[gentoo-commits] proj/sci:master commit in: dev-java/htsjdk/
commit: a12a2d7f3f65eb66e44d3fc907f4b24e85ef201a Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Mon Mar 25 11:50:28 2019 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Mon Mar 25 11:50:28 2019 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=a12a2d7f dev-java/htsjdk: drop old 2.1.0 version dev-java/htsjdk/htsjdk-2.1.0.ebuild | 47 - 1 file changed, 47 deletions(-) diff --git a/dev-java/htsjdk/htsjdk-2.1.0.ebuild b/dev-java/htsjdk/htsjdk-2.1.0.ebuild deleted file mode 100644 index c94f79781..0 --- a/dev-java/htsjdk/htsjdk-2.1.0.ebuild +++ /dev/null @@ -1,47 +0,0 @@ -# Copyright 1999-2019 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=7 - -JAVA_PKG_IUSE="doc source" - -inherit java-pkg-2 java-ant-2 - -DESCRIPTION="Java API for high-throughput sequencing data (HTS) formats" -HOMEPAGE="https://samtools.github.io/htsjdk/"; -SRC_URI="https://github.com/samtools/htsjdk/archive/${PV}.tar.gz -> ${P}.tar.gz" - -LICENSE="MIT" -SLOT="0" -IUSE="" -KEYWORDS="~amd64 ~x86" - -CDEPEND="dev-java/commons-jexl:2 - dev-java/commons-compress:0 - dev-java/commons-logging:0" - -DEPEND=">=virtual/jdk-1.8 - ${CDEPEND}" -RDEPEND=">=virtual/jre-1.8 - ${CDEPEND}" - -EANT_BUILD_TARGET="all" -EANT_NEEDS_TOOLS="true" -JAVA_ANT_REWRITE_CLASSPATH="true" -EANT_GENTOO_CLASSPATH="commons-jexl-2,commons-compress,commons-logging" - -java_prepare() { - default - rm -v lib/{commons-compress,commons-jexl,commons-logging}*.jar || die -} - -src_install() { - cd dist || die - - for i in *.jar; do - java-pkg_newjar $i ${i/-[0-9]*.jar/.jar} - done - - use source && java-pkg_dosrc "${S}"/src/java/* - use doc && java-pkg_dojavadoc "${S}"/javadoc -}
[gentoo-commits] proj/sci:master commit in: dev-java/htsjdk/
commit: 6d3f8d736bf1a9653f516c3e959a97948c61f843 Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Mon Mar 25 11:08:21 2019 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Mon Mar 25 11:08:21 2019 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6d3f8d73 dev-java/htsjdk: 2.3.0 which was the last using Apache ant Bump to EAPI7 Building does not work since sandbox has now no network access. Downloading https://services.gradle.org/distributions/gradle-5.2.1-bin.zip Exception in thread "main" java.net.SocketException: Network is unreachable (connect failed) htsjdk calls some `gradlew` wrapper so the recent ebuilds need more work to use dev-java/gradle-bin package. Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs fold.natur.cuni.cz> dev-java/htsjdk/htsjdk-2.1.0.ebuild | 4 ++-- dev-java/htsjdk/{htsjdk-2.5.1.ebuild => htsjdk-2.19.0.ebuild} | 7 --- dev-java/htsjdk/{htsjdk-2.2.2.ebuild => htsjdk-2.3.0.ebuild} | 4 ++-- dev-java/htsjdk/htsjdk-.ebuild| 7 --- 4 files changed, 12 insertions(+), 10 deletions(-) diff --git a/dev-java/htsjdk/htsjdk-2.1.0.ebuild b/dev-java/htsjdk/htsjdk-2.1.0.ebuild index fc2dd6e8a..c94f79781 100644 --- a/dev-java/htsjdk/htsjdk-2.1.0.ebuild +++ b/dev-java/htsjdk/htsjdk-2.1.0.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2019 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 JAVA_PKG_IUSE="doc source" diff --git a/dev-java/htsjdk/htsjdk-2.5.1.ebuild b/dev-java/htsjdk/htsjdk-2.19.0.ebuild similarity index 91% rename from dev-java/htsjdk/htsjdk-2.5.1.ebuild rename to dev-java/htsjdk/htsjdk-2.19.0.ebuild index 755a6fa1f..349e56673 100644 --- a/dev-java/htsjdk/htsjdk-2.5.1.ebuild +++ b/dev-java/htsjdk/htsjdk-2.19.0.