February 2014 Commit Log

Number of Commits:
60
Number of Active Developers:
2
westram 2014-02-28 20:30 Rev.: 11705


- allow injection of ARBBUILDHOST and ARBBUILDUSER

10 lines of code changed in 1 file:

westram 2014-02-28 20:08 Rev.: 11702


- added 'tag_custom' (create tag for custom version anywhere outside 'rc'/'stable')

37 lines of code changed in 1 file:

westram 2014-02-28 17:20 Rev.: 11698


* full update from child 'rc' into 'trunk'
* adds:
- log:branches/rc@11679:11696

7148 lines of code changed in 11 files:

westram 2014-02-27 16:52 Rev.: 11676


- test version upgrade

2 lines of code changed in 1 file:

westram 2014-02-27 16:49 Rev.: 11675


- stub for release script

11 lines of code changed in 2 files:

westram 2014-02-27 16:30 Rev.: 11674


* make show_version
* fix hostname (@->.)

9 lines of code changed in 2 files:

westram 2014-02-27 12:26 Rev.: 11673


* try to retrieve some host/domain/user-info (if nothing defined in variables 'USER', 'HOST'/'HOSTNAME')
* dump version info to jenkins buildlog
* hack arb_ntree to dump version info w/o starting GUI

60 lines of code changed in 3 files:

westram 2014-02-27 10:45 Rev.: 11672


- execute svnversion via pipe (to catch failure). should fix u1304 builds

16 lines of code changed in 1 file:

westram 2014-02-26 19:31 Rev.: 11671


* handle revision number similar as svn-url is handled since [11669]

32 lines of code changed in 1 file:

westram 2014-02-26 19:05 Rev.: 11670


* detect errors in forked command @ close ([http://mm.iit.uni-miskolc.hu/data/texts/Manuals/Perl5/faq/Q5.16.html perl faq])

3 lines of code changed in 1 file:

westram 2014-02-26 18:31 Rev.: 11669


* reverted [11648]
* retrieve svn information using
- method1: svn info
- method2: variable SVN_URL (as set inside jenkins builds)
* accept failure in method1 (AFAIK only happens inside jenkins if svn version differs between master and slave) and fallback to result of method2
* if both methods succeed, fail on conflicts
* dump contents of version-related files to build log

303 lines of code changed in 5 files:

westram 2014-02-26 17:56 Rev.: 11668


- store result of pkg-config in variables (instead of storing the call to pkg-config)

5 lines of code changed in 2 files:

westram 2014-02-26 17:39 Rev.: 11667


- use SHARED_LIB_SUFFIX instead of 'so'

1 lines of code changed in 1 file:

westram 2014-02-26 17:21 Rev.: 11666


cmon make, make it my way!

3 lines of code changed in 1 file:

westram 2014-02-26 16:09 Rev.: 11665


* COMPILE_COMPAT
- binaries now depend on libARBDB and libCORE (were not rebuild)
- eliminate obsolete 'clean_old'
- link vs glib

9 lines of code changed in 1 file:

westram 2014-02-26 13:35 Rev.: 11664


* use glib
- dependency added to CORE (several functions in CORE may be replace by glib equivalents)
- use g_ascii_strtod in ARBDB unittest (failing in [https://colab.mpi-bremen.de/jenkins/job/ARB/564/ build #564]; expected to pass now)

18 lines of code changed in 8 files:

westram 2014-02-26 12:32 Rev.: 11663


- missing header (u1004)

1 lines of code changed in 1 file:

westram 2014-02-26 12:09 Rev.: 11662


- dump SVN related envvars passed in by jenkins

5 lines of code changed in 2 files:

westram 2014-02-26 12:00 Rev.: 11661


- create situation described in #473 inside a unit-test (expected to fail on centOS)

9 lines of code changed in 1 file:

westram 2014-02-26 11:54 Rev.: 11660


- hardcode "C" locale ("fixes" centos/ubuntu 13.10 builds started with german locale set by user)

2 lines of code changed in 1 file:

westram 2014-02-26 09:39 Rev.: 11659


* changes done in [11622] seem to be responsible for [https://colab.mpi-bremen.de/jenkins/job/SINA/467/ failing SINA-build #467]
* fix:
- do not rm arb.tgz in non-RELEASE-build, instead rename it into 'arb..-bin...tgz'
- (jenkins cfg) do not copy such tarballs to ftp server

