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 AD7E8138334 for ; Sat, 30 Mar 2019 06:43:04 +0000 (UTC) Received: from pigeon.gentoo.org (localhost [127.0.0.1]) by pigeon.gentoo.org (Postfix) with SMTP id 39B33E0855; Sat, 30 Mar 2019 06:43:03 +0000 (UTC) Received: from smtp.gentoo.org (woodpecker.gentoo.org [IPv6:2001:470:ea4a:1:5054:ff:fec7:86e4]) (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 EC20AE0855 for ; Sat, 30 Mar 2019 06:43:02 +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 07BCD335CCD for ; Sat, 30 Mar 2019 06:43:00 +0000 (UTC) Received: from localhost.localdomain (localhost [IPv6:::1]) by oystercatcher.gentoo.org (Postfix) with ESMTP id 6C38A57D for ; Sat, 30 Mar 2019 06:42:58 +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: <1553928162.a6b601e64f7b9313fc7d7c2fec43d0f4d4d7ec1f.mmokrejs@gentoo> Subject: [gentoo-commits] proj/sci:master commit in: sci-biology/ncbi-tools++/ X-VCS-Repository: proj/sci X-VCS-Files: sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild X-VCS-Directories: sci-biology/ncbi-tools++/ X-VCS-Committer: mmokrejs X-VCS-Committer-Name: Martin Mokrejs X-VCS-Revision: a6b601e64f7b9313fc7d7c2fec43d0f4d4d7ec1f X-VCS-Branch: master Date: Sat, 30 Mar 2019 06:42:58 +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-Auto-Response-Suppress: DR, RN, NRN, OOF, AutoReply X-Archives-Salt: 89d497a6-1e4d-44f8-a56e-39450740c0d0 X-Archives-Hash: 92eb09cbc9ad5ac6ad7dee695373452c commit: a6b601e64f7b9313fc7d7c2fec43d0f4d4d7ec1f Author: Martin Mokrejs fold natur cuni cz> AuthorDate: Sat Mar 30 06:42:42 2019 +0000 Commit: Martin Mokrejs fold natur cuni cz> CommitDate: Sat Mar 30 06:42:42 2019 +0000 URL: https://gitweb.gentoo.org/proj/sci.git/commit/?id=a6b601e6 sci-biology/ncbi-tools++: document possible issue with builds I have the following defined due to ncbi-tools++-18.0.0 installed on my system: /usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0/32: /usr/lib/gcc/x86_64-pc-linux-gnu/8.3.0: /usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0/32: /usr/lib/gcc/x86_64-pc-linux-gnu/7.3.0: /usr/lib/llvm/7/lib32: /usr/lib/llvm/7/lib64: /usr/lib64/itcl4.1.1: /usr/lib64/itk4.1.0: /lib64: /usr/lib64: /usr/local/lib64: /lib32: /usr/lib32: /usr/lib64/rust-1.29.2: /usr/lib64/R/lib: /usr/lib64/fltk: /usr/lib64/ncbi-tools++: /usr/lib64/staden: grep: /etc: No such file or directory grep: /etc/env.d: No such file or directory /etc/env.d/99ncbi-tools++:LDPATH=/usr/lib64/ncbi-tools++ ... That in turn makes linker pick "${WORKDIR}"/ncbi_cxx--22_0_0_build/lib/* files but later overrides some of them with /usr/lib64/ncbi-tools++/*, depending on the ordering of -lXXXXXX arguments. Package-Manager: Portage-2.3.62, Repoman-2.3.12 Signed-off-by: Martin Mokrejs fold.natur.cuni.cz> sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild | 5 +++-- sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild | 5 +++-- sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild | 3 ++- 3 files changed, 8 insertions(+), 5 deletions(-) diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild index 14e1fabda..68341a338 100644 --- a/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild +++ b/sci-biology/ncbi-tools++/ncbi-tools++-12.0.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2019 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -36,11 +36,12 @@ KEYWORDS="~amd64" REQUIRED_USE="${PYTHON_REQUIRED_USE}" # sys-libs/db should be compiled with USE=cxx +# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then? DEPEND=" !sci-biology/sra_sdk app-arch/cpio berkdb? ( sys-libs/db:4.3[cxx] ) - boost? ( dev-libs/boost ) + boost? ( dev-libs/boost[tools] ) curl? ( net-misc/curl ) sqlite? ( dev-db/sqlite:3 ) mysql? ( virtual/mysql ) diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild index 3f1fc7bd1..c737392fd 100644 --- a/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild +++ b/sci-biology/ncbi-tools++/ncbi-tools++-18.0.0.ebuild @@ -1,4 +1,4 @@ -# Copyright 1999-2017 Gentoo Foundation +# Copyright 1999-2019 Gentoo Authors # Distributed under the terms of the GNU General Public License v2 EAPI=5 @@ -35,11 +35,12 @@ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" REQUIRED_USE="${PYTHON_REQUIRED_USE}" # sys-libs/db should be compiled with USE=cxx +# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then? DEPEND=" !sci-biology/sra_sdk app-arch/cpio berkdb? ( sys-libs/db:4.3[cxx] ) - boost? ( dev-libs/boost ) + boost? ( dev-libs/boost[tools] ) curl? ( net-misc/curl ) sqlite? ( dev-db/sqlite:3 ) mysql? ( virtual/mysql ) diff --git a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild index 585042f9f..971789fb4 100644 --- a/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild +++ b/sci-biology/ncbi-tools++/ncbi-tools++-22.0.0.ebuild @@ -35,11 +35,12 @@ KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux" REQUIRED_USE="${PYTHON_REQUIRED_USE}" # sys-libs/db should be compiled with USE=cxx +# dev-libs/boost must have Boost.Test suite, probably dev-libs/boost[test] then? DEPEND=" !sci-biology/sra_sdk app-arch/cpio berkdb? ( sys-libs/db:4.3[cxx] ) - boost? ( dev-libs/boost ) + boost? ( dev-libs/boost[tools] ) curl? ( net-misc/curl ) sqlite? ( >=dev-db/sqlite-3.6.6:3 ) mysql? ( virtual/mysql )