gentoo resync : 28.04.2019

17 files changed, 102 insertions, 23 deletions

diff --git a/sci-biology/HTSeq/HTSeq-0.9.1.ebuild b/sci-biology/HTSeq/HTSeq-0.9.1.ebuild
index 446bbef36efb..8f27fec4c5a7 100644
--- a/sci-biology/HTSeq/HTSeq-0.9.1.ebuild
+++ b/sci-biology/HTSeq/HTSeq-0.9.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
 
-PYTHON_COMPAT=( python2_7 python3_{4,5,6} )
+PYTHON_COMPAT=( python2_7 python3_{5,6} )
 
 inherit distutils-r1
 
diff --git a/sci-biology/HTSeq/HTSeq-9999.ebuild b/sci-biology/HTSeq/HTSeq-9999.ebuild
index 446bbef36efb..8f27fec4c5a7 100644
--- a/sci-biology/HTSeq/HTSeq-9999.ebuild
+++ b/sci-biology/HTSeq/HTSeq-9999.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
 
-PYTHON_COMPAT=( python2_7 python3_{4,5,6} )
+PYTHON_COMPAT=( python2_7 python3_{5,6} )
 
 inherit distutils-r1
 
diff --git a/sci-biology/HTSeq/Manifest b/sci-biology/HTSeq/Manifest
index e56056cd897b..66c1a76c57df 100644
--- a/sci-biology/HTSeq/Manifest
+++ b/sci-biology/HTSeq/Manifest
@@ -1,4 +1,4 @@
 DIST HTSeq-0.9.1.tar.gz 596941 BLAKE2B 6865c36056bff2008ae8bf18d0ac81dbf721fb97cdcc8bbd9150356fc80ae99e0cb872033fac274b40df3d1c95e9bcfd83c4f7d033184725596ffc96081e26d1 SHA512 ec3e1ec9cf66918f2afacf7997ab5da02015896ddd97260f5abec8343a9013cf6e857872be38b2cd3bb5bde655abe602a3c22c32448190f32e1a8f1153a19344
-EBUILD HTSeq-0.9.1.ebuild 715 BLAKE2B 13320f7fb8b3693641f1422096a30d8463cbbd563d0f924e51861c287c4cebfe37a7e65e01e89f772e8fbe4030e7484d020c5878765a7687e6a600643c404aa2 SHA512 eee6989a6910b4022b94982f1c8f598215431c6e0674609d8f30b992a4b9036fde82156fbec0bb4fad1b6bfbd56aa33dcb05cff136cb90a7f5678f18218f3fd0
-EBUILD HTSeq-9999.ebuild 715 BLAKE2B 13320f7fb8b3693641f1422096a30d8463cbbd563d0f924e51861c287c4cebfe37a7e65e01e89f772e8fbe4030e7484d020c5878765a7687e6a600643c404aa2 SHA512 eee6989a6910b4022b94982f1c8f598215431c6e0674609d8f30b992a4b9036fde82156fbec0bb4fad1b6bfbd56aa33dcb05cff136cb90a7f5678f18218f3fd0
+EBUILD HTSeq-0.9.1.ebuild 710 BLAKE2B 30f42cfd491af94a9f7adad9c99a74fa53607b0068bbae29f60197dad1fdb212e580ac8baa4878fb507ebd5be1b15fdd007fa07a110dd096cdc5cf1e274f0dd3 SHA512 d8e15adc39e65a8579853ef98faf1a77052d9d52532506f64d1028d1e60a185f4696bde425fcb5bcce7bffff6ad7863780f79ff47ae80bbe53e4dfb6538505fb
+EBUILD HTSeq-9999.ebuild 710 BLAKE2B 30f42cfd491af94a9f7adad9c99a74fa53607b0068bbae29f60197dad1fdb212e580ac8baa4878fb507ebd5be1b15fdd007fa07a110dd096cdc5cf1e274f0dd3 SHA512 d8e15adc39e65a8579853ef98faf1a77052d9d52532506f64d1028d1e60a185f4696bde425fcb5bcce7bffff6ad7863780f79ff47ae80bbe53e4dfb6538505fb
