August 2023 Commit Log

Number of Commits:
19
Number of Active Developers:
1
westram 2023-08-11 12:40 Rev.: 19480


* reintegrates 'gde' into 'trunk'
* adds: log:branches/gde@19460:19479

2421 lines of code changed in 138 files:

westram 2023-08-05 13:43 Rev.: 19459


* activate warnings (reverts parts of r15483).

3 lines of code changed in 1 file:

westram 2023-08-05 13:41 Rev.: 19458


* do NOT suppress warnings in MrBAYES => {{{-Werror-implicit-function-declaration}}} now active. No error reported.

1 lines of code changed in 1 file:

westram 2023-08-05 13:38 Rev.: 19457


* pass down {{{onlyC_flags}}}.
* use onlyC_flags in all Makefiles (inject using seq).
* patch SATIVA raxml code in tarball (one missing prototype).

7 lines of code changed in 2 files:

westram 2023-08-05 13:34 Rev.: 19456


* fix builds of AxML, FASTDNAML + SUPPORT
- mostly fixed by add missing includes.
- had to change code order to avoid otherwise required definition of protytypes in SUPPORT.

455 lines of code changed in 10 files:

westram 2023-08-05 13:22 Rev.: 19455


* keep {{{-W -Wall}}} everywhere in GDE => activates -Werror-implicit-function-declaration.
- Note: (re)build of GDE tools fails.

1 lines of code changed in 1 file:

westram 2023-08-05 13:19 Rev.: 19454


* hide message from autoreconf (misinterpreted by emacs).

4 lines of code changed in 1 file:

westram 2023-08-05 13:17 Rev.: 19453


* use {{{-W -Wall}}} in FASTTREE + fix warnings.

15 lines of code changed in 2 files:

westram 2023-08-05 13:15 Rev.: 19452


* get rid of {{{tmpnam()}}}.

18 lines of code changed in 2 files:

westram 2023-08-05 13:13 Rev.: 19451


* fix a bug (and silence {{{-Wparentheses}}}).
* fix other warnings

22 lines of code changed in 2 files:

westram 2023-08-05 12:53 Rev.: 19450


* keep {{{-W -Wall}}} in READSEQ => build does fail due to implicit-function-declaration.
* include {{{stdlib.h}}} for missing prototypes => fixes build error.

2 lines of code changed in 2 files:

westram 2023-08-05 12:50 Rev.: 19449


* shadow-location does appear as warning AND note (depending on gcc version)
- handle both.

67 lines of code changed in 1 file:

westram 2023-08-05 12:48 Rev.: 19448


* enable + fix warnings in ISLAND_HOPPING.

8 lines of code changed in 2 files:

westram 2023-08-05 12:46 Rev.: 19447


* suppression of warnings for source-subtrees:
- comment + warn when suppressed (currently suppressed in GDE)

16 lines of code changed in 5 files:

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.

73 lines of code changed in 21 files:

westram 2023-08-05 12:32 Rev.: 19445


* check all {{{A_CC}}} calls (=plain C compilations) whether they are used.

0 lines of code changed in 1 file:

westram 2023-08-05 12:29 Rev.: 19444


* add header (fixes previous commit)

64 lines of code changed in 1 file:

westram 2023-08-05 12:27 Rev.: 19443


* fix use of {{{gets()}}} (globally):
- provide a drop-in replacement for {{{gets()}}}
* only requires to specify buffersize.
- use {{{gets_noOverflow()}}} in READSEQ, SUPPORT, CLUSTAL + CLUSTALW.
* adapt {{{getstr()}}}

95 lines of code changed in 16 files:

westram 2023-08-05 12:24 Rev.: 19442


* reactivate implicit-fallthrough warnings and fix code.

3 lines of code changed in 2 files:

July 2023 »

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