5 lines of code changed in 1 file:

westram 2014-02-25 18:35 Rev.: 11658


- remove hardcoded locale (hardcoded in [11657])

2 lines of code changed in 1 file:

westram 2014-02-25 17:57 Rev.: 11657


- tested several locale settings (ubuntu 13.10)
- temporarily hardcode locale (german for LC_NUMERIC; C for rest) to see whether tests fail in jenkins

50 lines of code changed in 1 file:

westram 2014-02-25 17:50 Rev.: 11656


- added dependencies to main-object(s)

20 lines of code changed in 5 files:

westram 2014-02-25 16:56 Rev.: 11655


* fix (manual) dependencies for arb_main.o
* attempt to fix clang failure (see [https://colab.mpi-bremen.de/jenkins/job/ARB/555/MODE=DEBUG,TGT=osx/consoleText build #555 osx failure])

5 lines of code changed in 2 files:

westram 2014-02-25 16:05 Rev.: 11654


* added place to execute some code at start_of_main()
- called before every ARB_main
- called in unittests (at start of test launcher and when preparing environment)
* start_of_main() currently does not execute anything!

38 lines of code changed in 5 files:

westram 2014-02-25 16:02 Rev.: 11653


* terminate when GB_atof() fails
* add test for GB_atof()

17 lines of code changed in 1 file:

westram 2014-02-21 18:27 Rev.: 11652


- fix broken url

1 lines of code changed in 1 file:

westram 2014-02-21 13:52 Rev.: 11651


- warn only once about incomplete LOCUS data

7 lines of code changed in 1 file:

westram 2014-02-21 13:32 Rev.: 11650


- init !TreeAwarRegistry in startup_mainwindow_and_dbserver (fixes #472)

2 lines of code changed in 1 file:

westram 2014-02-21 12:44 Rev.: 11649


- fix test for "no tree selected" in arb_raxml
- passing an empty tree to RAxML caused it to run forever under some circumstances
- added comments at "no tree selected"-tests

3 lines of code changed in 2 files:

westram 2014-02-21 12:02 Rev.: 11648


* revert [11640] and [11634] until i found a possibility to retrieve branch information w/o using 'svn'

(reintroduced by [11669])

94 lines of code changed in 5 files:

westram 2014-02-20 17:54 Rev.: 11645


* fix missing/duplicated/invalid mnemonics in rest of arb (completes [11643])

16 lines of code changed in 7 files:

westram 2014-02-20 17:53 Rev.: 11644


* show available mnemonics which are NOT matching the problematic topic, if no matching mnemonic exists

32 lines of code changed in 1 file:

westram 2014-02-20 16:55 Rev.: 11643


* fix missing/duplicated/invalid mnemonics in ARB_NTREE (incl. genome)

34 lines of code changed in 9 files:

westram 2014-02-20 16:53 Rev.: 11642


* top-level mnemonics
- now checked as well
- deny use of non-alpha mnemonics
* all mnemonics
- warn case mismatch

52 lines of code changed in 2 files:

westram 2014-02-20 16:51 Rev.: 11641


- automatically assign mnemonics to user-mask menu entries

67 lines of code changed in 1 file:

westram 2014-02-20 13:15 Rev.: 11640


* trace output from 'svn info' to buildlog

(reverted by [11648]; reintroduced by [11669])

2 lines of code changed in 1 file:

westram 2014-02-20 12:46 Rev.: 11639


- mark duplicated mnemonic check by separate define

12 lines of code changed in 1 file:

westram 2014-02-18 17:18 Rev.: 11635


* make 'inc_minor' (test version upgrade)

4 lines of code changed in 1 file:

westram 2014-02-18 17:16 Rev.: 11634


* change rel_[minor|major] into inc_[minor|major]
- no longer builds the release (will be done by jenkins)
- only increment version numbers
* added targets
- 'inc_candi' (to increment RC number; only needed for RC2 and following)
- 'inc_patch' (to increment patchlevel; in case release gets a hotfix => version number will be MAJOR.MINOR.PATCHLEVEL instead of just MAJOR.MINOR)
* extract branch/tag from svn (if in SVN-WC) and save into svn_revision.h
- if not in SVN-WC -> parse branch/tag info from svn_revision.h
- added code to create SVN-tagname; if building from tag -> guess branch, rebuild tag and fail on mismatch
* define ARB_VERSION_DETAILED (always containing revision)
- ARB_VERSION
* used in intro
* contains no revision in release
* always show user/host where build (was skipped for our builds in the past)