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2019 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 JAVA_PKG_IUSE="doc source" @@ -18,7 +18,8 @@ KEYWORDS="" CDEPEND="dev-java/commons-jexl:2 dev-java/commons-compress:0 - dev-java/commons-logging:0" + dev-java/commons-logging:0 + dev-java/gradle-bin:*" DEPEND=">=virtual/jdk-1.8 ${CDEPEND}" diff --git a/dev-java/htsjdk/htsjdk-2.2.2.ebuild b/dev-java/htsjdk/htsjdk-2.3.0.ebuild similarity index 95% rename from dev-java/htsjdk/htsjdk-2.2.2.ebuild rename to dev-java/htsjdk/htsjdk-2.3.0.ebuild index fc2dd6e8a..c94f79781 100644 --- a/dev-java/htsjdk/htsjdk-2.2.2.ebuild +++ b/dev-java/htsjdk/htsjdk-2.3.0.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2016 Gentoo Foundation +# Copyright 1999-2019 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 JAVA_PKG_IUSE="doc source" diff --git a/dev-java/htsjdk/htsjdk-.ebuild b/dev-java/htsjdk/htsjdk-.ebuild index b4a3c1441..2123bbc55 100644 --- a/dev-java/htsjdk/htsjdk-.ebuild +++ b/dev-java/htsjdk/htsjdk-.ebuild @@ -1,7 +1,7 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2019 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=6 +EAPI=7 JAVA_PKG_IUSE="doc source" @@ -18,7 +18,8 @@ KEYWORDS="" CDEPEND="dev-java/commons-jexl:2 dev-java/commons-compress:0 - dev-java/commons-logging:0" + dev-java/commons-logging:0 + dev-java/gradle-bin:*" DEPEND=">=virtual/jdk-1.8 ${CDEPEND}"
[gentoo-commits] proj/sci:master commit in: dev-java/htsjdk/
commit: 6e6616f8521d20074bbca6522e2a5570718d5736 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Wed Jan 11 23:26:50 2017 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Wed Jan 11 23:26:50 2017 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=6e6616f8 dev-java/htsjdk: add a live ebuild, add a note Not sure if current build system still creates $HOME/.git but from reading github Issues it seem it is still needed: users are even asked to run 'git clone' to work around the issue when gradle fails to do that. Package-Manager: Portage-2.3.3, Repoman-2.3.1 dev-java/htsjdk/htsjdk-2.5.1.ebuild| 4 ++-- .../{htsjdk-2.5.1.ebuild => htsjdk-.ebuild}| 26 +++--- 2 files changed, 15 insertions(+), 15 deletions(-) diff --git a/dev-java/htsjdk/htsjdk-2.5.1.ebuild b/dev-java/htsjdk/htsjdk-2.5.1.ebuild index 0f1e162..6ba163f 100644 --- a/dev-java/htsjdk/htsjdk-2.5.1.ebuild +++ b/dev-java/htsjdk/htsjdk-2.5.1.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 # $Id$ @@ -36,7 +36,7 @@ java_prepare(){ } src_compile(){ - # work around gradle writing $HOME/.gradle + # work around gradle writing $HOME/.gradle and $HOME/.git # https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965 GRADLE_USER_HOME="${WORKDIR}" ./gradlew build || die } diff --git a/dev-java/htsjdk/htsjdk-2.5.1.ebuild b/dev-java/htsjdk/htsjdk-.ebuild similarity index 59% copy from dev-java/htsjdk/htsjdk-2.5.1.ebuild copy to dev-java/htsjdk/htsjdk-.ebuild index 0f1e162..e957674 100644 --- a/dev-java/htsjdk/htsjdk-2.5.1.ebuild +++ b/dev-java/htsjdk/htsjdk-.