[med-svn] [lambda-align] 01/01: fix builds with new SeqAn2
Sascha Steinbiss
satta at debian.org
Sat Jan 21 14:03:03 UTC 2017
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satta pushed a commit to branch master
in repository lambda-align.
commit 086b7876a3b7413f9bca63bfb893e7718ab63706
Author: Sascha Steinbiss <satta at debian.org>
Date: Sat Jan 21 14:01:48 2017 +0000
fix builds with new SeqAn2
---
debian/changelog | 8 +++
debian/patches/cast-min-initializer.patch | 20 --------
debian/patches/fix-documentation.patch | 59 ----------------------
debian/patches/series | 2 +-
...qan-modules.patch => set-seqan-cmake-dir.patch} | 7 ++-
5 files changed, 12 insertions(+), 84 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 437d15a..03247b0 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,3 +1,11 @@
+lambda-align (1.0.1-2) unstable; urgency=medium
+
+ * Set SeqAn_DIR to make sure SeqAn modules are found.
+ This fixes FTBFS against libseqan2-dev 2.3.1.
+ * Delete obsolete patch files.
+
+ -- Sascha Steinbiss <satta at debian.org> Sat, 21 Jan 2017 13:32:49 +0000
+
lambda-align (1.0.1-1) unstable; urgency=medium
* New upstream release.
diff --git a/debian/patches/cast-min-initializer.patch b/debian/patches/cast-min-initializer.patch
deleted file mode 100644
index e61163a..0000000
--- a/debian/patches/cast-min-initializer.patch
+++ /dev/null
@@ -1,20 +0,0 @@
-Description: fix 32bit builds
- This patch fixes FTBFS on 32-bit platforms by making sure all members
- of an initializer list are 64-bit values. Previously these were arch-
- dependent.
-Author: Sascha Steinbiss <sascha at steinbiss.name>
-Forwarded: https://github.com/seqan/lambda/issues/68
-Applied-Upstream: https://github.com/seqan/lambda/commit/cdb7e755af9829e26bf6e5f9ddbb07b5102038ef
---- a/src/lambda.hpp
-+++ b/src/lambda.hpp
-@@ -701,8 +701,8 @@
- }
-
- effectiveLength = std::min({
-- length(lH.gH.qrySeqs[m.qryId]) - effectiveQBegin,
-- length(lH.gH.subjSeqs[m.subjId]) - effectiveSBegin,
-+ static_cast<uint64_t>(length(lH.gH.qrySeqs[m.qryId]) - effectiveQBegin),
-+ static_cast<uint64_t>(length(lH.gH.subjSeqs[m.subjId]) - effectiveSBegin),
- effectiveLength});
- // std::cout << effectiveQBegin << "\t" << effectiveSBegin << "\t"
- // << effectiveLength << "\n";
diff --git a/debian/patches/fix-documentation.patch b/debian/patches/fix-documentation.patch
deleted file mode 100644
index 3fa5502..0000000
--- a/debian/patches/fix-documentation.patch
+++ /dev/null
@@ -1,59 +0,0 @@
-Description: fix documentation strings
-Author: Sascha Steinbiss <satta at debian.org>
-Forwarded: https://github.com/seqan/lambda/pull/65
-Applied-Upstream: https://github.com/seqan/lambda/pull/65
---- a/src/holders.hpp
-+++ b/src/holders.hpp
-@@ -174,7 +174,7 @@
- << "\033[0m\n\n";
-
- if (rem != stats.hitsFinal)
-- std::cout << "WARNING: hits dont add up\n";
-+ std::cout << "WARNING: hits don't add up\n";
- }
-
- if (options.verbosity >= 1)
---- a/src/options.hpp
-+++ b/src/options.hpp
-@@ -587,14 +587,14 @@
- // "STR"));
- // setValidValues(parser, "query-alphabet", "dna5 aminoacid");
- // setDefaultValue(parser, "query-alphabet", "dna5");
--//
-+//
- // addOption(parser, ArgParseOption("da", "db-alphabet",
- // "original alphabet of the subject sequences",
- // ArgParseArgument::STRING,
- // "STR"));
- // setValidValues(parser, "db-alphabet", "dna5 aminoacid");
- // setDefaultValue(parser, "db-alphabet", "aminoacid");
--//
-+//
- // addOption(parser, ArgParseOption("sa", "seeding-alphabet",
- // "alphabet to use during seeding (reduction possible)",
- // ArgParseArgument::STRING,
-@@ -710,7 +710,7 @@
- addSection(parser, "Scoring");
-
- addOption(parser, ArgParseOption("sc", "scoring-scheme",
-- "'45' for Blosum45; '62' for Blosum62 (default); '80' for Blosum80; "
-+ "use '45' for Blosum45; '62' for Blosum62 (default); '80' for Blosum80; "
- "[ignored for BlastN]",
- ArgParseArgument::INTEGER));
- setDefaultValue(parser, "scoring-scheme", "62");
-@@ -1033,12 +1033,14 @@
- // Setup ArgumentParser.
- ArgumentParser parser("lambda_indexer");
-
-+ setShortDescription(parser, "indexer for creating lambda-compatible databases");
-+
- // Define usage line and long description.
- addUsageLine(parser, "[\\fIOPTIONS\\fP] \\-d DATABASE.fasta\\fP");
-
- sharedSetup(parser);
-
-- addDescription(parser, "This is the indexer_binary for creating a lambda-compatible databases.");
-+ addDescription(parser, "This is the indexer_binary for creating lambda-compatible databases.");
-
- addSection(parser, "Input Options");
- addOption(parser, ArgParseOption("d", "database",
diff --git a/debian/patches/series b/debian/patches/series
index 11691ed..c5b28a6 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,2 +1,2 @@
-cmake-seqan-modules.patch
+set-seqan-cmake-dir.patch
force-link-rt-pthread.patch
diff --git a/debian/patches/cmake-seqan-modules.patch b/debian/patches/set-seqan-cmake-dir.patch
similarity index 62%
rename from debian/patches/cmake-seqan-modules.patch
rename to debian/patches/set-seqan-cmake-dir.patch
index f4aa2a8..6050852 100644
--- a/debian/patches/cmake-seqan-modules.patch
+++ b/debian/patches/set-seqan-cmake-dir.patch
@@ -1,13 +1,12 @@
-Description: add path to SeqAn CMake modules
+Description: set SeqAn_DIR to find CMake modules
Author: Sascha Steinbiss <satta at debian.org>
--- a/src/CMakeLists.txt
+++ b/src/CMakeLists.txt
-@@ -22,6 +22,9 @@
+@@ -22,6 +22,8 @@
# Dependencies (continued)
# ----------------------------------------------------------------------------
-+LIST(APPEND CMAKE_MODULE_PATH "/usr/share/seqan/cmake")
-+message (STATUS "CMAKE_MODULE_PATH is ${CMAKE_MODULE_PATH}")
++set (SeqAn_DIR "/usr/share/cmake")
+
# Search SeqAn and select dependencies.
find_package(OpenMP QUIET)
--
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