 MISC metadata.xml 555 BLAKE2B 9cb1b8a7b9beeeb137209a73b0f4687f3134f08ac17119daddcdff8f12c74b5724ea45e1de7a5259b1ffa39c06f103e1280065a72b26d73576bad377ed5c86b9 SHA512 a9402ce0e04f242a4509d6f8e3bfc998b32703a9e1ac619d618d761f03e76a92eb5ab625bba7b72dabf23d36d587d48815652764e9f62b317482495ecf59a97e
diff --git a/sci-biology/Manifest.gz b/sci-biology/Manifest.gz
index 7fba99cc1be4..89bff10b7570 100644
--- a/sci-biology/Manifest.gz
+++ b/sci-biology/Manifest.gz
diff --git a/sci-biology/bedtools/Manifest b/sci-biology/bedtools/Manifest
index 301c707d979c..3e0a0a3f796c 100644
--- a/sci-biology/bedtools/Manifest
+++ b/sci-biology/bedtools/Manifest
@@ -1,4 +1,4 @@
 DIST bedtools-2.26.0-fix-buildsystem.patch.bz2 2584 BLAKE2B 550cd03a0c01217adb347587cb75bdc2ffa4e03ad6ad66535b22d423e6f030e237b0ccfd3d1bd3e434cb9cc2a007971517f03e9ceabc08b63c725bac786e23e8 SHA512 0a7835f560102ce6183736faea6a2be05609b69bb8efdaf98b9d7057e24aa1ebe9d6067118b95c76470ca341b151970db532094ee70ca333075aed7c47509ba3
 DIST bedtools-2.26.0.tar.gz 19939711 BLAKE2B 8f6ee6ed755c638dbdd0a4750a5348c28a865f36eaafef6160e90f62912cb0a6b719713935ba68dad74bc591e3f37db49eab54a06a316dc00e4ec82a5dca71dc SHA512 b224adcc09322e90ef389e8172e14572b68f164185fe1a8814db1c47bb4f15656ca8c0ff0061017eb54d76affbe0d0f5793d893b8ab489b56eaf0818616a5def
-EBUILD bedtools-2.26.0.ebuild 949 BLAKE2B 901f59ab0d26b9daf0be6a09e7188c100bbede23dd64473979b4f5ee2e647919b9692ff31f7e7ce305f121959ca515b86fa2661c8490676155a47c06ac87b015 SHA512 21abd3ed3d8d56ae3410519aff15371a989c9e44297d938f1adfc18fdfd684f062cdc1e491ce8b752cb31b54e9fafaa7a7808dbf1f0d28cfcf5aa71ad5fcf269
+EBUILD bedtools-2.26.0.ebuild 945 BLAKE2B 05e926ee12cb2ad650d611990e8d9d8bca0b52fdb24ef90cc162c4c891dfd96b3eec31c5cdf873d518540015f1d7daa9ffe5791ef850fcc911fb8696f56e55c1 SHA512 ee68e91063f9f310a93af8dc3fcfc9c359636ba24b70080df3b5fe89ce40cd3877dfa0f75fea018277181fdf49fb9681378a963904d9f01f89b437cc2c311d07
 MISC metadata.xml 761 BLAKE2B 35d57919e32a4b8bd6070ab5a513f62578394d43098d9e7b9b0765fd57d684c049dad9ec1b315044518bf01535d505e9d9d3fee540308df40c0b70886db8e49f SHA512 2d98b9559ef00bee2b741f9e7d22645442ba161f3cadb32c6366b39fcd71b6eac52afd210f59ae709a15cba36a2d0a47341345740e0cab6a1f6bfdffed064770
diff --git a/sci-biology/bedtools/bedtools-2.26.0.ebuild b/sci-biology/bedtools/bedtools-2.26.0.ebuild
index 084192dd4419..25f91921363a 100644
--- a/sci-biology/bedtools/bedtools-2.26.0.ebuild
+++ b/sci-biology/bedtools/bedtools-2.26.0.ebuild
@@ -3,7 +3,7 @@
 