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 # $Id$ @@ -6,11 +6,11 @@ EAPI="6" JAVA_PKG_IUSE="doc source" -inherit java-pkg-2 java-ant-2 +inherit git-r3 java-pkg-2 java-ant-2 DESCRIPTION="Java API for high-throughput sequencing data (HTS) formats." HOMEPAGE="https://samtools.github.io/htsjdk/"; -SRC_URI="https://github.com/samtools/htsjdk/archive/${PV}.tar.gz -> ${P}.tar.gz" +EGIT_REPO_URI="https://github.com/samtools/htsjdk.git"; LICENSE="MIT" SLOT="0" @@ -36,18 +36,18 @@ java_prepare(){ } src_compile(){ - # work around gradle writing $HOME/.gradle + # work around gradle writing $HOME/.gradle and $HOME/.git # https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965 - GRADLE_USER_HOME="${WORKDIR}" ./gradlew build || die + GRADLE_USER_HOME="${WORKDIR}" ./gradlew || die } src_install() { - cd dist || die - - for i in *.jar; do - java-pkg_newjar $i ${i/-[0-9]*.jar/.jar} - done - - use source && java-pkg_dosrc "${S}"/src/java/* - use doc && java-pkg_dojavadoc "${S}"/javadoc + cd build/libs || die + + #for i in *-SNAPSHOT.jar; do + # java-pkg_newjar $i ${i/-[0-9]*.jar/.jar} + #done + java-pkg_newjar "${S}"/build/libs/*-SNAPSHOT.jar htsjdk.jar + use source && java-pkg_dosrc "${S}"/build/libs/*-sources.jar + use doc && java-pkg_dojavadoc "${S}"/build/libs/*-javadoc.jar }
[gentoo-commits] proj/sci:master commit in: dev-java/htsjdk/
commit: d0811884dba63b23093aa0cf580171e4ba51a36f Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Tue Jul 12 21:42:07 2016 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Tue Jul 12 21:42:07 2016 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=d0811884 dev-java/htsjdk: make gradle use relocated $HOME/.gradle/ inside sanbox paths This dies later because .git/ directory does not exist (probably $HOME/.git/ was looked up). Package-Manager: portage-2.2.28 dev-java/htsjdk/htsjdk-2.5.1.ebuild | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/dev-java/htsjdk/htsjdk-2.5.1.ebuild b/dev-java/htsjdk/htsjdk-2.5.1.ebuild index b63c0d2..0f1e162 100644 --- a/dev-java/htsjdk/htsjdk-2.5.1.ebuild +++ b/dev-java/htsjdk/htsjdk-2.5.1.ebuild @@ -36,7 +36,9 @@ java_prepare(){ } src_compile(){ - ./gradlew build || die + # work around gradle writing $HOME/.gradle + # https://github.com/samtools/htsjdk/issues/660#issuecomment-232155965 + GRADLE_USER_HOME="${WORKDIR}" ./gradlew build || die } src_install() {
[gentoo-commits] proj/sci:master commit in: dev-java/htsjdk/
commit: 691de03a081a82665985b69eb879c6be3ecd7f7e Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Tue Jul 12 16:31:39 2016 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Tue Jul 12 16:31:39 2016 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=691de03a dev-java/htsjdk: added 2.1.0 version needed=bundled so far in cramtools-3.0 Package-Manager: portage-2.2.28 dev-java/htsjdk/htsjdk-2.1.0.ebuild | 48 + 1 file changed, 48 insertions(+) diff --git a/dev-java/htsjdk/htsjdk-2.1.0.ebuild b/dev-java/htsjdk/htsjdk-2.1.0.ebuild new file mode 100644 index 000..ca2cdd9 --- /dev/null +++ b/dev-java/htsjdk/htsjdk-2.1.0.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="6" + +JAVA_PKG_IUSE="doc source" + +inherit java-pkg-2 java-ant-2 + +DESCRIPTION="Java API for high-throughput sequencing data (HTS) formats." +HOMEPAGE="https://samtools.github.io/htsjdk/"; +SRC_URI="https://github.com/samtools/htsjdk/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +CDEPEND="dev-java/commons-jexl:2 + dev-java/commons-compress:0 + dev-java/commons-logging:0" + +DEPEND=">=virtual/jdk-1.8 + ${CDEPEND}" +RDEPEND=">=virtual/jre-1.8 + ${CDEPEND}" + +EANT_BUILD_TARGET="all" +EANT_NEEDS_TOOLS="true" +JAVA_ANT_REWRITE_CLASSPATH="true" +EANT_GENTOO_CLASSPATH="commons-jexl-2,commons-compress,commons-logging" + +java_prepare() { + default + rm -v lib/{commons-compress,commons-jexl,commons-logging}*.jar || die +} + +src_install() { + cd dist || die + + for i in *.jar; do + java-pkg_newjar $i ${i/-[0-9]*.jar/.jar} + done + + use source && java-pkg_dosrc "${S}"/src/java/* + use doc && java-pkg_dojavadoc "${S}"/javadoc +}
