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commit 086b7876a3b7413f9bca63bfb893e7718ab63706 Author: Sascha Steinbiss <[email protected]> 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 <[email protected]> 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 <[email protected]> -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 <[email protected]> -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 <[email protected]> --- 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) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/lambda-align.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