 EAPI=6
 
-PYTHON_COMPAT=( python{2_7,3_4,3_5,3_6} )
+PYTHON_COMPAT=( python{2_7,3_5,3_6} )
 
 inherit flag-o-matic python-any-r1 toolchain-funcs
 
diff --git a/sci-biology/biopandas/Manifest b/sci-biology/biopandas/Manifest
index 7e79ddd4d104..078e8397d3a2 100644
--- a/sci-biology/biopandas/Manifest
+++ b/sci-biology/biopandas/Manifest
@@ -1,3 +1,3 @@
 DIST biopandas-0.2.1.tar.gz 209379 BLAKE2B 839a6f569f12b95c9b1c75dc755d009c77d7ef8224e517aed5026ffa6c33bd3826fe3862fec03469e967005a500600782fc372951d61358e2fe3bb56af734228 SHA512 0ea7aec84251d8d6ec4736c4968228133bd8622afb17d6916287168cb9f9757c5a97a4d5a52ac0e2f30027bf0edf9d76413db142f70d606f1359b8a4e06de7c8
-EBUILD biopandas-0.2.1.ebuild 1066 BLAKE2B 6e435b3e5cec6751551eacfaf351df69b16dfd43b4e4173aed3a7dfea3740dd7e395b4d78092267a43a38d6e4b5ccee0d5e4f688174125b6a8498f594ab3bbf7 SHA512 7226499bd7d132150b6c2caeb7fcbdda3ff8d2fd47755d535834584c6d3aa426b65d30a87d7265f638be9019b0fbf0f5f73e9dd3495c468c6a79624a1e908916
+EBUILD biopandas-0.2.1.ebuild 1061 BLAKE2B adc9dcd6248cf5a720efd53a0db7d64701ece870fe4f851210d312aff1f8ccea29187bdb732254f80b2bfbbd6acc24ea7f5f74f4b5c1fb7798170c894e6eb455 SHA512 af6888f773aca4c9e93ea53de9861542398d952bab8f817cae9dba2b6613a993f051c260e7aa0a6919644561cc0f37df466a5e23b3d8fb727f674ee38e49a0c9
 MISC metadata.xml 536 BLAKE2B e3cb776d0332fff486a7e1ea1353c54694ff687d4685bbb51728db0ed2025bb3d09d39cf7c9ea9f11546cbf9c4727661348e2f5fdfc13ffac2329ef6dfbe7450 SHA512 502803e30ecfac53516b56501a7bffeb49c3c0bc44ce5b3dd87aac5c745de614c235523ba3be374fcbede1a9a7bcf11c328abb27d82e087b275303f38b80b166
diff --git a/sci-biology/biopandas/biopandas-0.2.1.ebuild b/sci-biology/biopandas/biopandas-0.2.1.ebuild
index 315f6a4e0160..4260d0a440a1 100644
--- a/sci-biology/biopandas/biopandas-0.2.1.ebuild
+++ b/sci-biology/biopandas/biopandas-0.2.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
 
