change
Totals 1199 (100.0%) 16735 (100.0%) 13.9
westram 1092 (91.1%) 15441 (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 2023-11-23 11:44 Rev.: 19492


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

1 lines of code changed in 1 file:

  • arb_INSTALL.txt (+1)
westram 2023-08-05 12:40 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 16:44 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 09:52 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 14:31 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 12:36 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 15:47 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 13:59 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 15:01 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 18:23 Rev.: 19260


* cosmetic changes to text output.

5 lines of code changed in 1 file:

  • arb_install.sh (+5 -5)
westram 2022-09-03 18:22 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 18:21 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 18:19 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 18:17 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 18:15 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 18:13 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 18:10 Rev.: 19253


* indent case sections.

109 lines of code changed in 1 file:

  • arb_install.sh (+109 -103)
westram 2022-09-03 18:08 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 15:19 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 13:01 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 08:50 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 09:44 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 12:29 Rev.: 19060


* align version numbers (cosmetic).

11 lines of code changed in 1 file:

  • Makefile (+11 -11)
westram 2022-06-17 12:28 Rev.: 19059


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

1 lines of code changed in 1 file:

  • Makefile (+1)
westram 2022-06-17 10:56 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 10:41 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 10:39 Rev.: 19054


* accept gcc 8.5.0

1 lines of code changed in 1 file:

  • Makefile (+1 -1)
westram 2022-05-20 08:39 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 12:59 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 13:34 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 13:33 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 13:29 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 15:08 Rev.: 18960


* updated

5 lines of code changed in 1 file:

  • arb_CHANGES.txt (+5)
westram 2022-03-04 11:26 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 16:32 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 16:28 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 16:25 Rev.: 18923


* move cloc section.
* use system-cloc.

20 lines of code changed in 1 file:

  • Makefile (+20 -20)
westram 2022-02-07 16:22 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 16:20 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 15:11 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)

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