commit: cdd700699de2b2f26d6265fc317f7003d89a2b68 Author: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> AuthorDate: Tue Jan 19 10:46:45 2021 +0000 Commit: Andrew Ammerlaan <andrewammerlaan <AT> riseup <DOT> net> CommitDate: Tue Jan 19 10:47:03 2021 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=cdd70069
sci-biology/OBO-Edit: fix fetching Package-Manager: Portage-3.0.13, Repoman-3.0.2 Signed-off-by: Andrew Ammerlaan <andrewammerlaan <AT> riseup.net> profiles/package.mask | 1 - sci-biology/OBO-Edit/OBO-Edit-2.1.0.ebuild | 53 ---------------------- ...O-Edit-2.1.1.6.ebuild => OBO-Edit-2.3.1.ebuild} | 41 +++++++---------- 3 files changed, 16 insertions(+), 79 deletions(-) diff --git a/profiles/package.mask b/profiles/package.mask index 6afd1ca5c..297270976 100644 --- a/profiles/package.mask +++ b/profiles/package.mask @@ -89,4 +89,3 @@ sci-biology/mreps sci-biology/mRNAmarkup sci-biology/mrsfast sci-biology/MuSeqBox -sci-biology/OBO-Edit diff --git a/sci-biology/OBO-Edit/OBO-Edit-2.1.0.ebuild b/sci-biology/OBO-Edit/OBO-Edit-2.1.0.ebuild deleted file mode 100644 index 1724e13c3..000000000 --- a/sci-biology/OBO-Edit/OBO-Edit-2.1.0.ebuild +++ /dev/null @@ -1,53 +0,0 @@ -# Copyright 1999-2020 Gentoo Authors -# Distributed under the terms of the GNU General Public License v2 - -EAPI=5 - -inherit eutils toolchain-funcs versionator java-pkg-2 - -MY_PV=$(replace_all_version_separators '-') - -DESCRIPTION="Java-based editor optimized for the OBO biological ontology file format" -HOMEPAGE="http://www.oboedit.org/"; # no https, invalid certificate -SRC_URI=" - https://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%20${PV}/${MY_PV}_unix_install4j.sh/download -> OBO-Edit_unix_install4j-${PV}.sh - https://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%20${PV}/ReleaseNotes-${PV}.txt"; - -LICENSE="OBO-Edit" # Artistic-like -SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" - -DEPEND="app-arch/rpm2targz" -RDEPEND="virtual/jre" - -S="${WORKDIR}" - -src_install(){ - dodir /opt/OBO-Edit2/.install4j - - sed \ - -e "s#\"\${D}\"#"${D}"#g" \ - "${FILESDIR}"/response.varfile \ - > "${D}"/opt/OBO-Edit2/.install4j/response.varfile || die "sed failed" - - sed \ - -e "s#/bin/java\" -Dinstall4j.jvmDir#/bin/java\" -Duser.home="${D}"/../temp -Dinstall4j.jvmDir#" \ - -i "${DISTDIR}"/OBO-Edit_unix_install4j-"${PV}".sh || die "failed to set userHome value" - - sh "${DISTDIR}"/OBO-Edit_unix_install4j-"${PV}".sh \ - -q -overwrite \ - --varfile="${D}"/opt/OBO-Edit2/.install4j/response.varfile \ - --destination="${D}"/opt/OBO-Edit2 \ - -dir "${D}"/opt/OBO-Edit2 \ - || die "Failed to run the self-extracting ${DISTDIR}/OBO-Edit_unix_install4j-"${PV}".sh file" - find . -name firstrun -delete || die - - esvn_clean - - insinto /opt/ - doins -r OBO-Edit2 - chmod 755 "${ED}"/opt/OBO-Edit2/* || die - - dodoc "${DISTDIR}"/ReleaseNotes-2.1.0.txt -} diff --git a/sci-biology/OBO-Edit/OBO-Edit-2.1.1.6.ebuild b/sci-biology/OBO-Edit/OBO-Edit-2.3.1.ebuild similarity index 60% rename from sci-biology/OBO-Edit/OBO-Edit-2.1.1.6.ebuild rename to sci-biology/OBO-Edit/OBO-Edit-2.3.1.ebuild index e4d3b9304..29550a0fc 100644 --- a/sci-biology/OBO-Edit/OBO-Edit-2.1.1.6.ebuild +++ b/sci-biology/OBO-Edit/OBO-Edit-2.3.1.ebuild @@ -1,25 +1,19 @@ -# Copyright 1999-2020 Gentoo Authors +# Copyright 1999-2021 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 -EAPI=5 +EAPI=7 -inherit eutils toolchain-funcs versionator java-pkg-2 +inherit