-PYTHON_COMPAT=( python2_7 python3_{4,5,6} )
+PYTHON_COMPAT=( python2_7 python3_{5,6} )
 
 inherit distutils-r1
 
diff --git a/sci-biology/biopython/Manifest b/sci-biology/biopython/Manifest
index 8d1a080b69ee..acc4141192b8 100644
--- a/sci-biology/biopython/Manifest
+++ b/sci-biology/biopython/Manifest
@@ -1,5 +1,7 @@
 DIST biopython-1.68.tar.gz 14445813 BLAKE2B 566931c4e522e95278f7f6a9dc07ecc091dc54b69cdea8bb07603339af4f1fd38e3df87482e97729acb776dd2df19a4e61d49ee7608ec5cb0f24966e28c2e3dd SHA512 0ca994475654bb68ff326c8e86cbd4547cd87b42e1633dda039ad668e1298884b22e169f6b25ab514e929861334a93b7db6d057a3486cea9997ca2de95c61a69
 DIST biopython-1.71.tar.gz 16031832 BLAKE2B 2062065b77fc35ea8a3f09ec967482c233a6e0bbfc7d09187ff5e892848b45fa7bd6d7b6027b38c3d4c9a9c601785521fa7edb91fa960b46c8e49aed91b1f5dc SHA512 003955e92295e98526c88abb573db9bdc37877fc41395551b541e7106ffa603327a36c6f4d999838c0be38b378901235c9dbd7cb7fc25c14a5d7001939fe23bd
-EBUILD biopython-1.68.ebuild 1641 BLAKE2B a66e9c4a4c4987809faa18742b345fad45c6c6e536c1a87dfc552345637f1b7df28426a314df4b2f7e523002229395e978b75548b907f0a7aac6d80ee893d1b3 SHA512 e30c9f8b542ef0508a6fea508461521cbdc140a0c1e1f08eddfaef6dd73c10496f1d2fdc26261c26a5c860ffba845c1e6bb6f82d8722d0c7a1a89253c3a7a7f1
-EBUILD biopython-1.71.ebuild 1621 BLAKE2B c880eb5d4bde244ee427a576400d5a3fb2703f85fe07a68949a4ff1b0fa7ac1def332cd67b12731bd3629e62ffef318ce55f0768300c20d05eda72fef82a594c SHA512 1c9147003fc3a47e515e94b89bb718e80358db9956382937b9e675240d08608ef57090013a824c7cf504b517697c182385a6073c7cb1e8037a439fde75ca3935
+DIST biopython-1.73.tar.gz 15715102 BLAKE2B b2c40f9ed02681f19607c88f91b469784985acefc6e81770a54e5c13c715915344bc7fd72e4a88ae50879a2463965ac6d0d04c6d263908887028d1e065620b95 SHA512 d067330ef8e25ca6881b56f4e5e89e16a816c89760473e2f32a6236ab202f805294650aa944f0b098987425bcb65727317da7a26deb4d4937f02b00123ea9a8f
+EBUILD biopython-1.68.ebuild 1634 BLAKE2B 43d435496fc239c847b19a4e66bf52f920454ee6fd810b94d0d32bde6381059abb9561f90d06e5d1ca83a80721958c6051f79d0c92e5b76dc8d930ed54254f78 SHA512 70b8d2a8f84f70edc6a6225a8958328d8657dbb8b01c0716b7b1c15320914e827129c30da32b670f6ba9ab4d24a8f6cf01ea728b5d14e1607e9cef5c35f7b47f
+EBUILD biopython-1.71.ebuild 1616 BLAKE2B e1e4b60cfe88dd00ef28135f137657147112249bc60738d145c5036bab3d1436878834f9ac03c829aa39c40696d0350d9ea98040be43e7f393752f9baf63ac21 SHA512 ae8fa77eefe2bb67c430bd6351a60e2a5d1e0193be4c8e6330f81edbac90b4730d5ec59b1bd25baf04452a9d8ea4f9b7550b703ecf20b1af9c9473b6465b2e5a
+EBUILD biopython-1.73.ebuild 1684 BLAKE2B c98e92b2e989b2a398912b1335049750565933b202cc1e1d77d83f1aa13071bb5dd1ce63ac37113a2bf03cc1394dcb7011fb2346728d3463c353460101b847a5 SHA512 b71c3acc6b6f97564b31b3bfc4a8fe47ad1c95fcd07f265964f3cf381ef3d2c2917d2bc2ef8446ef3290eaf447a1c77ff38fc7d1459694c8884dc45cd8350e9a
 MISC metadata.xml 267 BLAKE2B 7cf386952842945148119de3263231db4d1046d5f54811f7e303ed8ec4d27cbc1960b99c92daf6f32e5b981c2fb9f50ec666be6193865d6e18541b7427a152a9 SHA512 91ab266d9ab24401bc0fec759c5b6cfcf44a3c5669fc31c7301d79770839bb5dfa0e155d949392ef06176b4a0b2c32b91b1b54b0027f972db61f0a5e54644403
diff --git a/sci-biology/biopython/biopython-1.68.ebuild b/sci-biology/biopython/biopython-1.68.ebuild
index 9c8442e39090..f76da59c1b84 100644
--- a/sci-biology/biopython/biopython-1.68.ebuild
+++ b/sci-biology/biopython/biopython-1.68.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
 
