diff options
| author | V3n3RiX <venerix@redcorelinux.org> | 2017-12-25 17:37:52 +0000 |
|---|---|---|
| committer | V3n3RiX <venerix@redcorelinux.org> | 2017-12-25 17:37:52 +0000 |
| commit | 2f51c9978dda4c6e8debca43e4235ecc86914032 (patch) | |
| tree | bc41e1c4383040034174c327504f702c8517a123 /sci-biology/mosaik | |
| parent | 51536d2fe4697ba9114d611178bb9e20d3d5b729 (diff) | |
gentoo resync : 25.12.2017
Diffstat (limited to 'sci-biology/mosaik')
| -rw-r--r-- | sci-biology/mosaik/Manifest | 3 | ||||
| -rw-r--r-- | sci-biology/mosaik/files/mosaik-2.2.30-gcc7.patch | 40 | ||||
| -rw-r--r-- | sci-biology/mosaik/mosaik-2.2.30.ebuild | 13 |
3 files changed, 47 insertions, 9 deletions
diff --git a/sci-biology/mosaik/Manifest b/sci-biology/mosaik/Manifest index 0a6c6c678ede..e70550f4ed6a 100644 --- a/sci-biology/mosaik/Manifest +++ b/sci-biology/mosaik/Manifest @@ -1,6 +1,7 @@ AUX mosaik-2.2.30-Wformat-security.patch 3296 BLAKE2B f75a4dde6fb88e0175989ff9ddfd6dfd2450eb0df24e4e5f60943fbd9fcc40b798d7d7bca2d57e25c4201f6a7cbf8eb66b2f3573f54fc05b5b3a46e3e01a1ddb SHA512 e72fa7cac8798425ac1dd4d3358bfdff640cc831a01531749ee2fad99f8b53bd64e8c7fcdddce205e9f6dd312cc74376afcba395ab8d508d92416190b7eed1df AUX mosaik-2.2.30-fix-build-system.patch 8056 BLAKE2B 4c795e790718dca2a46e25fd67499612ad1226c6e6ad73d7543cd1c1aa1dacabc0ed77ade798b2602d8f661eeb9cd7b033bd8945d4384d01e2d279762f40fa14 SHA512 ed4a6efd9fb2fabd6c24adaa5894fde80024d8ee930450711c07388b62969a41e801f052ee88d7890355f1ddfc5ef9fbb40bfdabfbfae364c64c673ce08958c6 +AUX mosaik-2.2.30-gcc7.patch 1252 BLAKE2B 896d662807c223cc69eacfa2e1fcb457c696e0d198dfa718f0f7eb9060d9c0491a18017901385227c2c0906e02c61a8fb9a9deb71f228d4c6195cdf0b5696515 SHA512 fc7dd31d2fcce7a4e624e759ee08b8997757bf4ce3ae3f98080e6e6252dfc647de4848f6a736b35090e8c8da37618baaf08e19be9ddfc408bbc5f7200f44cbba AUX mosaik-2.2.30-remove-platform-code.patch 399 BLAKE2B ec711a9b112efa87b2811e4545bfc58716393576915f71167ff700ccd809be4fad5e07bac7a5cb7df911615f4c996284cd711c1d1cb62c5a18695e719e6574c6 SHA512 4aec709660b41fb61bb9219a587255a5f416992a4478c2a7eb67374d1425f0a4e0b4d356827a9214e2f2718b635169c95d3288bf10388a74e50d498c39c2f259 DIST mosaik-2.2.30.tar.gz 4387062 BLAKE2B 6f373aeae4f68be2455556e7f79a5850e25d804bd482d85a846b44f8adaabb2513ffc7ced774f5ead6dbc8fc9dca9d64f76f83bc5b55b1be4073a8cf309e121b SHA512 1acf534e6defc927fc22937a7bae6786e85ab7aa234b4209169f1267f1a9bd68415b441c6aed2e7cd667f694a562017ebc9457251958f77386259ffce9812b10 -EBUILD mosaik-2.2.30.ebuild 1104 BLAKE2B a567a6ce6f232eff13980b0d1d9ad54f4ff486539c8bbb594412c4dd8798e59ca23df40af0acd93d17f552683b39adc6e0212e8c09ab308d186206c6dfa225f3 SHA512 34863af564b085b85d1670b9c20fdc8ca8c5367e210a041c81d2cb67e5380e91636620214ebe06c347cb0ac556581d304374e527738c36b01029cf38a4846a4b +EBUILD mosaik-2.2.30.ebuild 1105 BLAKE2B 842b161c8fc0cda9cab8101ca6ae0879cedb191983a61a25d21afe0ef5edb4a87e7e62edad27f2642444c2dc58387328c275f7830abd7917146d6febee812ba5 