[gentoo-commits] proj/sci:master commit in: dev-java/htsjdk/
commit: 9ce6536356df2dffa9672161ae47b8de609c7682 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Tue Jul 12 16:28:58 2016 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Tue Jul 12 16:28:58 2016 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=9ce65363 dev-java/htsjdk: re-added back 2.2.2 version due to picard-2 Package-Manager: portage-2.2.28 dev-java/htsjdk/htsjdk-2.2.2.ebuild | 48 + 1 file changed, 48 insertions(+) diff --git a/dev-java/htsjdk/htsjdk-2.2.2.ebuild b/dev-java/htsjdk/htsjdk-2.2.2.ebuild new file mode 100644 index 000..ca2cdd9 --- /dev/null +++ b/dev-java/htsjdk/htsjdk-2.2.2.ebuild @@ -0,0 +1,48 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="6" + +JAVA_PKG_IUSE="doc source" + +inherit java-pkg-2 java-ant-2 + +DESCRIPTION="Java API for high-throughput sequencing data (HTS) formats." +HOMEPAGE="https://samtools.github.io/htsjdk/"; +SRC_URI="https://github.com/samtools/htsjdk/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +CDEPEND="dev-java/commons-jexl:2 + dev-java/commons-compress:0 + dev-java/commons-logging:0" + +DEPEND=">=virtual/jdk-1.8 + ${CDEPEND}" +RDEPEND=">=virtual/jre-1.8 + ${CDEPEND}" + +EANT_BUILD_TARGET="all" +EANT_NEEDS_TOOLS="true" +JAVA_ANT_REWRITE_CLASSPATH="true" +EANT_GENTOO_CLASSPATH="commons-jexl-2,commons-compress,commons-logging" + +java_prepare() { + default + rm -v lib/{commons-compress,commons-jexl,commons-logging}*.jar || die +} + +src_install() { + cd dist || die + + for i in *.jar; do + java-pkg_newjar $i ${i/-[0-9]*.jar/.jar} + done + + use source && java-pkg_dosrc "${S}"/src/java/* + use doc && java-pkg_dojavadoc "${S}"/javadoc +}
[gentoo-commits] proj/sci:master commit in: dev-java/htsjdk/
commit: 091fd4549ad2edd83419e0f645cc902a2f71ae23 Author: Martin Mokrejš fold natur cuni cz> AuthorDate: Tue Jul 12 15:53:53 2016 + Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Tue Jul 12 15:53:53 2016 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=091fd454 dev-java/htsjdk: version bump, moved from ant to gradle, SANDBOX VIOLATION Package-Manager: portage-2.2.28 dev-java/htsjdk/{htsjdk-2.2.2.ebuild => htsjdk-2.5.1.ebuild} | 9 ++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/dev-java/htsjdk/htsjdk-2.2.2.ebuild b/dev-java/htsjdk/htsjdk-2.5.1.ebuild similarity index 89% rename from dev-java/htsjdk/htsjdk-2.2.2.ebuild rename to dev-java/htsjdk/htsjdk-2.5.1.ebuild index ca2cdd9..b63c0d2 100644 --- a/dev-java/htsjdk/htsjdk-2.2.2.ebuild +++ b/dev-java/htsjdk/htsjdk-2.5.1.ebuild @@ -15,7 +15,7 @@ SRC_URI="https://github.com/samtools/htsjdk/archive/${PV}.tar.gz -> ${P}.tar.gz" LICENSE="MIT" SLOT="0" IUSE="" -KEYWORDS="~amd64 ~x86" +KEYWORDS="" # SANDBOX VIOLATION CDEPEND="dev-java/commons-jexl:2 dev-java/commons-compress:0 @@ -31,9 +31,12 @@ EANT_NEEDS_TOOLS="true" JAVA_ANT_REWRITE_CLASSPATH="true" EANT_GENTOO_CLASSPATH="commons-jexl-2,commons-compress,commons-logging" -java_prepare() { +java_prepare(){ default - rm -v lib/{commons-compress,commons-jexl,commons-logging}*.jar || die +} + +src_compile(){ + ./gradlew build || die } src_install() {