-PYTHON_COMPAT=( python2_7 python3_{4,5} pypy )
+PYTHON_COMPAT=( python2_7 python3_5 pypy )
 
 inherit distutils-r1 eutils
 
diff --git a/sci-biology/biopython/biopython-1.71.ebuild b/sci-biology/biopython/biopython-1.71.ebuild
index 73a714248aea..8b9a0cd7112e 100644
--- a/sci-biology/biopython/biopython-1.71.ebuild
+++ b/sci-biology/biopython/biopython-1.71.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2018 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=7
 
-PYTHON_COMPAT=( python2_7 python3_{4,5,6} )
+PYTHON_COMPAT=( python2_7 python3_{5,6} )
 
 inherit distutils-r1 eutils
 
diff --git a/sci-biology/biopython/biopython-1.73.ebuild b/sci-biology/biopython/biopython-1.73.ebuild
new file mode 100644
index 000000000000..f0d335a5933a
--- /dev/null
+++ b/sci-biology/biopython/biopython-1.73.ebuild
@@ -0,0 +1,58 @@
+# Copyright 1999-2019 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=7
+
+PYTHON_COMPAT=( python2_7 python3_{5,6,7} )
+
+inherit distutils-r1 eutils
+
+DESCRIPTION="Python modules for computational molecular biology"
+HOMEPAGE="https://www.biopython.org/ https://pypi.org/project/biopython/"
+SRC_URI="mirror://pypi/${PN:0:1}/${PN}/${P}.tar.gz"
+
+LICENSE="HPND"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+RDEPEND="
+	dev-python/matplotlib[${PYTHON_USEDEP}]
+	dev-python/networkx[${PYTHON_USEDEP}]
+	dev-python/numpy[${PYTHON_USEDEP}]
+	dev-python/rdflib[${PYTHON_USEDEP}]
+	dev-python/pygraphviz[${PYTHON_USEDEP}]
+	>=dev-python/reportlab-3.5.13-r1[${PYTHON_USEDEP}]
+	dev-python/pydot[${PYTHON_USEDEP}]"
+DEPEND="${RDEPEND}
+	dev-python/setuptools[${PYTHON_USEDEP}]
+	sys-devel/flex"
+
+DOCS=( {CONTRIB,DEPRECATED,NEWS,README}.rst Doc/. )
+
+python_test() {
+	distutils_install_for_testing
+	cp -r "${S}"/{Doc,Tests} "${TEST_DIR}"/lib/ || die
+	cd "${TEST_DIR}"/lib/Tests || die
+	rm test_BioSQL_{psycopg2.py,MySQLdb.py,mysql_connector.py} || die
+	"${EPYTHON}" run_tests.py --offline --verbose || die
+}
+
+python_install_all() {
+	# remove files causing ecompressdir to fail
+	rm Doc/examples/ls_orchid.gbk.{gz,bz2} || die
