November 2014 Commit Log

Number of Commits:

13

Number of Active Developers:

2

akozlov 2014-11-27 00:11 #13 Rev.: 13264

- partial merge from sativa branch
* log:branches/sativa@13263:13263

0 lines of code changed in 1 file:

• GDE/SATIVA: sativa-RAxML-8.1.3.tar.gz (changed)

akozlov 2014-11-26 03:56 #12 Rev.: 13243

- partial merge from sativa branch
* log:branches/sativa@13241:13241

370 lines of code changed in 14 files:

• GDE/SATIVA: arb_sativa.pl (+14 -10), sativa-RAxML-8.1.3.tar.gz (new)
• GDE/SATIVA/sativa: epa_trainer.py (new), find_mislabels.py (+144 -55)
• GDE/SATIVA/sativa/epac: classify_util.py (+124), config.py (+22 -2), erlang.py (+10 -3), taxonomy_util.py (new)

westram 2014-11-19 09:13 #11 Rev.: 13204

* +lib/sativa, -bin/sativa
- source-tarball-generation
- svn-ignores

1 lines of code changed in 1 file:

• util: arb_srclst.pl (+1 -1)

akozlov 2014-11-19 02:34 #10 Rev.: 13203

- partial merge from sativa branch
* log:branches/sativa@13202:13202

0 lines of code changed in 8 files:

• GDE/SATIVA: Makefile (changed), arb_sativa.pl (changed)
• GDE/SATIVA/sativa: epac.cfg.sativa (changed)
• GDE/SATIVA/sativa/epac: config.py (changed)

westram 2014-11-18 15:36 #9 Rev.: 13197

- delete sub-mergeinfo accidentally introduced with [13191]

0 lines of code changed in 2 files:

• TOOLS: arb_export_sequences.cxx (changed), arb_probe_match.cxx (changed)

westram 2014-11-17 16:42 #8 Rev.: 13191

* reintegrates 'slv' into 'trunk'
* performs #624
* adds:
- log:branches/slv@13152:13190

1010 lines of code changed in 22 files:

• AISC_COM/AISC: keys.README (+4)
• ARBDB: ad_prot.h (+1), arbdb.cxx (+36)
• PROBE: PT_match.cxx (+15 -5), probe.h (+21), pt_prototypes.h (+4 -1)
• PROBE_COM: PT.aisc (+17 -14)
• SL/PTCLEAN: ptclean.cxx (+4 -3)
• SL/SEQIO: seq_export.cxx (+9 -2)
• TOOLS: Makefile (+55 -1), arb_export_sequences.cxx (new 447), arb_probe.cxx (+1), arb_probe_match.cxx (new 230), arb_test.cxx (+71)
• UNIT_TESTER/run: TEST_pt_cleaned_expected.arb (+4), TEST_pt_src.arb (+5 -1)
• UNIT_TESTER/run/tools: acc.list (new 1), exseq.fasta.expected (new 6), exseq_ascii.arb.expected (new 63), exseq_via_eft.fasta.expected (new 2), min_template.arb (new 13)
• util: arb_srclst.pl (+1)

westram 2014-11-12 18:51 #7 Rev.: 13163

* accidently activated location checks with gcc>=4.8 for others with [13019]

7 lines of code changed in 1 file:

• UNIT_TESTER: UnitTester.cxx (+7 -5)

westram 2014-11-06 17:12 #6 Rev.: 13136

- fix clang compilation (broken by [13134])

3 lines of code changed in 1 file:

• NTREE: ColumnStat_2_gnuplot.cxx (+3 -1)

westram 2014-11-06 16:07 #5 Rev.: 13135

- disable {{{-Wmaybe-uninitialized}}} in DEBUG mode (too many bogus warnings that do NOT appear in NDEBUG)

4 lines of code changed in 1 file:

• Makefile (+4)

westram 2014-11-06 15:51 #4 Rev.: 13134

- fix warnings reported by NDEBUG compilation

16 lines of code changed in 11 files:

• ARBDB: adindex.cxx (+1 -1), arbdb.cxx (+1 -3)
• ARB_GDE: GDE.cxx (-2), GDE_event.cxx (+2 -1)
• CORE: arb_progress.cxx (+1 -1)
• DIST: DI_clusters.cxx (+1 -1)
• NTREE: ColumnStat_2_gnuplot.cxx (+2), ad_transpro.cxx (+5 -1)
• SL/ARB_TREE: ARB_Tree.cxx (+1 -1)
• SL/TREEDISP: TreeCallbacks.cxx (+1 -1), TreeDisplay.cxx (+1 -1)

westram 2014-11-06 15:50 #3 Rev.: 13133

- enable warnings in NDEBUG and RELEASE

6 lines of code changed in 1 file:

• Makefile (+6 -6)

westram 2014-11-06 14:31 #2 Rev.: 13130

* fix undefined behavior in loops over enum values
- only checked for-loops, other manual loops still might exist
- NDEBUG compilation with some gcc versions (e.g. 4.3.3, 4.4.3) optimize out the loop condition:
* in case of the loop added in [13129] the condition {{{at<=MY_AA}}} is regarded as "always true", because standard defines the variable {{{at}}} '''may not''' contain any value greater than MY_AA
* newer gccs do no longer perform such rigid optimizations
* the "bug" is described [https://gcc.gnu.org/bugzilla/show_bug.cgi?id=42810 here]
- as you can see the test {{{TEST_EXPECT(at>=1 && at<=3);}}} is optimized out as well
- this patch shows two different ways to remove undefined behavior:
* add another value (greater than tested loop condition) to enum (done in GEN_graphic.cxx). may easily be broken by removing that (unused) value later .
* use int as loop-variable, then assign to enum variable

11 lines of code changed in 4 files:

• CORE: arb_string.cxx (+2 -1)
• DIST: DI_view_matrix.cxx (+2 -1)
• GENOM: GEN_graphic.cxx (+4 -1)
• SL/TREEDISP: TreeDisplay.cxx (+3 -2)

westram 2014-11-05 17:09 #1 Rev.: 13129

- check some undefined behavior

19 lines of code changed in 1 file:

• CORE: arb_string.cxx (+19)

October 2014 »