[med-svn] [Git][med-team/bppsuite][master] 3 commits: d/patches/hardening: Added patch to not shadow dpkg-buildflags
Michael R. Crusoe (@crusoe)
gitlab at salsa.debian.org
Mon Mar 25 23:52:42 GMT 2024
Michael R. Crusoe pushed to branch master at Debian Med / bppsuite
Commits:
bf0f8909 by Michael R. Crusoe at 2024-03-25T11:43:17+01:00
d/patches/hardening: Added patch to not shadow dpkg-buildflags
- - - - -
bd09aff2 by Michael R. Crusoe at 2024-03-25T11:43:17+01:00
d/rules: specifying RelWithDebInfo isn't necessary for getting unstripped binaries.
- - - - -
42f8582a by Michael R. Crusoe at 2024-03-25T15:25:32+01:00
d/patches/spelling: new patch to fix typos.
- - - - -
5 changed files:
- debian/changelog
- + debian/patches/hardening
- debian/patches/series
- + debian/patches/spelling
- debian/rules
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+bppsuite (2.4.1-7) UNRELEASED; urgency=medium
+
+ * Team upload.
+ * d/patches/hardening: Added patch to not shadow dpkg-buildflags
+ * d/rules: specifying RelWithDebInfo isn't necessary for getting
+ unstripped binaries.
+ * d/patches/spelling: new patch to fix typos.
+
+ -- Michael R. Crusoe <crusoe at debian.org> Mon, 25 Mar 2024 11:37:18 +0100
+
bppsuite (2.4.1-6) unstable; urgency=medium
* Relax autopkgtest for arm64
=====================================
debian/patches/hardening
=====================================
@@ -0,0 +1,14 @@
+From: Michael R. Crusoe <crusoe at debian.org>
+Subject: Append to CXXFLAGS, don't overwrite them
+Forwarded: https://github.com/BioPP/bppsuite/pull/18
+--- bppsuite.orig/CMakeLists.txt
++++ bppsuite/CMakeLists.txt
+@@ -8,7 +8,7 @@
+ project (bppsuite CXX)
+
+ # Compile options
+-SET (CMAKE_CXX_FLAGS "-std=c++11 -Wall -Weffc++ -Wshadow -Wconversion")
++add_compile_options(-std=c++11 -Wall -Weffc++ -Wshadow -Wconversion)
+
+ IF(NOT CMAKE_BUILD_TYPE)
+ SET(CMAKE_BUILD_TYPE RelWithDebInfo CACHE STRING
=====================================
debian/patches/series
=====================================
@@ -1 +1,3 @@
# fix_includes_path.patch
+spelling
+hardening
=====================================
debian/patches/spelling
=====================================
@@ -0,0 +1,80 @@
+From: Michael R. Crusoe <crusoe at debian.org>
+Subject: typo fixes
+Forwarded: https://github.com/BioPP/bppsuite/pull/19
+--- bppsuite.orig/bppSuite/bppAlnScore.cpp
++++ bppsuite/bppSuite/bppAlnScore.cpp
+@@ -152,7 +152,7 @@
+ try
+ {
+ BasicSequence motif("motif", phaseOpt, sitesTest->getAlphabet());
+- ApplicationTools::displayResult("Phase based on 1st occurence of", motif.toString());
++ ApplicationTools::displayResult("Phase based on 1st occurrence of", motif.toString());
+ size_t pos = sitesTest->getNumberOfSites();
+ for (size_t i = 0; i < sitesTest->getNumberOfSequences(); ++i)
+ {
+--- bppsuite.orig/bppSuite/bppAncestor.cpp
++++ bppsuite/bppSuite/bppAncestor.cpp
+@@ -270,7 +270,7 @@
+ {
+ (*ApplicationTools::error << "Site " << sites->getSite(i).getPosition() << "\tlog likelihood = " << tl->getLogLikelihoodForASite(i)).endLine();
+ }
+- ApplicationTools::displayError("!!! 0 values (inf in log) may be due to computer overflow, particularily if datasets are big (>~500 sequences).");
++ ApplicationTools::displayError("!!! 0 values (inf in log) may be due to computer overflow, particularly if datasets are big (>~500 sequences).");
+ exit(-1);
+ }
+ tree = new TreeTemplate<Node>(tl->getTree());
+--- bppsuite.orig/bppSuite/bppML.cpp
++++ bppsuite/bppSuite/bppML.cpp
+@@ -511,7 +511,7 @@
+ }
+ debug.close();
+ ApplicationTools::displayError("!!! Site-specific likelihood have been written in file DEBUG_likelihoods.txt .");