+
+	distutils-r1_python_install_all
+
+	dodir /usr/share/${PN}
+	cp -r --preserve=mode Scripts Tests "${ED}"/usr/share/${PN} || die
+}
+
+pkg_postinst() {
+	elog "For database support you need to install:"
+	optfeature "MySQL" dev-python/mysql-python
+	optfeature "PostgreSQL" dev-python/psycopg
+
+	elog "Some applications need extra packages:"
+	optfeature "EMBOSS (The European Molecular Biology Open Software Suite)" sci-biology/emboss
+}
diff --git a/sci-biology/consed/Manifest b/sci-biology/consed/Manifest
index 9694dbfdb96e..07e6a1839807 100644
--- a/sci-biology/consed/Manifest
+++ b/sci-biology/consed/Manifest
@@ -1,7 +1,7 @@
-AUX consed-29-fix-build-system.patch 5614 BLAKE2B 8b145d01e5fa6935715e7775d8e415b43184c4dd067bb3ad3eb72ef870b6f18d254f73a1e512dfb55376473df5cd3af70b4050daddf354cbe7a61773aaa9a13a SHA512 ea649079d5dbff21206bf8f56729fc559f374120dd3336499677eb65fde247739f41efdb29a3df60225ec38efc6802608aa2410bf4ab77f8d76bfd31fdc710fa
+AUX consed-29-fix-build-system.patch 5614 BLAKE2B 2ec980906ee2f9c7b0cede7b3eabad78cdc3e9c3d95c58275dc849ff36ee4ef9fa53dd3b321729ae60c9f2d2fc1ca4cd0ee2448175410acca7ffe6266d66ac44 SHA512 92df40d6465685aec77d73db1f0eb7a79d4c26fbbf7d9764c4e0a83208e4ef97b45db1a8175239bd174bd56aeed7a5aa0111c7b99764910f7d6c0ac63aba187d
 AUX consed-29-fix-c++14.patch 9261 BLAKE2B ff70814b39780dbbabc70eb7555359e8aee2ef72b40b7e149e2f63ccaeedfe7e0dc8822cb2b5c79d57c33e621a59e0e1cd273e49a0976daef0bdeb52f4f46569 SHA512 be5cd76d36cf437c1113d09e540d98d0eb92b7e2e732f4a5a308066b8046b5628048203e791a0fa316e44a4cc127d027418a7f038406df22c3f60552f5b87789
 AUX consed-29-fix-perl-shebang.patch 17375 BLAKE2B e34a358569d594f4ab60fc3745a6a84cab781cbad860421f5ac322154df9635e13b2e2349c92f4271b0ca161eda87285ba89bf0801992954fecaa11575c8baf9 SHA512 4caed1ab7229e2b3e367f03a8d650cafed2974232fcd6daa08e62c90512d49e09caceb34c5bb65c67a588bab314165d72d8c1687393549d4107425df78e3218d
-AUX consed-29-fix-qa.patch 11168 BLAKE2B 139b52d402f27c8121a43f933a181aabf150c0c8836f2facc7b42909db3808fab1ceede30956d6b3c2462ad31b43e054c0bbf8552e57e6e41479d25eb111738b SHA512 088d774159b421666bf75f6f9f17ee83d488625d482d8d404bde12671025b1f03322bee5c50e792fbbd822c223fa5ee697cf99c7efc9fcbebc119314d02df604
