Directory CONVERTALN/

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westram 2022-03-04 11:26 Rev.: 18959

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

1 lines of code changed in 1 file:

• CONVERTALN: Makefile (+1)

westram 2022-02-02 12:41 Rev.: 18914

* fix error handling for piped commands in perl
- when forking piped commands
* use error message ($!) instead of exitcode ($?).
* use message 'failed to fork'.
- when closing piped commands
* show IPC errors and exitcode of command.

2 lines of code changed in 1 file:

• CONVERTALN: show_error_list.pl (+2 -2)

westram 2021-09-15 12:52 Rev.: 18730

* remove trailing whitespace from c source.

4 lines of code changed in 2 files:

• CONVERTALN: date.cxx (+3 -3), phylip.cxx (+1 -1)

westram 2021-08-17 14:15 Rev.: 18665

* change many WARN_TODO triggered warnings into todo markers.

1 lines of code changed in 1 file:

• CONVERTALN: convert.cxx (+1 -3)

westram 2019-09-18 08:25 Rev.: 18100

* mark loop failing with 4.9.2

1 lines of code changed in 1 file:

• CONVERTALN: genbank.cxx (+1 -1)

westram 2019-08-16 11:53 Rev.: 18011

* document vectorizations failing with gcc 9.2.
* document vectorizations refused as "not worthwhile" by gcc 9.2.
* cannot check loop vectorization in header (seq.h).

1 lines of code changed in 1 file:

• CONVERTALN: seq.h (+1 -1)

westram 2019-05-10 12:57 Rev.: 17877

* reintegrates 'gcc' into 'trunk'
* adds: log:branches/gcc@17850:17876

14 lines of code changed in 3 files:

• CONVERTALN: genbank.cxx (+1 -1), reader.h (+12 -1), seq.h (+1 -1)

westram 2018-10-24 14:58 Rev.: 17534

* partial merge from 'fix' into 'trunk'
- globally define what are "gaps"
- kept behavioral changes to a minimum:
* defaults for (user-defined) gap-definition in EDIT4 changed
* EDIT sequence search also uses user-defined gaps
* adds: log:branches/fix@17529:17533

21 lines of code changed in 2 files:

• CONVERTALN: Makefile (+17), global.h (+4 -1)

westram 2018-05-04 17:06 Rev.: 16986

* reintegrates 'gcc' into 'trunk'
- ports arb to gcc 8.1 (fixing warnings)
* adds: log:branches/gcc@16965:16985

Update: continued by [17178]

4 lines of code changed in 3 files:

• CONVERTALN: date.cxx (+1 -1), macke.cxx (+2 -2), mg.cxx (+1 -1)

westram 2018-02-15 11:51 Rev.: 16861

* reintegrates 'unittest' into 'trunk'
- fixed non-deterministic behavior of add-species:
* 2 sequences in test-DB were identical (changed 1 bp)
* {{{AP_tree_edge}}} cannot be used to store insert-positions (uses pair of {{{AP_tree_nlen}}} instead)
* corrected some undefined behavior (results did depend on compiler version+flags):
- general order of inserts was undefined
- order of initial-insert was undefined (used by complete tree reconstruction)
- bugs fixed:
* not all possible insert-positions were tested
* sometimes species were added at wrong positions
* if multiple species were inserted at the same position, the following optimization
- did modify topology
- now optimizes all multi-inserts globally
- at leaf-positions: includes the leaf (Note: this does not modify the original topology)
* insert order now is "longest sequence first" (was "shortest sequence first")
- fixed unwanted behavior when testing for content of generated files
* adds: log:branches/unittest@16807:16860

1 lines of code changed in 1 file:

• CONVERTALN: fconv.cxx (+1 -1)

westram 2017-11-28 18:22 Rev.: 16766

* reintegrates 'gcc' into 'trunk'
- mostly cosmetics changes
* adds: log:branches/gcc@16655,16741:16743,16752:16765

26 lines of code changed in 8 files:

• CONVERTALN: date.cxx (+2 -2), embl.cxx (+8 -9), genbank.cxx (+1 -1), global.h (+1 -3), mg.cxx (+5 -5), rdp_info.h (+7 -6), seq.h (+1 -2), util.cxx (+1 -1)

westram 2017-11-28 17:09 Rev.: 16763

* partial merge from 'gcc' into 'trunk'
- use {{{nullptr}}} in Cxx11 (with backward compatibility)
* adds: log:branches/gcc@16683:16740,16744:16746,16751

48 lines of code changed in 21 files:

• CONVERTALN: convert.cxx (+1 -1), date.cxx (+1 -1), embl.cxx (+2 -2), fconv.cxx (+6 -6), fun.h (+1 -1), gcg.cxx (+1 -1), genbank.cxx (+4 -4), global.h (+3 -3), input_format.h (+1 -1), macke.cxx (+6 -6), macke.h (+1 -1), main.cxx (+2 -2), mg.cxx (+1 -1), rdp_info.h (+1 -1), reader.cxx (+6 -6), reader.h (+4 -4), refs.h (+1 -1), seq.h (+1 -1), util.cxx (+3 -3), wrap.cxx (+1 -1), wrap.h (+1 -1)

westram 2017-11-19 15:19 Rev.: 16683

* full update from child 'gcc' into 'trunk'
- more warning fixes
- fix bug in prettyprint
* adds: log:branches/gcc@16668:16682

1 lines of code changed in 1 file:

• CONVERTALN: embl.cxx (+1 -1)

westram 2017-11-12 14:53 Rev.: 16649

* partial merge from 'gcc' into 'trunk'
- handles #770 by reducing optimizations of several bleeding test functions
* adds: log:branches/gcc@16636:16648

1 lines of code changed in 1 file:

• CONVERTALN: date.cxx (+1 -1)

westram 2017-01-09 15:10 Rev.: 15529

* reintegrates 'warnings' into 'trunk'
- use gnu++14-standard for gcc>=6
- use gnu++0x-standard for gcc<4.7 (bugfix)
- defines many inlines as constexpr
* adds: log:branches/warnings@15515:15522,15525:15528

15 lines of code changed in 3 files:

• CONVERTALN: fun.h (+1 -1), global.h (+10 -10), macke.h (+4 -4)

westram 2017-01-04 17:06 Rev.: 15513

* reintegrates 'warnings' into 'trunk'
- activate additional warnings (gcc 5.x++)
- Cxx11-forward final (classes+methods)
- fix tag problems caused by using preprocessor
* adds: log:branches/warnings@15486:15489,15491:15501,15506:15512

18 lines of code changed in 6 files:

• CONVERTALN: date.cxx (+2 -2), embl.h (+1 -1), genbank.h (+1 -1), macke.h (+1 -1), reader.cxx (-10), reader.h (+13 -2)

westram 2016-08-17 19:39 Rev.: 15198

* remove {{{virtual}}} if {{{OVERRIDE}}} is present
- OVERRIDE implies 'implicit virtual' (if code compiles as C++11 <- tested on build server!)

5 lines of code changed in 4 files:

• CONVERTALN: embl.h (+1 -1), genbank.h (+1 -1), input_format.h (+2 -2), macke.h (+1 -1)

westram 2016-08-11 10:05 Rev.: 15176

* reintegrates 'fixres' into 'trunk'
- fixes #715
* adds: log:branches/fixres@15127:15175

103 lines of code changed in 15 files:

• CONVERTALN: Makefile (+33), date.cxx (+1 -1), embl.cxx (+5 -5), embl.h (+12 -9), genbank.cxx (+3 -3), genbank.h (+10 -7), global.h (+7 -5), macke.cxx (+2 -2), macke.h (+6 -3), paup.cxx (+1 -1), prototypes.h (-1), reader.cxx (+1 -1), seq.h (+16 -14), util.cxx (+5 -22), wrap.h (+1 -1)

westram 2015-12-23 16:13 Rev.: 14655

* spelling

2 lines of code changed in 1 file:

• CONVERTALN: date.cxx (+2 -2)

westram 2015-12-03 17:50 Rev.: 14587

* fix error-forwarding (from external tools -> ARB GUI)
- {{{GBK_singlequote}}} error message (replaces various wrong ways to do that)
- always call {{{arb_message}}} asynchronously

6 lines of code changed in 2 files:

• CONVERTALN: Makefile (+1), main.cxx (+5 -8)

westram 2015-12-03 17:48 Rev.: 14586

* fix truncated error-messages

6 lines of code changed in 1 file:

• CONVERTALN: util.cxx (+6 -3)

westram 2015-01-23 14:19 Rev.: 13443

* reintegrates 'vectorize' into 'trunk'
- adds vectorization check for gcc 4.9.x / NDEBUG compile
* adds:
- log:branches/vectorize@13428:13442

1 lines of code changed in 1 file:

• CONVERTALN: Makefile (+1 -1)

westram 2014-10-17 15:43 Rev.: 13077

* reintegrates 'sanitize' into 'trunk'
* adds:
- log:branches/sanitize@13023:13076

28 lines of code changed in 1 file:

