From mboxrd@z Thu Jan 1 00:00:00 1970 Return-Path: Received: from lists.gentoo.org (pigeon.gentoo.org [208.92.234.80]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (No client certificate requested) by finch.gentoo.org (Postfix) with ESMTPS id 2DDA7138334 for ; Mon, 25 Jun 2018 12:14:28 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 1F932E09BB; Mon, 25 Jun 2018 12:14:26 +0000 (UTC) Received: from smtp.gentoo.org (smtp.gentoo.org [140.211.166.183]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by pigeon.gentoo.org (Postfix) with ESMTPS id C9A8DE09BB for ; Mon, 25 Jun 2018 12:14:25 +0000 (UTC) Received: from oystercatcher.gentoo.org (unknown [IPv6:2a01:4f8:202:4333:225:90ff:fed9:fc84]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (No client certificate requested) by smtp.gentoo.org (Postfix) with ESMTPS id 14397335CA3 for ; Mon, 25 Jun 2018 12:14:23 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 5CE3B2E2 for ; Mon, 25 Jun 2018 12:14:21 +0000 (UTC) From: "Martin Mokrejs" To: gentoo-commits@lists.gentoo.org Content-Transfer-Encoding: 8bit Content-type: text/plain; charset=UTF-8 Reply-To: gentoo-dev@lists.gentoo.org, "Martin Mokrejs" Message-ID: <1529928846.0f24b4873a8cc38eaf05aa590d26f40a640e4b4b.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/salmon/files/, sci-biology/salmon/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/salmon/files/salmon-0.10.2_fix_lib_dir.patch sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch sci-biology/salmon/salmon-0.10.2.ebuild sci-biology/salmon/salmon-9999.ebuild X-VCS-Directories: sci-biology/salmon/ sci-biology/salmon/files/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: 0f24b4873a8cc38eaf05aa590d26f40a640e4b4b X-VCS-Branch: master Date: Mon, 25 Jun 2018 12:14:21 +0000 (UTC) Precedence: bulk List-Post: List-Help: List-Unsubscribe: List-Subscribe: List-Id: Gentoo Linux mail X-BeenThere: gentoo-commits@lists.gentoo.org X-Archives-Salt: a11d5507-cba8-41dd-86be-1ba960926e56 X-Archives-Hash: 3ad39262690829ceef6738241fbf4397 commit: 0f24b4873a8cc38eaf05aa590d26f40a640e4b4b Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Mon Jun 25 12:14:06 2018 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Mon Jun 25 12:14:06 2018 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=0f24b487 sci-biology/salmon: drop calls to curl, fix libdir This zaps all calls to curl downloads during compile time except those for Google tbb. It should not get executed anyway as the dev-cpp/tbb dependency is enforced. Package-Manager: Portage-2.3.40, Repoman-2.3.9 .../salmon/files/salmon-0.10.2_fix_lib_dir.patch | 22 +++ .../files/salmon-0.10.2_remove_curl_calls.patch | 200 +++++++++++++++++++++ sci-biology/salmon/salmon-0.10.2.ebuild | 23 ++- sci-biology/salmon/salmon-9999.ebuild | 9 +- 4 files changed, 244 insertions(+), 10 deletions(-) diff --git a/sci-biology/salmon/files/salmon-0.10.2_fix_lib_dir.patch b/sci-biology/salmon/files/salmon-0.10.2_fix_lib_dir.patch new file mode 100644 index 000000000..eb606c00c --- /dev/null +++ b/sci-biology/salmon/files/salmon-0.10.2_fix_lib_dir.patch @@ -0,0 +1,22 @@ +--- salmon-0.10.2/src/CMakeLists.txt 2018-06-25 13:35:45.723519730 +0200 ++++ salmon-0.10.2/src/CMakeLists.txt 2018-06-25 13:44:01.326139539 +0200 +@@ -296,6 +296,8 @@ + ) + ENDIF(CMAKE_INSTALL_PREFIX_INITIALIZED_TO_DEFAULT) + ++include(GNUInstallDirs) ++ + set(INSTALL_LIB_DIR lib ) + set(INSTALL_BIN_DIR bin ) + set(INSTALL_INCLUDE_DIR include ) +@@ -311,8 +313,8 @@ + + install(TARGETS salmon salmon_core + RUNTIME