[gentoo-commits] proj/sci:master commit in: sci-biology/trinityrnaseq/, sci-biology/libBigWig/, sci-biology/graf-bin/, ...

[Justin Lecher]

commit:     307a9995cc3b29bd9726ad7ade53132c7c08f7fa
Author:     Justin Lecher <jlec <AT> gentoo <DOT> org>
AuthorDate: Sat Oct 27 20:03:05 2018 +0000
Commit:     Justin Lecher <jlec <AT> gentoo <DOT> org>
CommitDate: Sat Oct 27 20:07:56 2018 +0000
URL:        https://gitweb.gentoo.org/proj/sci.git/commit/?id=307a9995

Sort keywords

Signed-off-by: Justin Lecher <jlec <AT> gentoo.org>

 sci-biology/MolBioLib/MolBioLib-5.ebuild               | 2 +-
 sci-biology/bwa/bwa-0.7.17.ebuild                      | 2 +-
 sci-biology/gatk/gatk-3.8.1.ebuild                     | 2 +-
 sci-biology/gatk/gatk-9999.ebuild                      | 2 +-
 sci-biology/graf-bin/graf-bin-20171212.ebuild          | 2 +-
 sci-biology/igv/igv-2.3.81.ebuild                      | 2 +-
 sci-biology/igv/igv-2.3.88.ebuild                      | 2 +-
 sci-biology/igv/igv-2.3.92.ebuild                      | 2 +-
 sci-biology/jtreeview-bin/jtreeview-bin-1.1.6.4.ebuild | 2 +-
 sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild         | 2 +-
 sci-biology/jtreeview/jtreeview-9999.ebuild            | 2 +-
 sci-biology/libBigWig/libBigWig-0.4.0.ebuild           | 2 +-
 sci-biology/libBigWig/libBigWig-9999.ebuild            | 2 +-
 sci-biology/mira/mira-4.9.5.ebuild                     | 2 +-
 sci-biology/nxtrim/nxtrim-9999.ebuild                  | 2 +-
 sci-biology/oncotator/oncotator-1.9.2.0.ebuild         | 2 +-
 sci-biology/phusion/phusion-2.1c.ebuild                | 2 +-
 sci-biology/portrait/portrait-1.1.ebuild               | 3 +--
 sci-biology/pysamstats/pysamstats-0.24.2.ebuild        | 2 +-
 sci-biology/trinityrnaseq/trinityrnaseq-2.6.6.ebuild   | 2 +-
 sci-libs/fast5/fast5-0.6.4.ebuild                      | 2 +-
 sci-libs/openblas/openblas-0.2.19-r1.ebuild            | 2 +-
 sci-libs/openblas/openblas-0.2.20.ebuild               | 2 +-
 23 files changed, 23 insertions(+), 24 deletions(-)

diff --git a/sci-biology/MolBioLib/MolBioLib-5.ebuild b/sci-biology/MolBioLib/MolBioLib-5.ebuild
index 2775e2faf..681758724 100644
--- a/sci-biology/MolBioLib/MolBioLib-5.ebuild
+++ b/sci-biology/MolBioLib/MolBioLib-5.ebuild
@@ -9,7 +9,7 @@ SRC_URI="https://sourceforge.net/projects/molbiolib/files/MolBioLib_public.versi
 
 LICENSE="GPL-3"
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="" # does not build
 IUSE="doc"
 
 # contains bundled samtools-0.1.18 and bamtools (pezmaster31-bamtools-d553a62) which contains jsoncpp

diff --git a/sci-biology/bwa/bwa-0.7.17.ebuild b/sci-biology/bwa/bwa-0.7.17.ebuild
index 9d4e13e57..429ba43e6 100644
--- a/sci-biology/bwa/bwa-0.7.17.ebuild
+++ b/sci-biology/bwa/bwa-0.7.17.ebuild
@@ -12,7 +12,7 @@ SRC_URI="mirror://sourceforge/bio-bwa/${P}.tar.bz2"
 LICENSE="GPL-3"
 SLOT="0"
 IUSE=""
-KEYWORDS="~amd64 ~x64-macos ~x86"
+KEYWORDS="~amd64 ~x86 ~x64-macos"
 