• CONVERTALN: printable.cxx (+28 -23)

westram 2014-10-09 17:48 Rev.: 13018

* merge a bunch of fixes from 'gcc' into 'trunk'
- detected using !AddressSanitizer
- fixing #613, #580 and other (undetected) bugs
* adds:
- log:branches/gcc@12996,13001:13003,13005:13006,13010:13014,13016

35 lines of code changed in 3 files:

• CONVERTALN: embl.h (+16 -16), genbank.h (+19 -19), global.h (-7)

westram 2014-10-06 16:02 Rev.: 12992

* ~~valgrind was reporting 'invalid reads' in CONVERTALN when compiled with gcc-4.8.2 + NDEBUG~~
- ~~added (weird) workaround for broken optimizer~~
- ~~added some comments about broken gcc version; afaik problems are similar to those of gcc 4.9.0 (see [12988])~~

(reverted by [12996])

7 lines of code changed in 1 file:

• CONVERTALN: global.h (+7)

westram 2014-06-09 05:16 Rev.: 12411

- CONVERTALN.a was relinked unconditionally (fixed)

10 lines of code changed in 1 file:

• CONVERTALN: Makefile (+10 -6)

westram 2014-04-04 17:22 Rev.: 11947

* merge misc changes from 'customize' into 'trunk'
* adds:
- log:branches/customize@11920,11943:11944

1 lines of code changed in 1 file:

• CONVERTALN: fconv.cxx (+1 -1)

westram 2014-03-22 09:34 Rev.: 11844

* merge [11840:11843] from 'customize' into 'trunk'
* adds:
- log:branches/customize@11841:11843
* skipped changes in ARB_GDE
- log:branches/customize/ARB_GDE@11841:11843 ~~(might fail to reintegrate)~~

28 lines of code changed in 5 files:

• CONVERTALN: Makefile (+17 -17), fun.h (+2 -2), reader.cxx (+1 -1), reader.h (+7 -7), util.cxx (+1 -1)

westram 2014-02-21 12:52 Rev.: 11651

- warn only once about incomplete LOCUS data

7 lines of code changed in 1 file:

• CONVERTALN: genbank.cxx (+7 -2)

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

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

24 lines of code changed in 1 file:

• CONVERTALN: main.cxx (+24 -3)

westram 2013-10-31 15:40 Rev.: 11002

* 'class { public' -> struct

2 lines of code changed in 2 files:

• CONVERTALN: input_format.h (+1 -2), reader.h (+1 -2)

westram 2013-10-31 14:10 Rev.: 10996

* use cflags before cxxflags

1 lines of code changed in 1 file:

• CONVERTALN: Makefile (+1 -1)

westram 2013-10-30 16:04 Rev.: 10975

* fixed wrong include variables (CC-CXX-mix). Harmless since includes do not differ atm

1 lines of code changed in 1 file:

• CONVERTALN: Makefile (+1 -1)

westram 2013-10-30 15:58 Rev.: 10974

* renamed include variables

1 lines of code changed in 1 file:

• CONVERTALN: Makefile (+1 -1)

westram 2013-10-29 12:55 Rev.: 10956

* made A_CC and A_CXX consistent
- A_CXX previously contained cxxflags
- cxxflags are now passed down and used separately

1 lines of code changed in 1 file:

• CONVERTALN: Makefile (+1 -1)

westram 2013-10-29 12:23 Rev.: 10955

- renamed
* ACC -> A_CC
* CPP -> A_CXX (misleading atm, since it contains c++flags)

1 lines of code changed in 1 file:

• CONVERTALN: Makefile (+1 -1)

westram 2013-10-09 10:07 Rev.: 10764

* renamed file- and mem-cmp-functions
* added parameter 'blockStartAddress' to ARB_test_mem_equal
- use it to show correct file-offset when called from ARB_files_are_equal
* removed unused function files_are_equal()

1 lines of code changed in 1 file:

• CONVERTALN: fconv.cxx (+1 -1)

westram 2013-10-03 12:11 Rev.: 10704

- reintegrated branch 'helptest'

2 lines of code changed in 2 files:

• CONVERTALN: Makefile (+1), fconv.cxx (+1)

westram 2013-09-09 15:36 Rev.: 10563

- include downcast.h from arbdbt.h
(this break C++11 compilation, i.e. gcc4.8 or newer)[[BR]]
amendment:
* also broke compilation on ubuntu 13.04 and with gcc 4.7.3 (due to nameclash with boost)

1 lines of code changed in 1 file:

• CONVERTALN: Makefile (+1)

westram 2013-09-09 11:55 Rev.: 10557

- rename

3 lines of code changed in 1 file:

• CONVERTALN: fconv.cxx (+3 -3)

(105 more)