From owner-freebsd-ports-bugs@freebsd.org  Thu Jan 12 19:01:53 2017
Return-Path: <owner-freebsd-ports-bugs@freebsd.org>
Delivered-To: freebsd-ports-bugs@mailman.ysv.freebsd.org
Received: from mx1.freebsd.org (mx1.freebsd.org
 [IPv6:2001:1900:2254:206a::19:1])
 by mailman.ysv.freebsd.org (Postfix) with ESMTP id 06F86CABFFA
 for <freebsd-ports-bugs@mailman.ysv.freebsd.org>;
 Thu, 12 Jan 2017 19:01:53 +0000 (UTC)
 (envelope-from bugzilla-noreply@freebsd.org)
Received: from kenobi.freebsd.org (kenobi.freebsd.org
 [IPv6:2001:1900:2254:206a::16:76])
 (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits))
 (Client did not present a certificate)
 by mx1.freebsd.org (Postfix) with ESMTPS id EB07912F5
 for <freebsd-ports-bugs@FreeBSD.org>; Thu, 12 Jan 2017 19:01:52 +0000 (UTC)
 (envelope-from bugzilla-noreply@freebsd.org)
Received: from bugs.freebsd.org ([127.0.1.118])
 by kenobi.freebsd.org (8.15.2/8.15.2) with ESMTP id v0CJ1q4k030875
 for <freebsd-ports-bugs@FreeBSD.org>; Thu, 12 Jan 2017 19:01:52 GMT
 (envelope-from bugzilla-noreply@freebsd.org)
From: bugzilla-noreply@freebsd.org
To: freebsd-ports-bugs@FreeBSD.org
Subject: [Bug 216004] biology/ncbi-blast+: package requires libgomp
Date: Thu, 12 Jan 2017 19:01:53 +0000
X-Bugzilla-Reason: AssignedTo
X-Bugzilla-Type: new
X-Bugzilla-Watch-Reason: None
X-Bugzilla-Product: Ports & Packages
X-Bugzilla-Component: Individual Port(s)
X-Bugzilla-Version: Latest
X-Bugzilla-Keywords: 
X-Bugzilla-Severity: Affects Some People
X-Bugzilla-Who: weeks@iastate.edu
X-Bugzilla-Status: New
X-Bugzilla-Resolution: 
X-Bugzilla-Priority: ---
X-Bugzilla-Assigned-To: freebsd-ports-bugs@FreeBSD.org
X-Bugzilla-Flags: 
X-Bugzilla-Changed-Fields: bug_id short_desc product version rep_platform
 op_sys bug_status bug_severity priority component assigned_to reporter
Message-ID: <bug-216004-13@https.bugs.freebsd.org/bugzilla/>
Content-Type: text/plain; charset="UTF-8"
Content-Transfer-Encoding: quoted-printable
X-Bugzilla-URL: https://bugs.freebsd.org/bugzilla/
Auto-Submitted: auto-generated
MIME-Version: 1.0
X-BeenThere: freebsd-ports-bugs@freebsd.org
X-Mailman-Version: 2.1.23
Precedence: list
List-Id: Ports bug reports <freebsd-ports-bugs.freebsd.org>
List-Unsubscribe: <https://lists.freebsd.org/mailman/options/freebsd-ports-bugs>, 
 <mailto:freebsd-ports-bugs-request@freebsd.org?subject=unsubscribe>
List-Archive: <http://lists.freebsd.org/pipermail/freebsd-ports-bugs/>
List-Post: <mailto:freebsd-ports-bugs@freebsd.org>
List-Help: <mailto:freebsd-ports-bugs-request@freebsd.org?subject=help>
List-Subscribe: <https://lists.freebsd.org/mailman/listinfo/freebsd-ports-bugs>, 
 <mailto:freebsd-ports-bugs-request@freebsd.org?subject=subscribe>
X-List-Received-Date: Thu, 12 Jan 2017 19:01:53 -0000

https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=3D216004

            Bug ID: 216004
           Summary: biology/ncbi-blast+: package requires libgomp
           Product: Ports & Packages
           Version: Latest
          Hardware: Any
                OS: Any
            Status: New
          Severity: Affects Some People
          Priority: ---
         Component: Individual Port(s)
          Assignee: freebsd-ports-bugs@FreeBSD.org
          Reporter: weeks@iastate.edu

It appears that the amd64 ncbi-blast+-2.5.0 package was compiled with gcc >=
=3D
5.0, as it requires a libgomp supporting OpenMP 4.0; however, this is not
reflected in the dependencies:


$ pkg which /usr/local/bin/blastn
/usr/local/bin/blastn was installed by package ncbi-blast+-2.5.0
$ pkg info -d ncbi-blast+=20=20=20=20=20=20=20=20
ncbi-blast+-2.5.0:
        python27-2.7.13_1
        pcre-8.39_1
        p5-List-MoreUtils-0.416
        perl5-5.24.1.r4_1
        gcc-4.9.4
$ blastn -version
/usr/lib/libgomp.so.1: version GOMP_4.0 required by /usr/local/bin/blastn n=
ot
found
weeks@cicer:ncbi-blast+$ LD_LIBRARY_PATH=3D/usr/local/lib/gcc49 blastn -ver=
sion
/usr/lib/libgomp.so.1: version GOMP_4.0 required by /usr/local/bin/blastn n=
ot
found
$ LD_LIBRARY_PATH=3D/usr/local/lib/gcc50 blastn -version
/usr/lib/libgomp.so.1: version GOMP_4.0 required by /usr/local/bin/blastn n=
ot
found

--=20
You are receiving this mail because:
You are the assignee for the bug.=