 RDEPEND="dev-lang/perl"
 

diff --git a/sci-biology/gatk/gatk-3.8.1.ebuild b/sci-biology/gatk/gatk-3.8.1.ebuild
index c5e44747a..f46c1d322 100644
--- a/sci-biology/gatk/gatk-3.8.1.ebuild
+++ b/sci-biology/gatk/gatk-3.8.1.ebuild
@@ -18,7 +18,7 @@ EGIT_COMMIT="41147a655594c2aae6e2cad8462bd1648570b32b"
 LICENSE="MIT"
 SLOT="0"
 IUSE=""
-KEYWORDS=""${W} # 134MB 608.21 MiB and download git ~amd64""
+KEYWORDS="~amd64" # 608.21 MiB git download and 134MB "${W}"/.m2 download
 
 COMMON_DEPS=""
 DEPEND="

diff --git a/sci-biology/gatk/gatk-9999.ebuild b/sci-biology/gatk/gatk-9999.ebuild
index 83149fb0f..fc9db8986 100644
--- a/sci-biology/gatk/gatk-9999.ebuild
+++ b/sci-biology/gatk/gatk-9999.ebuild
@@ -21,7 +21,7 @@ EGIT_CLONE_TYPE="mirror"
 LICENSE="BSD-3" # since gatk-4
 SLOT="0"
 IUSE=""
-KEYWORDS=""${W} # 134MB 148.19 MB and download git"
+KEYWORDS="" # 148.19 MB git download and 134MB "${W}"/.m2 download
 
 COMMON_DEPS=""
 # gatk-4 needs java-1.8

diff --git a/sci-biology/graf-bin/graf-bin-20171212.ebuild b/sci-biology/graf-bin/graf-bin-20171212.ebuild
index 710eb5595..93d554892 100644
--- a/sci-biology/graf-bin/graf-bin-20171212.ebuild
+++ b/sci-biology/graf-bin/graf-bin-20171212.ebuild
@@ -12,7 +12,7 @@ SRC_URI="http://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/GetZip.cgi?zip_name=GR
 
 LICENSE="public-domain"
 SLOT="0"
-KEYWORDS="~amd64"
+KEYWORDS="~amd64" # 64bit exe only
 IUSE=""
 
 DEPEND=""

diff --git a/sci-biology/igv/igv-2.3.81.ebuild b/sci-biology/igv/igv-2.3.81.ebuild
index b870b0e98..5fabefeb3 100644
--- a/sci-biology/igv/igv-2.3.81.ebuild
+++ b/sci-biology/igv/igv-2.3.81.ebuild
@@ -26,7 +26,7 @@ HOMEPAGE="http://www.broadinstitute.org/igv/"
 LICENSE="LGPL-2.1"
 SLOT="0"
 IUSE=""
-KEYWORDS=""
+KEYWORDS="" # igv-2.3.81/src/com/iontorrent/views/FlowSignalDistributionPanel.java:222: error: cannot access PublicCloneable
 
 # actually more exactly the COMMON_DEPS should contain:
 #   >=dev-java/commons-compress-1.11 # use bundled library until dev-java/commons-compress is bumped, see bug #591696

diff --git a/sci-biology/igv/igv-2.3.88.ebuild b/sci-biology/igv/igv-2.3.88.ebuild
index b870b0e98..8011ea888 100644
--- a/sci-biology/igv/igv-2.3.88.ebuild
+++ b/sci-biology/igv/igv-2.3.88.ebuild
@@ -26,7 +26,7 @@ HOMEPAGE="http://www.broadinstitute.org/igv/"
 LICENSE="LGPL-2.1"
 SLOT="0"
 IUSE=""
-KEYWORDS=""
+KEYWORDS="" # see upstream issue #332
 