SHA512 55377965262d7942229a269bc1c0c56ff930d544b422305994f0995ca68d06ea3a1745fb759dc70225ff6b76d338b8761236079eb7107edb6225ae7c6d2f372e MISC metadata.xml 414 BLAKE2B 3c19ab9f4c6a0f4e73d67fe4f280fd252d68120a28e045a39c3ad78a4741921b2141c4433c6babcdc33b16083d4949fc28448f57fcb6c65be8719dd1d0bff8f3 SHA512 2e6887226a0ac7457d1bbce1d76ac0953f0c1d5ff1d4261b7e11e4fa38803f01f8a67a285c2071671d58fcb8912ca8bb66bdfca93e2481be043ec5f2f2353c5b diff --git a/sci-biology/mosaik/files/mosaik-2.2.30-gcc7.patch b/sci-biology/mosaik/files/mosaik-2.2.30-gcc7.patch new file mode 100644 index 000000000000..ebf925a0cbb7 --- /dev/null +++ b/sci-biology/mosaik/files/mosaik-2.2.30-gcc7.patch @@ -0,0 +1,40 @@ +--- a/CommonSource/ExternalReadFormats/BamWriter.cpp ++++ b/CommonSource/ExternalReadFormats/BamWriter.cpp +@@ -496,7 +496,7 @@ + buffer[6] = 0xffffffff; // mate_pos + buffer[7] = 0; // ins_size + +- const char* startChar = '\0'; ++ const char* startChar = NULL; + + // write the block size + const unsigned int dataBlockSize = nameLen + packedCigarLen + encodedQueryLen + queryLen; +@@ -652,7 +652,7 @@ + unsigned int zaTagLen = 0; + string zaTag; + char* pZaTag; +- if ((zaString != 0) && (zaString != (char)0)) { ++ if ((zaString != 0) && (zaString[0] != '\0')) { + zaTagLen = 3 + strlen( zaString ) + 1; + zaTag.resize( zaTagLen ); + pZaTag = (char*)zaTag.data(); +@@ -776,7 +776,7 @@ + BgzfWrite(mdTag.data(), mdTagLen); + + // write the ZA tag +- if ( zaString != 0 && (zaString != (char)0)) ++ if ( zaString != 0 && (zaString[0] != '\0')) + BgzfWrite(zaTag.data(), zaTagLen); + + // write the ZN tag +--- a/MosaikAligner/AlignmentThread.cpp ++++ b/MosaikAligner/AlignmentThread.cpp +@@ -591,7 +591,7 @@ + buffer.al = al; + buffer.noCigarMdNm = noCigarMdNm; + buffer.notShowRnamePos = notShowRnamePos; +- if ( zaString == (char)0 ) ++ if ( zaString == NULL ) + buffer.zaString.clear(); + else + buffer.zaString = zaString; diff --git a/sci-biology/mosaik/mosaik-2.2.30.ebuild b/sci-biology/mosaik/mosaik-2.2.30.ebuild index 45633c47dab5..874edba4504d 100644 --- a/sci-biology/mosaik/mosaik-2.2.30.ebuild +++ b/sci-biology/mosaik/mosaik-2.2.30.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2017 Gentoo Foundation # Distributed under the terms of the GNU General Public License v2 EAPI=6 @@ -11,18 +11,15 @@ SRC_URI="https://github.com/wanpinglee/MOSAIK/archive/5c25216d3522d6a33e53875cd7 LICENSE="GPL-2" SLOT="0" -IUSE="" KEYWORDS="~amd64 ~x86" -DEPEND="" -RDEPEND="" - S="${WORKDIR}/${P}/src" PATCHES=( - "${FILESDIR}/${P}-remove-platform-code.patch" - "${FILESDIR}/${P}-fix-build-system.patch" - "${FILESDIR}/${P}-Wformat-security.patch" + "${FILESDIR}"/${P}-remove-platform-code.patch + "${FILESDIR}"/${P}-fix-build-system.patch + "${FILESDIR}"/${P}-Wformat-security.patch + "${FILESDIR}"/${P}-gcc7.patch ) src_configure() { |