DESTINATION bin +- LIBRARY DESTINATION lib +- ARCHIVE DESTINATION lib ++ LIBRARY DESTINATION "${CMAKE_INSTALL_FULL_LIBDIR}" ++ ARCHIVE DESTINATION "${CMAKE_INSTALL_FULL_LIBDIR}" + ) + + add_custom_command(TARGET unitTests POST_BUILD diff --git a/sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch b/sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch new file mode 100644 index 000000000..438763960 --- /dev/null +++ b/sci-biology/salmon/files/salmon-0.10.2_remove_curl_calls.patch @@ -0,0 +1,200 @@ +--- salmon-0.10.2/CMakeLists.txt 2018-06-25 13:12:49.275828719 +0200 ++++ salmon-0.10.2/CMakeLists.txt 2018-06-25 13:12:38.945565690 +0200 +@@ -235,31 +235,7 @@ + + find_package (LibLZMA) + if (NOT LIBLZMA_FOUND) +- message ("Will attempt to fetch and build liblzma") +- message ("=======================================") +-ExternalProject_Add(liblzma +- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external +- ## +- DOWNLOAD_COMMAND curl -k -L http://tukaani.org/xz/xz-5.2.2.tar.gz -o xz-5.2.2.tar.gz && +- ${SHASUM} 73df4d5d34f0468bd57d09f2d8af363e95ed6cc3a4a86129d2f2c366259902a2 xz-5.2.2.tar.gz && +- tar -xzvf xz-5.2.2.tar.gz +- #URL http://tukaani.org/xz/xz-5.2.2.tar.gz +- #URL_HASH SHA1=14663612422ab61386673be78fbb2556f50a1f08 +- ## +- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.2 +- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install +- BUILD_IN_SOURCE TRUE +- CONFIGURE_COMMAND ${CMAKE_CURRENT_SOURCE_DIR}/external/xz-5.2.2/configure --prefix= CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} CFLAGS=${EXTRA_CMAKE_INCLUDE_FLAGS} CPPFLAGS=${EXTRA_CMAKE_INCLUDE_FLAGS} LDFLAGS=${EXTRA_CMAKE_LIBRARY_FLAGS} +- BUILD_COMMAND make ${QUIET_MAKE} +- INSTALL_COMMAND make ${QUIET_MAKE} install +-) +- +-# Tell cmake that the external project generated a library so we can +-# add dependencies here instead of later +-set (LIBLZMA_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/liblzma.a) +-set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib") +-set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include") +-set (FETCHED_LIBLZMA TRUE) ++ message (FATAL_ERROR "liblzma must be installed before configuration & building can proceed") + else() + message("Found liblzma library: ${LIBLZMA_LIBRARIES}") + message("===========================================") +@@ -267,28 +243,7 @@ + + find_package (BZip2) + if (NOT BZIP2_FOUND) +- message ("Will attempt to fetch and build libbz2") +- message ("=======================================") +-ExternalProject_Add(libbz2 +- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external +- DOWNLOAD_COMMAND curl -k -L http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz -o bzip2-1.0.6.tar.gz && +- ${SHASUM} a2848f34fcd5d6cf47def00461fcb528a0484d8edef8208d6d2e2909dc61d9cd bzip2-1.0.6.tar.gz && +- tar -xzvf bzip2-1.0.6.tar.gz +- #URL http://www.bzip.org/1.0.6/bzip2-1.0.6.tar.gz +- #URL_HASH SHA1=3f89f861209ce81a6bab1fd1998c0ef311712002 +- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bzip2-1.0.6 +- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install +- BUILD_IN_SOURCE TRUE +- CONFIGURE_COMMAND "" +- BUILD_COMMAND make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} +- INSTALL_COMMAND make ${QUIET_MAKE} install PREFIX= +-) +-# Tell cmake that the external project generated a library so we can +-# add dependencies here instead of later +-set (BZIP2_LIBRARIES ${GAT_SOURCE_DIR}/external/install/lib/libbz2.a) +-set (LIBSTADEN_LDFLAGS "-L${GAT_SOURCE_DIR}/external/install/lib -I${GAT_SOURCE_DIR}/external/install/include") +-set (LIBSTADEN_CFLAGS "-I${GAT_SOURCE_DIR}/external/install/include") +-set (FETCHED_LIBBZ2 TRUE) ++ message (FATAL_ERROR "libbz2 must be installed before configuration & building can proceed") + else() + message("Found libbz2 library: ${BZIP2_LIBRARIES}") + message("===========================================") +@@ -333,61 +288,15 @@ + # Either inform the user of how to obtain Boost, or, if they passed in the FETCH_BOOST + # option, go and grab it for them. + ## +-if ((NOT Boost_FOUND) AND (NOT FETCH_BOOST)) ++if (NOT Boost_FOUND) + message(FATAL_ERROR + "Salmon cannot be compiled without Boost.\n" + "It is recommended to visit http://www.boost.org/ and install Boost according to those instructions.\n" + "This build system can also download and install a local version of boost for you (this takes a lot of time).\n" + "To fetch and build boost locally, call cmake with -DFETCH_BOOST=TRUE" + ) +-elseif(FETCH_BOOST) +- ## Let the rest of the build process know we're going to be fetching boost +- set (BOOST_LIB_SUBSET --with-iostreams --with-atomic --with-chrono --with-container --with-date_time --with-exception +- --with-filesystem --with-graph --with-graph_parallel --with-math +- --with-program_options --with-system --with-thread +- --with-timer) +- set (BOOST_WILL_RECONFIGURE TRUE) +- set (FETCH_BOOST FALSE) +- message("Build system will fetch and build Boost") +- message("==================================================================") +- ExternalProject_Add(libboost +- DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external +- DOWNLOAD_COMMAND curl -k -L http://downloads.sourceforge.net/project/boost/boost/1.66.0/boost_1_66_0.tar.gz -o boost_1_66_0.tar.gz && +- ${SHASUM} bd0df411efd9a585e5a2212275f8762079fed8842264954675a4fddc46cfcf60 boost_1_66_0.tar.gz && +- tar xzf boost_1_66_0.tar.gz +- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0 +- INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install +- #PATCH_COMMAND patch -p2 < ${CMAKE_CURRENT_SOURCE_DIR}/external/boost156.patch +- CONFIGURE_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0/bootstrap.sh ${BOOST_CONFIGURE_TOOLSET} ${BOOST_BUILD_LIBS} --prefix= +- BUILD_COMMAND CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER} ${CMAKE_CURRENT_SOURCE_DIR}/external/boost_1_66_0/b2 -d0 -j2 ${BOOST_LIB_SUBSET} toolset=${BOOST_TOOLSET} ${BOOST_EXTRA_FLAGS} cxxflags=${BOOST_CXX_FLAGS} link=static install +- BUILD_IN_SOURCE 1 +- INSTALL_COMMAND "" +- ) +- +- ## +- # After we've installed boost, +- ## +- SET( RECONFIG_FLAGS ${RECONFIG_FLAGS} -DBOOST_WILL_RECONFIGURE=FALSE -DBOOST_RECONFIGURE=TRUE -DFETCH_BOOST=FALSE) +- ExternalProject_Add_Step(libboost reconfigure +- COMMAND ${CMAKE_COMMAND} ${CMAKE_CURRENT_SOURCE_DIR} ${RECONFIG_FLAGS} +- DEPENDEES install +- ) +- set (FETCHED_BOOST TRUE) + endif() + +-## +-# If we're fetching boost and we need to have dummy paths for these variables +-# so that CMake won't complain +-## +-if (BOOST_WILL_RECONFIGURE) +- message("Setting Temporary Boost paths") +- set(Boost_INCLUDE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include) +- set(Boost_INCLUDE_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/include) +- set(Boost_LIBRARY_DIRS ${CMAKE_CURRENT_SOURCE_DIR}/external/install/lib) +- set(Boost_FOUND TRUE) +-endif() +- +- + message("BOOST INCLUDE DIR = ${Boost_INCLUDE_DIR}") + message("BOOST INCLUDE DIRS = ${Boost_INCLUDE_DIRS}") + message("BOOST LIB DIR = ${Boost_LIBRARY_DIRS}") +@@ -422,9 +331,9 @@ + include(ExternalProject) + ExternalProject_Add(libcereal + DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external +- DOWNLOAD_COMMAND curl -k -L https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz -o cereal-v1.2.2.tar.gz && +- ${SHASUM} 1921f26d2e1daf9132da3c432e2fd02093ecaedf846e65d7679ddf868c7289c4 cereal-v1.2.2.tar.gz && +- tar -xzvf cereal-v1.2.2.tar.gz ++ DOWNLOAD_COMMAND cp ../../../distdir/cereal-1.2.2.tar.gz . && ++ ${SHASUM} 1921f26d2e1daf9132da3c432e2fd02093ecaedf846e65d7679ddf868c7289c4 cereal-1.2.2.tar.gz && ++ tar -xzvf cereal-1.2.2.tar.gz + + ## + #URL https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz +@@ -455,12 +364,12 @@ + ExternalProject_Add(libbwa + DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external + #URL https://github.com/COMBINE-lab/bwa/archive/0.7.12.3.tar.gz +- #DOWNLOAD_NAME bwa-master.tar.gz +- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/bwa/archive/v0.7.12.5.tar.gz -o bwa-master.tar.gz && +- ${SHASUM} 1ac5661d9e12e9017a47f0264201a75d9128f28dbd9a26952925f7745ddf6036 bwa-master.tar.gz && +- mkdir -p bwa-master && +- tar -xzvf bwa-master.tar.gz --strip-components=1 -C bwa-master +- SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bwa-master ++ #DOWNLOAD_NAME bwa-0.7.12.5.tar.gz ++ DOWNLOAD_COMMAND cp ../../../distdir/bwa-0.7.12.5.tar.gz . && ++ ${SHASUM} 1ac5661d9e12e9017a47f0264201a75d9128f28dbd9a26952925f7745ddf6036 bwa-0.7.12.5.tar.gz && ++ mkdir -p bwa-0.7.12.5 && ++ tar -xzvf bwa-0.7.12.5.tar.gz --strip-components=1 -C bwa-0.7.12.5 ++ SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/bwa-0.7.12.5 + INSTALL_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/install + CONFIGURE_COMMAND "" + BUILD_COMMAND sh -c "make ${QUIET_MAKE} CC=${CMAKE_C_COMPILER} CXX=${CMAKE_CXX_COMPILER}" +@@ -562,9 +471,9 @@ + message("==================================================================") + ExternalProject_Add(libgff + DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external +- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -o libgff.tgz && +- ${SHASUM} 34597ecd3718e6d6e7a1dd4350220664be2c1cd992070d1218564a20d7aa5697 libgff.tgz && +- tar -xzvf libgff.tgz ++ DOWNLOAD_COMMAND cp ../../../distdir/libgff-1.1.tgz . && ++ ${SHASUM} 34597ecd3718e6d6e7a1dd4350220664be2c1cd992070d1218564a20d7aa5697 libgff-1.1.tgz && ++ tar -xzvf libgff-1.1.tgz + ## + #URL https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz + #DOWNLOAD_NAME libff.tgz +@@ -600,10 +509,10 @@ + message("==================================================================") + ExternalProject_Add(libstadenio + DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external +- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/staden-io_lib/archive/v1.14.8.1.tar.gz -o staden-io_lib-v1.14.8.tar.gz && +- ${SHASUM} f6f30eefa478cfb708f3109a35fb6ffa0e24951d9d971985df2cef5919dd0bc3 staden-io_lib-v1.14.8.tar.gz && ++ DOWNLOAD_COMMAND cp ../../../distdir/staden-io_lib-1.14.8.tar.gz . && ++ ${SHASUM} f6f30eefa478cfb708f3109a35fb6ffa0e24951d9d971985df2cef5919dd0bc3 staden-io_lib-1.14.8.tar.gz && + mkdir -p staden-io_lib-1.14.8 && +- tar -xzf staden-io_lib-v1.14.8.tar.gz --strip-components=1 -C staden-io_lib-1.14.8 && ++ tar -xzf staden-io_lib-1.14.8.tar.gz --strip-components=1 -C staden-io_lib-1.14.8 && + rm -fr staden-io_lib && + mv -f staden-io_lib-1.14.8 staden-io_lib + SOURCE_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external/staden-io_lib +@@ -620,9 +529,9 @@ + message("==================================================================") + ExternalProject_Add(libspdlog + DOWNLOAD_DIR ${CMAKE_CURRENT_SOURCE_DIR}/external +- DOWNLOAD_COMMAND curl -k -L https://github.com/COMBINE-lab/spdlog/archive/v0.16.1.tar.gz -o spdlog-v0.16.1.tar.gz && +- ${SHASUM} 733260e1fbdcf1b3dc307fc585e4476240026de8be28eb905731d2ab0942deae spdlog-v0.16.1.tar.gz && +- tar -xzf spdlog-v0.16.1.tar.gz ++ DOWNLOAD_COMMAND cp ../../../distdir/spdlog-0.16.1.tar.gz . && ++ ${SHASUM} 733260e1fbdcf1b3dc307fc585e4476240026de8be28eb905731d2ab0942deae spdlog-0.16.1.tar.gz && ++ tar -xzf spdlog-0.16.1.tar.gz + ## + #URL https://github.com/COMBINE-lab/spdlog/archive/v0.12.0.tar.gz + #DOWNLOAD_NAME spdlog-v0.12.0.tar.gz diff --git a/sci-biology/salmon/salmon-0.10.2.ebuild b/sci-biology/salmon/salmon-0.10.2.ebuild index 540225019..b3bdc6d53 100644 --- a/sci-biology/salmon/salmon-0.10.2.ebuild +++ b/sci-biology/salmon/salmon-0.10.2.ebuild @@ -8,7 +8,12 @@ inherit cmake-utils DESCRIPTION="Transcript-level quantification from RNA-seq reads using lightweight alignments" HOMEPAGE="https://github.com/COMBINE-lab/salmon" SRC_URI="https://github.com/COMBINE-lab/${PN}/archive/v${PV}.tar.gz -> ${P}.tar.gz - https://github.com/COMBINE-lab/RapMap/archive/salmon-v0.10.2.zip -> ${P}_RapMap.zip" + https://github.com/COMBINE-lab/RapMap/archive/salmon-v0.10.2.zip -> ${P}_RapMap.zip + https://github.com/USCiLab/cereal/archive/v1.2.2.tar.gz -> cereal-1.2.2.tar.gz + https://github.com/COMBINE-lab/bwa/archive/v0.7.12.5.tar.gz -> bwa-0.7.12.5.tar.gz + https://github.com/COMBINE-lab/libgff/archive/v1.1.tar.gz -> libgff-1.1.tgz + https://github.com/COMBINE-lab/staden-io_lib/archive/v1.14.8.1.tar.gz -> staden-io_lib-1.14.8.tar.gz + https://github.com/COMBINE-lab/spdlog/archive/v0.16.1.tar.gz -> spdlog-0.16.1.tar.gz" LICENSE="GPL-3" SLOT="0" @@ -16,7 +21,9 @@ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" IUSE="" PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch - "${FILESDIR}"/salmon-0.10.2_remove_curl_call.patch ) + "${FILESDIR}"/salmon-0.10.2_remove_curl_call.patch + "${FILESDIR}"/salmon-0.10.2_remove_curl_calls.patch + "${FILESDIR}"/salmon-0.10.2_fix_lib_dir.patch ) RDEPEND="${DEPEND}" # budled copies of: @@ -31,15 +38,15 @@ RDEPEND="${DEPEND}" # # dev-libs/spdlog-0.16.1 # cereal-1.2.2 -DEPEND="sys-libs/zlib + +# see the many curl executions: +# salmon-0.10.2$ find . -type f | xargs grep curl 2>/dev/null +# +DEPEND="net-misc/curl + sys-libs/zlib app-arch/bzip2 app-arch/xz-utils dev-libs/boost:0[threads] >=dev-libs/jemalloc-5.0.1 >=dev-cpp/tbb-2018.20180312" RDEPEND="${DEPEND}" - -src_install() { - cmake-utils_src_install - rm -r "${ED}"/usr/tests || die -} diff --git a/sci-biology/salmon/salmon-9999.ebuild b/sci-biology/salmon/salmon-9999.ebuild index 0083648fb..b5e748fd2 100644 --- a/sci-biology/salmon/salmon-9999.ebuild +++ b/sci-biology/salmon/salmon-9999.ebuild @@ -29,7 +29,8 @@ PATCHES=( "${FILESDIR}"/${P}-no-boost-static.patch # # dev-libs/spdlog-0.16.1 # cereal-1.2.2 -DEPEND="sys-libs/zlib +DEPEND="net-misc/curl + sys-libs/zlib app-arch/bzip2 app-arch/xz-utils dev-libs/boost:0[threads] @@ -53,6 +54,10 @@ RDEPEND="${DEPEND}" # and maybe more # See https://github.com/COMBINE-lab/salmon/issues/236 for Cmake tweaks needed by Debian + +# see the many curl executions: +# salmon-0.10.2$ find . -type f | xargs grep curl 2>/dev/null +# src_configure(){ local mycmakeargs=( "-DBOOST_INCLUDEDIR=${EPREFIX}/usr/include/boost/" @@ -67,5 +72,5 @@ src_configure(){ src_install() { cmake-utils_src_install - rm -r "${ED}"/usr/tests || die + rm -rf "${ED}"/usr/tests || die }