+AUX consed-29-fix-qa.patch 11639 BLAKE2B 3b80fd91b60c09e69cb9fa9b8deb88393fd89f02a3a650076db275567725aeb4636bfe1fcc35f44c72be33ed9494796fa6dab1b4da8b4b9444ecc73ea9b141fb SHA512 083b23d03ef9a473b41fae21ce433cdd5cdd0948819fa9dcc6dbed3022e93674aaa8769894b9be69b5bccf47dd6e67435bdf0549a719ecc4c5517f89010c3988
 DIST consed-29-linux.tar.gz 36172715 BLAKE2B 6706576b404c0bccb7ed28ab6fe2dec86fdac6f7651406d3f30e35caac3e49a66b4762edace2133d2dfb776bbeb730b74797c7323deb950f2648a46c4594fe98 SHA512 63a95d84cb58009045a9d898c8b1a94f98516bed9189f624a5930338cc8f51562504257f309d945fafcc07e0811ffeea122b640789f75fbd6c94535178dab4dd
 DIST consed-29-sources.tar.gz 3258845 BLAKE2B 508763ff2a240047cff0a43ba4b9b9a7f9302c0a023478c6b08f86bb77fb2c12a62a9b16165fe6257fe6c86af853dabe279bd9e05632c3e112e3fb7fad2c6bd3 SHA512 fd711a65a02ef1238cca12b90fe7fa9b67da6c37d43cd105f38c7b6475fbc073c1f4d7f99703dec9d3a0a7a2a9317cb14999a114bb6f52589cb9b6e34700eb93
 EBUILD consed-29.ebuild 2727 BLAKE2B 09c3d1619c7c751c1b084bcf1bc25bd87cfa23f4d83b0b6432b9229f7ecbd05c4a424522f6cc4117d571fa2ce34dbde805b4d0224a95db5af0f200e21688b1f3 SHA512 86160fe6b03dcfddc756c3f6a5c15bcbfe6a94b3002fe4deb39157adfc445a52ee557fa7732f07711a6859357c475bc31cfa535563cb91efee4511281fdef854
diff --git a/sci-biology/consed/files/consed-29-fix-build-system.patch b/sci-biology/consed/files/consed-29-fix-build-system.patch
index 27c9c552fe3f..30819f93ac80 100644
--- a/sci-biology/consed/files/consed-29-fix-build-system.patch
+++ b/sci-biology/consed/files/consed-29-fix-build-system.patch
@@ -45,7 +45,7 @@ Make build system semi-sane:
 -/usr/X11R6/lib/libICE.a /usr/X11R6/lib/libXext.a /usr/X11R6/lib/libXmu.a \
 -/usr/X11R6/lib/libXp.a /usr/lib/libm.a /me1/gordon/samtools/samtools-0.1.18/libbam.a /me1/gordon/samtools/samtools-0.1.18/bcftools/libbcf.a /me1/gordon/zlib/zlib-1.2.5/libz.a
 +
-+MOTIF_LIBS ?= -lXt -lXm
++MOTIF_LIBS ?= -lXm -lXt
 +ALL_LIBS = $(LIBS) $(MOTIF_LIBS) $(X11_LIBS) $(SAMTOOLS_LIBS)
  