toolchain-funcs java-pkg-2 -# MY_PV=$(replace_all_version_separators '-') -MY_PV="oboedit_2_1_1-b6" -MY_VER="2.1.1-b6" -MY_PV=$(replace_all_version_separators '-') +MY_PV="${PV//./_}" DESCRIPTION="Java-based editor optimized for the OBO biological ontology file format" HOMEPAGE="http://www.oboedit.org/"; # no https, invalid certificate -SRC_URI=" - https://downloads.sourceforge.net/project/geneontology/OBO-Edit%202%20%5BLatest%20versions%5D/${MY_VER}/${MY_PV}_unix_install4j.sh -> ${PN}_unix_install4j-${PV}.sh - https://sourceforge.net/projects/geneontology/files/OBO-Edit%202%20%5BLatest%20versions%5D/${MY_PV}/ReleaseNotes-${MY_VER}.txt -> ${PN}_ReleaseNotes-${PV}.txt" +SRC_URI="https://downloads.sourceforge.net/project/geneontology/OBO-Edit%202%20%5BLatest%20versions%5D/OBO-Edit%20${PV}/oboedit_${MY_PV}_unix_install4j.sh -> ${PN}_unix_install4j-${PV}.sh" LICENSE="OBO-Edit" # Artistic-like SLOT="0" -KEYWORDS="~amd64 ~x86" -IUSE="" +KEYWORDS="" DEPEND="app-arch/rpm2targz" RDEPEND="virtual/jre" @@ -35,14 +29,16 @@ pkg_setup() { } src_prepare(){ + default dodir /opt/OBO-Edit2/.install4j /usr/bin + cp "${DISTDIR}"/"${PN}"_unix_install4j-"${PV}".sh "${WORKDIR}" || die # /var/tmp/portage/sci-biology/OBO-Edit-2.1.1.6/image//opt/OBO-Edit2/.install4j/response.varfile sed -e "s#\"\${D}\"#"${D}"#g" "${FILESDIR}"/response.varfile | \ - sed -e "s#\"\${TMPDIR}\"#"${TMPDIR}"#g" | \ + sed -e "s#\"\${HOME}\"#"${HOME}"#g" | \ sed -e "[email protected]=/usr/local/bin@#sys.symlinkDir=/usr/local/bin@" \ > "${D}"/opt/OBO-Edit2/.install4j/response.varfile || die "sed failed" - cp -r "${D}"/opt/OBO-Edit2/.install4j "${TMPDIR}" || die + cp -r "${D}"/opt/OBO-Edit2/.install4j "${HOME}" || die # for user root install4j writes into /opt/icedtea-bin-7.2.0/jre/.systemPrefs or whatever it # found via JAVA_HOME or similar variables @@ -50,11 +46,11 @@ src_prepare(){ # trick setting -Djava.util.prefs.systemRoot="${TMPDIR}" does not work sed \ - -e "s@/bin/java\" -Dinstall4j.jvmDir=\"\$app_java_home\"@/bin/java\" -Duser.home="${TMPDIR}" -Dinstall4j.jvmDir="${TMPDIR}" -Dsys.symlinkDir="${D}"usr/bin -Djava.util.prefs.systemRoot="${TMPDIR}"@" \ - -i "${DISTDIR}"/"${PN}"_unix_install4j-"${PV}".sh \ + -e "s@/bin/java\" -Dinstall4j.jvmDir=\"\$app_java_home\"@/bin/java\" -Duser.home="${HOME}" -Dinstall4j.jvmDir="${HOME}" -Dsys.symlinkDir="${D}"usr/bin -Djava.util.prefs.systemRoot="${HOME}"@" \ + -i "${WORKDIR}"/"${PN}"_unix_install4j-"${PV}".sh \ || die "failed to set userHome and jvmDir where JAVA .systemPrefs can be found" - chmod u+rx "${DISTDIR}"/"${PN}"_unix_install4j-"${PV}".sh || die + chmod u+rx "${WORKDIR}/${PN}"_unix_install4j-"${PV}".sh || die } src_install(){ @@ -64,19 +60,14 @@ src_install(){ # chmod a-w "${TMPDIR}"/.install4j/response.varfile INSTALL4J_KEEP_TEMP="yes" \ - HOME="${TMPDIR}" \ - sh "${DISTDIR}"/"${PN}"_unix_install4j-"${PV}".sh -q \ - --varfile="${TMPDIR}"/.install4j/response.varfile \ + sh "${WORKDIR}"/"${PN}"_unix_install4j-"${PV}".sh -q \ + --varfile="${HOME}"/.install4j/response.varfile \ --destination="${D}"/opt/OBO-Edit2 \ -dir "${D}"/opt/OBO-Edit2 \ - || die "Failed to run the self-extracting ${DISTDIR}/${PN}_unix_install4j-${PV}.sh file" + || die "Failed to run the self-extracting ${WORKDIR}/${PN}_unix_install4j-${PV}.sh file" find . -name firstrun -delete || die - esvn_clean - - dodoc "${DISTDIR}"/"${PN}"_ReleaseNotes-"${PV}".txt - echo "PATH=/opt/OBO-Edit2" > 99OBO-Edit || die doenvd 99OBO-Edit }