 # actually more exactly the COMMON_DEPS should contain:
 #   >=dev-java/commons-compress-1.11 # use bundled library until dev-java/commons-compress is bumped, see bug #591696

diff --git a/sci-biology/igv/igv-2.3.92.ebuild b/sci-biology/igv/igv-2.3.92.ebuild
index b870b0e98..8011ea888 100644
--- a/sci-biology/igv/igv-2.3.92.ebuild
+++ b/sci-biology/igv/igv-2.3.92.ebuild
@@ -26,7 +26,7 @@ HOMEPAGE="http://www.broadinstitute.org/igv/"
 LICENSE="LGPL-2.1"
 SLOT="0"
 IUSE=""
-KEYWORDS=""
+KEYWORDS="" # see upstream issue #332
 
 # actually more exactly the COMMON_DEPS should contain:
 #   >=dev-java/commons-compress-1.11 # use bundled library until dev-java/commons-compress is bumped, see bug #591696

diff --git a/sci-biology/jtreeview-bin/jtreeview-bin-1.1.6.4.ebuild b/sci-biology/jtreeview-bin/jtreeview-bin-1.1.6.4.ebuild
index 345c4eaf6..365c534bf 100644
--- a/sci-biology/jtreeview-bin/jtreeview-bin-1.1.6.4.ebuild
+++ b/sci-biology/jtreeview-bin/jtreeview-bin-1.1.6.4.ebuild
@@ -16,7 +16,7 @@ SRC_URI="
 
 LICENSE="GPL-2"
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="" # src_install is wrong somehow, TreeView.jar does not start
 IUSE=""
 
 DEPEND="

diff --git a/sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild b/sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild
index fab52dbd7..f1e58af01 100644
--- a/sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild
+++ b/sci-biology/jtreeview/jtreeview-1.1.6.4.ebuild
@@ -17,7 +17,7 @@ SRC_URI="
 
 LICENSE="GPL-2"
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="" # resulting java binary does not execute for me
 IUSE=""
 
 DEPEND=">virtual/jdk-1.5:*

diff --git a/sci-biology/jtreeview/jtreeview-9999.ebuild b/sci-biology/jtreeview/jtreeview-9999.ebuild
index 35d361230..0d7a1be51 100644
--- a/sci-biology/jtreeview/jtreeview-9999.ebuild
+++ b/sci-biology/jtreeview/jtreeview-9999.ebuild
@@ -12,7 +12,7 @@ EGIT_REPO_URI="https://bitbucket.org/TreeView3Dev/treeview3.git"
 
 LICENSE="MIT"
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="" # builds and executes fines
 IUSE=""
 
 DEPEND=">virtual/jdk-1.7:*"

diff --git a/sci-biology/libBigWig/libBigWig-0.4.0.ebuild b/sci-biology/libBigWig/libBigWig-0.4.0.ebuild
index 92c7fc505..bd71899f7 100644
--- a/sci-biology/libBigWig/libBigWig-0.4.0.ebuild
+++ b/sci-biology/libBigWig/libBigWig-0.4.0.ebuild
@@ -9,7 +9,7 @@ SRC_URI="https://github.com/dpryan79/libBigWig/archive/${PV}.tar.gz -> ${P}.tar.
 
 LICENSE="MIT"
 SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64 ~x86" # https://github.com/dpryan79/libBigWig/issues/30
 IUSE=""
 
 DEPEND="net-misc/curl"

diff --git a/sci-biology/libBigWig/libBigWig-9999.ebuild b/sci-biology/libBigWig/libBigWig-9999.ebuild
index a90395b0e..d470de250 100644
--- a/sci-biology/libBigWig/libBigWig-9999.ebuild
+++ b/sci-biology/libBigWig/libBigWig-9999.ebuild
@@ -11,7 +11,7 @@ EGIT_REPO_URI="https://github.com/dpryan79/libBigWig.git"
 