(reverted by [11648]; reintroduced by [11669])

250 lines of code changed in 5 files:

westram 2014-02-17 13:19 Rev.: 11631


- depends updated

0 lines of code changed in 1 file:

epruesse 2014-02-16 15:06 Rev.: 11629

remove "SAI->Other->Positional Variability" feature (decided in #359)

the feature was broken and not deemed important enough to repair

0 lines of code changed in 9 files:

epruesse 2014-02-16 14:45 Rev.: 11628

reactivate "Export Column Statistic to !GnuPlot" (fixes part of #466)

1 lines of code changed in 1 file:

westram 2014-02-15 16:51 Rev.: 11626


* reintegrates 'fix' into 'trunk'
- implements: #158
- fixes: #386, #463, #459
* adds:
- log:branches/fix@11579:11625

649 lines of code changed in 38 files:

westram 2014-02-15 14:47 Rev.: 11622


- delete arb.tgz if MODE!=RELEASE (otherwise every build-directory contains one arb.tgz, containing the debug-version of the slowest build)

2 lines of code changed in 1 file:

westram 2014-02-13 15:30 Rev.: 11603


- use define for std::list interna

4 lines of code changed in 1 file:

westram 2014-02-13 15:21 Rev.: 11602


- do size detection in DEBUG mode only (only used by database browser). Should fix NDEBUG compile on Mavericks

4 lines of code changed in 2 files:

epruesse 2014-02-13 13:11 Rev.: 11598

add DJB2 as hash function for GB_hash (needs #define change to activate)

Based on a trace of the GB_hash calls executed when GB_open'ing a large SILVA
database, I've tried a few hashing methods. GB_hash fares better than
stl::unordered_map, and the DJB2 function got the best results among the
hash functions I tested.

27 lines of code changed in 1 file:

epruesse 2014-02-13 13:02 Rev.: 11597

remove "load sequences from PT server" option from SINA dialog
(since the PT server merge, the respective ARB files no longer
contain an alignment, so this is not possibly anymore)

2 lines of code changed in 1 file:

westram 2014-02-10 17:57 Rev.: 11582


- fix #460 (attempted to register tree awar w/o tree having a tree registry)

7 lines of code changed in 4 files:

westram 2014-02-10 17:56 Rev.: 11581


- warn when tree is unreadable while renaming species

1 lines of code changed in 1 file:

westram 2014-02-10 15:43 Rev.: 11578


* reintegrates 'alilink' into 'trunk'
- implements #420
* adds:
- log:branches/alilink@11490:11577

1093 lines of code changed in 28 files:

westram 2014-02-07 15:40 Rev.: 11574


* they really want me to take the sledgehammer to crack the nut (where i consider clang to be the nut :-p)

7 lines of code changed in 1 file:

westram 2014-02-07 15:17 Rev.: 11573


* fix NDEBUG compilation for clang 3.3 under linux
- TODO: unittests fail with 'Illegal instruction'

2 lines of code changed in 1 file:

westram 2014-02-07 12:22 Rev.: 11571


- silence some clang warnings

6 lines of code changed in 4 files:

westram 2014-02-07 12:21 Rev.: 11570


- isinf("negative infinity") is only garanteed to return non-zero (clang returns -1; gcc with glibc 2.01 and earlier returns 1)

1 lines of code changed in 1 file:

westram 2014-02-07 11:44 Rev.: 11569


- fix for clang (see http://stackoverflow.com/questions/13148513/does-stdmap-require-the-comparators-operator-to-be-const)

3 lines of code changed in 2 files:

westram 2014-02-04 17:16 Rev.: 11560


* reintegrates 'tree' into 'trunk'
* adds:
- log:branches/tree@11556:11559

63 lines of code changed in 4 files:

westram 2014-02-02 14:51 Rev.: 11547


* tests for equality that are marked as broken ({{{TEST_EXPECT_EQUAL__BROKEN}}}) did not protect vs regression
- added mandatory argument specifying the broken value (and fail when it changes)
- drawback: argument is evaluated twice

87 lines of code changed in 9 files:

January 2014 »

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