  
diff --git a/sci-biology/consed/files/consed-29-fix-qa.patch b/sci-biology/consed/files/consed-29-fix-qa.patch
index 5bdf0264d25b..90e180da0174 100644
--- a/sci-biology/consed/files/consed-29-fix-qa.patch
+++ b/sci-biology/consed/files/consed-29-fix-qa.patch
@@ -127,6 +127,25 @@ Fix various QA violations, due to
     printf( "x = %d\n", pEvent->x );
     printf( "y = %d\n", pEvent->y );
     printf( "x_root = %d\n", pEvent->x_root );
+--- a/parseAceFile.cpp
++++ b/parseAceFile.cpp
+@@ -45,6 +45,7 @@
+ using namespace std;
+ #include    "basesegment.h"
+ #include    <stdio.h>
++#include    <stddef.h>
+ #include    <string.h>
+ #include    <sstream>
+ #include    "mbt_errors.h"
+@@ -292,7 +293,7 @@
+    char* szPossibleComp = szReadName + nLength - nCOMP;
+ 
+    if (memcmp( szPossibleComp, szCOMP, nCOMP ) == 0 ) {
+-      szPossibleComp = '\0';
++      szPossibleComp = NULL;
+       return( true );
+    }
+    else
 --- a/phaster2PhdBall.cpp
 +++ b/phaster2PhdBall.cpp
 @@ -547,7 +547,7 @@
diff --git a/sci-biology/pysam/Manifest b/sci-biology/pysam/Manifest
index 0172dca78024..5f340369c755 100644
--- a/sci-biology/pysam/Manifest
+++ b/sci-biology/pysam/Manifest
@@ -1,4 +1,4 @@
 AUX pysam-0.12-fix-buildsystem.patch 2356 BLAKE2B 95542f99b411a00eeaa24836cb7489bf2bbf690d804669f69f6f1a8c07f66d9c6ef34624eb511036cd36b1268b49959d38db497cb557e9cc40f3a35b2d349f4d SHA512 24c5c521ddd2e8a88a713c2cab2aedb0cd9a589e2ae87696a60815f9714e2b222a5e0824c5ac293f9023f6f772a599256a5c07228b5a2df40b62a1bf7616c84a
 DIST pysam-0.12.0.1.tar.gz 2672020 BLAKE2B 4bc6330405724f7b1126da91ba3338687f4dd17f015895f42b971f22ffbb6c32eda65e2667035a4cc830c0370b34d95d3aa6ae0f026b2b3276af1fd6841eed28 SHA512 31460ca98ad2ac5489905ffce76bfbb5bf4a295159f3cc8e088c78dcfbfc34b30d6f7871fd1454de01da98f82b7438ac2aca678a771d7b97ae0029a418f29f1d
-EBUILD pysam-0.12.0.1.ebuild 1201 BLAKE2B 993515294284464b345fd755747a557fae1578e11fc2b37a7389cbd7432e1e2bb022c8d64e5012d152efae8a03b60f67e231c7124711b8b805eb1bf2ee0c5590 SHA512 8e54c955bc1e479b8ebbd4fe463a780c301c7819fab8685af77c00199d81a6b31706671f534233451d7769fad1dca25b86cc062288fc04ec6b8b05b9594864d6
+EBUILD pysam-0.12.0.1.ebuild 1196 BLAKE2B 7223e799c6deb2396c19bf218c9cdc6b1b19a15a9368798fa91dbca4e314b804da6b742bc5953fb72334e4256e69779d2a44f55c6b7dadd5ba5deff4ce3e5324 SHA512 826a36fc59ede855efdea8e8b5069c86f66db99ed0bbeb2c29d196bee8efa9ae8ccd831e89befdce0a9806689ff0f0a513646c07dca91ac59c35a985bce3893b
 MISC metadata.xml 410 BLAKE2B ed86e3ffe38a306e581762625b37cf6596dc2a2ba404406ab12f681d5b48529764e281d40411bedbdf6016bc57d02adb705e8c8703b8120cf89b4961f75bed67 SHA512 38bcd511561b2466ef5d39473a6d1a838af0aff6eeb520307331fe0fc3177be3062fa0be39f48a333bb8e31841115cafd9dfb80a5985c316c9b8df1609f00810
diff --git a/sci-biology/pysam/pysam-0.12.0.1.ebuild b/sci-biology/pysam/pysam-0.12.0.1.ebuild
index a3f81bd40a96..d4f7a7430501 100644
--- a/sci-biology/pysam/pysam-0.12.0.1.ebuild
+++ b/sci-biology/pysam/pysam-0.12.0.1.ebuild
@@ -1,9 +1,9 @@
-# Copyright 1999-2017 Gentoo Foundation
+# Copyright 1999-2019 Gentoo Authors
 # Distributed under the terms of the GNU General Public License v2
 
 EAPI=6
 
-PYTHON_COMPAT=( python2_7 python3_{4,5,6} )
+PYTHON_COMPAT=( python2_7 python3_{5,6} )
 
 inherit distutils-r1