 LICENSE="MIT"
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="" # https://github.com/dpryan79/libBigWig/issues/30
 IUSE=""
 
 DEPEND="net-misc/curl"

diff --git a/sci-biology/mira/mira-4.9.5.ebuild b/sci-biology/mira/mira-4.9.5.ebuild
index 5193618bc..7c888a5e7 100644
--- a/sci-biology/mira/mira-4.9.5.ebuild
+++ b/sci-biology/mira/mira-4.9.5.ebuild
@@ -21,7 +21,7 @@ S="${WORKDIR}"/"${PN}"-"${MY_PV}"
 
 SLOT="0"
 LICENSE="GPL-2"
-KEYWORDS="~amd64 ~x86 ~x86-macos ~amd64-linux ~x86-linux"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux ~x86-macos"
 IUSE="doc"
 
 CDEPEND="

diff --git a/sci-biology/nxtrim/nxtrim-9999.ebuild b/sci-biology/nxtrim/nxtrim-9999.ebuild
index 5c9da016c..9a12a0226 100644
--- a/sci-biology/nxtrim/nxtrim-9999.ebuild
+++ b/sci-biology/nxtrim/nxtrim-9999.ebuild
@@ -11,7 +11,7 @@ EGIT_REPO_URI="https://github.com/sequencing/NxTrim.git"
 
 LICENSE="BSD-2"
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="" # https://github.com/sequencing/NxTrim/issues/32
 IUSE=""
 
 DEPEND=""

diff --git a/sci-biology/oncotator/oncotator-1.9.2.0.ebuild b/sci-biology/oncotator/oncotator-1.9.2.0.ebuild
index 486c669b2..77f439b6d 100644
--- a/sci-biology/oncotator/oncotator-1.9.2.0.ebuild
+++ b/sci-biology/oncotator/oncotator-1.9.2.0.ebuild
@@ -12,7 +12,7 @@ SRC_URI="https://github.com/broadinstitute/oncotator/archive/v${PV}.tar.gz -> ${
 
 LICENSE="oncotator"
 SLOT="0"
-KEYWORDS="~amd64 ~x86"
+KEYWORDS="~amd64 ~x86" # breaks silently during install because of python syntax errors
 IUSE=""
 
 RESTRICT="fetch"

diff --git a/sci-biology/phusion/phusion-2.1c.ebuild b/sci-biology/phusion/phusion-2.1c.ebuild
index 54161ec02..7c72e31fd 100644
--- a/sci-biology/phusion/phusion-2.1c.ebuild
+++ b/sci-biology/phusion/phusion-2.1c.ebuild
@@ -14,7 +14,7 @@ LICENSE="all-rights-reserved" # temporarily placed value
 # Availability
 # Phusion is undergoing a rewrite of the code to make this a portable package. It will be made available free of charge to academic sites, but requires licensing for commercial use. For more information please contact the authors.
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="" # compile process does not exit upon errors
 # one file does not compile
 # x86_64-pc-linux-gnu-gcc  -O2 -pipe -maes -mpclmul -mpopcnt -mavx -march=native  -o contigoverlap  contigoverlap.o  -lm
 # contigoverlap.o: In function `HashFasta':

diff --git a/sci-biology/portrait/portrait-1.1.ebuild b/sci-biology/portrait/portrait-1.1.ebuild
index fd50849cb..424ccfcd6 100644
--- a/sci-biology/portrait/portrait-1.1.ebuild
+++ b/sci-biology/portrait/portrait-1.1.ebuild
@@ -22,8 +22,7 @@ RDEPEND="
 # was only tested with sci-libs/libsvm-2.84
 
 src_install(){
-	sed -e 's/
-//' -i *.pl || die "Failed to convert from DOS line endings to Unix"
+	sed -e 's/
//' -i *.pl || die "Failed to convert from DOS line endings to Unix"
 	sed -e 's#/home/rtarrial/prog#/usr/bin#' -i *.pl
 	dobin *.pl
 	dodoc README.txt