[gentoo-commits] proj/sci:master commit in: dev-java/htsjdk/
commit: f14032b578bf9d6b6bd840a05ad00f47867207f8 Author: Johann Schmitz gentoo org> AuthorDate: Sun Apr 24 06:13:12 2016 + Commit: Justin Lecher gentoo org> CommitDate: Sun Apr 24 06:13:12 2016 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=f14032b5 dev-java/htsjdk: Fixed error with EAPI=6 Package-Manager: portage-2.2.26 dev-java/htsjdk/htsjdk-2.2.2.ebuild | 1 + 1 file changed, 1 insertion(+) diff --git a/dev-java/htsjdk/htsjdk-2.2.2.ebuild b/dev-java/htsjdk/htsjdk-2.2.2.ebuild index 9950f1f..ca2cdd9 100644 --- a/dev-java/htsjdk/htsjdk-2.2.2.ebuild +++ b/dev-java/htsjdk/htsjdk-2.2.2.ebuild @@ -32,6 +32,7 @@ JAVA_ANT_REWRITE_CLASSPATH="true" EANT_GENTOO_CLASSPATH="commons-jexl-2,commons-compress,commons-logging" java_prepare() { + default rm -v lib/{commons-compress,commons-jexl,commons-logging}*.jar || die }
[gentoo-commits] proj/sci:master commit in: dev-java/htsjdk/
commit: c3ab7823c9462b681b308ab69346acc77cea683f Author: Johann Schmitz gentoo org> AuthorDate: Sun Apr 24 06:08:19 2016 + Commit: Justin Lecher gentoo org> CommitDate: Sun Apr 24 06:10:23 2016 + URL:https://gitweb.gentoo.org/proj/sci.git/commit/?id=c3ab7823 dev-java/htsjdk: New ebuild (dependency of picard-2) Package-Manager: portage-2.2.26 dev-java/htsjdk/htsjdk-2.2.2.ebuild | 47 + dev-java/htsjdk/metadata.xml| 15 2 files changed, 62 insertions(+) diff --git a/dev-java/htsjdk/htsjdk-2.2.2.ebuild b/dev-java/htsjdk/htsjdk-2.2.2.ebuild new file mode 100644 index 000..9950f1f --- /dev/null +++ b/dev-java/htsjdk/htsjdk-2.2.2.ebuild @@ -0,0 +1,47 @@ +# Copyright 1999-2016 Gentoo Foundation +# Distributed under the terms of the GNU General Public License v2 +# $Id$ + +EAPI="6" + +JAVA_PKG_IUSE="doc source" + +inherit java-pkg-2 java-ant-2 + +DESCRIPTION="Java API for high-throughput sequencing data (HTS) formats." +HOMEPAGE="https://samtools.github.io/htsjdk/"; +SRC_URI="https://github.com/samtools/htsjdk/archive/${PV}.tar.gz -> ${P}.tar.gz" + +LICENSE="MIT" +SLOT="0" +IUSE="" +KEYWORDS="~amd64 ~x86" + +CDEPEND="dev-java/commons-jexl:2 + dev-java/commons-compress:0 + dev-java/commons-logging:0" + +DEPEND=">=virtual/jdk-1.8 + ${CDEPEND}" +RDEPEND=">=virtual/jre-1.8 + ${CDEPEND}" + +EANT_BUILD_TARGET="all" +EANT_NEEDS_TOOLS="true" +JAVA_ANT_REWRITE_CLASSPATH="true" +EANT_GENTOO_CLASSPATH="commons-jexl-2,commons-compress,commons-logging" + +java_prepare() { + rm -v lib/{commons-compress,commons-jexl,commons-logging}*.jar || die +} + +src_install() { + cd dist || die + + for i in *.jar; do + java-pkg_newjar $i ${i/-[0-9]*.jar/.jar} + done + + use source && java-pkg_dosrc "${S}"/src/java/* + use doc && java-pkg_dojavadoc "${S}"/javadoc +} diff --git a/dev-java/htsjdk/metadata.xml b/dev-java/htsjdk/metadata.xml new file mode 100644 index 000..513e863 --- /dev/null +++ b/dev-java/htsjdk/metadata.xml @@ -0,0 +1,15 @@ + +http://www.gentoo.org/dtd/metadata.dtd";> + + + er...@gentoo.org + Johann Schmitz (ercpe) + + + sci-biol...@gentoo.org + Gentoo Biology Project + + + picard + +