+- ApplicationTools::displayError("!!! 0 values (inf in log) may be due to computer overflow, particularily if datasets are big (>~500 sequences).");
++ ApplicationTools::displayError("!!! 0 values (inf in log) may be due to computer overflow, particularly if datasets are big (>~500 sequences).");
+ ApplicationTools::displayError("!!! You may want to try input.sequence.remove_saturated_sites = yes to ignore positions with likelihood 0.");
+ exit(1);
+ } else {
+--- bppsuite.orig/bppSuite/bppMixedLikelihoods.cpp
++++ bppsuite/bppSuite/bppMixedLikelihoods.cpp
+@@ -254,7 +254,7 @@
+ {
+ (*ApplicationTools::error << "Site " << sites->getSite(i).getPosition() << "\tlog likelihood = " << tl->getLogLikelihoodForASite(i)).endLine();
+ }
+- ApplicationTools::displayError("!!! 0 values (inf in log) may be due to computer overflow, particularily if datasets are big (>~500 sequences).");
++ ApplicationTools::displayError("!!! 0 values (inf in log) may be due to computer overflow, particularly if datasets are big (>~500 sequences).");
+ exit(-1);
+ }
+
+--- bppsuite.orig/bppSuite/bppSeqGen.cpp
++++ bppsuite/bppSuite/bppSeqGen.cpp
+@@ -146,7 +146,7 @@
+ line += tmp;
+
+ index1 = line.find_first_of(" \t");
+- if (index1 == string::npos) throw Exception("Error when parsing tree file: no begining position.");
++ if (index1 == string::npos) throw Exception("Error when parsing tree file: no beginning position.");
+ index2 = line.find_first_of(" \t", index1 + 1);
+ if (index2 == string::npos) throw Exception("Error when parsing tree file: no ending position.");
+ begin = TextTools::toDouble(line.substr(0, index1));
+--- bppsuite.orig/doc/bppsuite.texi
++++ bppsuite/doc/bppsuite.texi
+@@ -1508,7 +1508,7 @@
+ @subsubsection Conditioned models
+
+ The transition probabilities on the branches are conditioned by the
+-occurence of given events. The model is then no-markovian, but
++occurrence of given events. The model is then no-markovian, but
+ semi-markovian. The sets of considered events follow the one (ie
+ register) defined for substitution mapping (see the testnh manual).
+
+--- bppsuite.orig/bppSuite/bppPopStats.cpp
++++ bppsuite/bppSuite/bppPopStats.cpp
+@@ -523,7 +523,7 @@
+ throw Exception("CodonSiteStatstics can only be used with a codon alignment. Check the input alphabet!");
+ }
+ string path = ApplicationTools::getAFilePath("output.file", cmdArgs, true, false);
+- if (path == "none") throw Exception("You must specify an ouptut file for CodonSiteStatistics");
++ if (path == "none") throw Exception("You must specify an output file for CodonSiteStatistics");
+ ApplicationTools::displayResult("Site statistics output to:", path);
+ ofstream out(path.c_str(), ios::out);
+ out << "Site\tMissingDataFrequency\tNbAlleles\tMinorAlleleFrequency\tMajorAlleleFrequency\tMinorAllele\tMajorAllele";
=====================================
debian/rules
=====================================
@@ -7,9 +7,5 @@ export DEB_BUILD_MAINT_OPTIONS = hardening=+all
%:
dh $@
-override_dh_auto_configure:
- dh_auto_configure -- -DCMAKE_BUILD_TYPE=RelWithDebInfo
-
-override_dh_fixperms:
- dh_fixperms
+execute_after_dh_fixperms:
find debian -name "*.dnd" -exec chmod -x \{\} \;
View it on GitLab: https://salsa.debian.org/med-team/bppsuite/-/compare/f366f4a21b08650fe6c73c8dbc7e367fb081045e...42f8582ada319a467c91438ece1a823c41c1f8f5
--
View it on GitLab: https://salsa.debian.org/med-team/bppsuite/-/compare/f366f4a21b08650fe6c73c8dbc7e367fb081045e...42f8582ada319a467c91438ece1a823c41c1f8f5
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