diff --git a/sci-biology/pysamstats/pysamstats-0.24.2.ebuild b/sci-biology/pysamstats/pysamstats-0.24.2.ebuild
index b81dd558d..d6e1350a4 100644
--- a/sci-biology/pysamstats/pysamstats-0.24.2.ebuild
+++ b/sci-biology/pysamstats/pysamstats-0.24.2.ebuild
@@ -14,7 +14,7 @@ SRC_URI="mirror://pypi/p/${PN}/${P}.tar.gz"
 
 LICENSE="MIT"
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="" # needs working pysam, see bug #645060
 IUSE=""
 
 DEPEND="dev-python/cython

diff --git a/sci-biology/trinityrnaseq/trinityrnaseq-2.6.6.ebuild b/sci-biology/trinityrnaseq/trinityrnaseq-2.6.6.ebuild
index 49865431b..238766eed 100644
--- a/sci-biology/trinityrnaseq/trinityrnaseq-2.6.6.ebuild
+++ b/sci-biology/trinityrnaseq/trinityrnaseq-2.6.6.ebuild
@@ -14,7 +14,7 @@ SRC_URI="https://github.com/trinityrnaseq/trinityrnaseq/archive/Trinity-v${PV}.t
 
 LICENSE="BSD-BroadInstitute"
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="" # PERL5INC path is wrong when /usr/bin/Trinity is executed
 IUSE=""
 
 DEPEND=""

diff --git a/sci-libs/fast5/fast5-0.6.4.ebuild b/sci-libs/fast5/fast5-0.6.4.ebuild
index bae49ffe0..181c2e593 100644
--- a/sci-libs/fast5/fast5-0.6.4.ebuild
+++ b/sci-libs/fast5/fast5-0.6.4.ebuild
@@ -13,7 +13,7 @@ SRC_URI="https://github.com/mateidavid/fast5/archive/v${PV}.tar.gz -> ${P}.tar.g
 
 LICENSE="MIT"
 SLOT="0"
-KEYWORDS=""
+KEYWORDS="" # the install step is broken (python modules integration, upstream binary code)
 IUSE=""
 
 DEPEND="

diff --git a/sci-libs/openblas/openblas-0.2.19-r1.ebuild b/sci-libs/openblas/openblas-0.2.19-r1.ebuild
index 1bbbc4d8c..11b5deefb 100644
--- a/sci-libs/openblas/openblas-0.2.19-r1.ebuild
+++ b/sci-libs/openblas/openblas-0.2.19-r1.ebuild
@@ -14,7 +14,7 @@ SRC_URI="https://github.com/xianyi/OpenBLAS/tarball/v${PV} -> ${P}.tar.gz
 
 LICENSE="BSD"
 SLOT="0"
-KEYWORDS="~amd64 ~x64-macos ~x86 ~x86-macos ~amd64-linux ~x86-linux"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x64-macos ~x86-linux ~x86-macos"
 IUSE="dynamic openmp static-libs threads"
 
 RDEPEND=""

diff --git a/sci-libs/openblas/openblas-0.2.20.ebuild b/sci-libs/openblas/openblas-0.2.20.ebuild
index 4a352163a..f65231aa7 100644
--- a/sci-libs/openblas/openblas-0.2.20.ebuild
+++ b/sci-libs/openblas/openblas-0.2.20.ebuild
@@ -13,7 +13,7 @@ SRC_URI="https://github.com/xianyi/OpenBLAS/tarball/v${PV} -> ${P}.tar.gz"
 
 LICENSE="BSD"
 SLOT="0"
-KEYWORDS="~amd64 ~x64-macos ~x86 ~x86-macos ~amd64-linux ~x86-linux"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x64-macos ~x86-linux ~x86-macos"
 IUSE="dynamic openmp static-libs threads"
 
 RDEPEND=""