Directory GDE/PHYML20130708/

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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.

1 lines of code changed in 1 file:

• GDE/PHYML20130708: Makefile (+1 -1)

westram 2019-03-04 14:22 Rev.: 17634

* reintegrates 'mix' into 'trunk'
* prepare arb for hybrid svn/git use (central svn + local git)
* adds: log:branches/mix@17631:17633

1 lines of code changed in 1 file:

• GDE/PHYML20130708: .gitignore (new 1)

westram 2018-11-25 19:19 Rev.: 17618

* full update from child 'fix' into 'trunk'
- fixes undefined variables in makefiles
- fixes perl tests
* adds: log:branches/fix@17599:17617

9 lines of code changed in 1 file:

• GDE/PHYML20130708: Makefile (+9 -3)

westram 2014-08-04 13:50 Rev.: 12662

* fixes build of GDE/PHYML20130708 (broken by [12660])

7 lines of code changed in 1 file:

• GDE/PHYML20130708: Makefile (+7 -5)

epruesse 2014-08-03 14:14 Rev.: 12660

add some files to make clean

3 lines of code changed in 1 file:

• GDE/PHYML20130708: Makefile (+3)

westram 2014-05-26 14:30 Rev.: 12299

* CC/CXX used by arb
- overwrite defaults after copying them into A_CC/A_CXX
- fix all errors (triggered by above change)
* remove fallbacks (probcons; MUSCLE; FASTTREE)
* set CC/CXX from A_CC/A_CXX (MrBAYES; PHYML20130708)

3 lines of code changed in 1 file:

• GDE/PHYML20130708: Makefile (+3)

westram 2014-02-28 16:20 Rev.: 11698

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

9 lines of code changed in 1 file:

• GDE/PHYML20130708: Makefile (+9 -1)

westram 2013-10-02 13:00 Rev.: 10690

- for some unknown reason calling PHYML-'make install' fails to install the binary under some condition and then even repeated arb-builds do not succeed
- AFAIK this does not happen in clean checkouts (so jenkins did never complain)
- when that happens, do a complete rebuild of PHYML

9 lines of code changed in 1 file:

• GDE/PHYML20130708: Makefile (+9)

westram 2013-09-04 09:58 Rev.: 10530

* UTF8 -> ASCII

1 lines of code changed in 1 file:

• GDE/PHYML20130708: Makefile (+1 -1)

westram 2013-08-28 15:16 Rev.: 10508

* PHYML20130708 Makefile
- did not always make final target ($(ARBHOME)/bin/phyml...)
- define complete dependency chain => no matter what is deleted from WC, it should be rebuild now
- no longer trigger configure-call by stamp (let it depend on Makefile, i.e. as long as Makefile is not changed, configure will be called exactly once)
- do auto-clean before configure
- directly call 'make install' (does build as well)

21 lines of code changed in 1 file:

• GDE/PHYML20130708: Makefile (+21 -17)

westram 2013-08-23 12:30 Rev.: 10479

* async GDE build
- pass down make flags (esp. -j) into subdirectories
- enclose subbuilds in $(SEP) as in main ARB Makefile (showing enter/exit timestamp for each subdir)
- mafft: build/clean core+extensions async
- mrbayes:
* define proper rules to make target 'mb' work with -j (no idea why that is needed)
* do not clear MAKEFLAGS in caller Makefile
- speedup for 'build' (on 8 cores)
* after GDE clean: 60s -> 30s
* after MrBAYES clean: 44s -> 17s

3 lines of code changed in 1 file:

• GDE/PHYML20130708: Makefile (+3 -7)

westram 2013-08-22 12:11 Rev.: 10476

* reverted [10467] and [10466] (build failed for 'cent5')

8 lines of code changed in 1 file:

• GDE/PHYML20130708: Makefile (+8 -3)

westram 2013-08-21 13:50 Rev.: 10466

* ~~'configure' is modified by compiling on a machine with different autoconf version~~
- ~~removed 'configure' from SVN; delete it on 'clean'~~
- ~~call autoconf before configure~~

(reverted by [10467])

3 lines of code changed in 1 file:

• GDE/PHYML20130708: Makefile (+3 -8)

aboeckma 2013-07-19 14:23 Rev.: 10308

Do not configure phyml on every build

17 lines of code changed in 1 file:

• GDE/PHYML20130708: Makefile (+17 -6)

aboeckma 2013-07-19 14:02 Rev.: 10307

added most recent version of phyml

21 lines of code changed in 1 file:

• GDE/PHYML20130708: Makefile (new 21)