Date: Sun, 28 Aug 2016 09:39:46 -0500 From: Jason Bacon <bacon4000@gmail.com> To: pkg-fallout@FreeBSD.org Subject: Re: [package - 93amd64-default][biology/ncbi-blast+] Failed for ncbi-blast+-2.2.30_2 in configure Message-ID: <125e3373-730e-cdec-c5fc-506412c760cf@gmail.com> In-Reply-To: <201608270726.u7R7QMo8030844@beefy2.nyi.freebsd.org> References: <201608270726.u7R7QMo8030844@beefy2.nyi.freebsd.org>
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Can't reproduce this on my Poudriere.
Regards,
JB
On 08/27/16 02:26, pkg-fallout@FreeBSD.org wrote:
> You are receiving this mail as a port that you maintain
> is failing to build on the FreeBSD package build server.
> Please investigate the failure and submit a PR to fix
> build.
>
> Maintainer: bacon4000@gmail.com
> Last committer: mat@FreeBSD.org
> Ident: $FreeBSD: head/biology/ncbi-blast+/Makefile 412344 2016=
-04-01 13:29:15Z mat $
> Log URL: http://beefy2.nyi.freebsd.org/data/93amd64-default/4209=
55/logs/ncbi-blast+-2.2.30_2.log
> Build URL: http://beefy2.nyi.freebsd.org/build.html?mastername=3D9=
3amd64-default&build=3D420955
> Log:
>
> =3D=3D=3D=3D>> Building biology/ncbi-blast+
> build started at Sat Aug 27 07:25:53 UTC 2016
> port directory: /usr/ports/biology/ncbi-blast+
> building for: FreeBSD 93amd64-default-job-14 9.3-RELEASE-p45 FreeBSD 9.=
3-RELEASE-p45 amd64
> maintained by: bacon4000@gmail.com
> Makefile ident: $FreeBSD: head/biology/ncbi-blast+/Makefile 412344=
2016-04-01 13:29:15Z mat $
> Poudriere version: 3.1.14
> Host OSVERSION: 1200001
> Jail OSVERSION: 903000
>
> ---Begin Environment---
> SHELL=3D/bin/csh
> UNAME_v=3DFreeBSD 9.3-RELEASE-p45
> UNAME_r=3D9.3-RELEASE-p45
> BLOCKSIZE=3DK
> MAIL=3D/var/mail/root
> STATUS=3D1
> OPSYS=3DFreeBSD
> ARCH=3Damd64
> SAVED_TERM=3D
> MASTERMNT=3D/usr/local/poudriere/data/.m/93amd64-default/ref
> UID=3D0
> PATH=3D/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/lo=
cal/bin:/root/bin
> _JAVA_VERSION_LIST_REGEXP=3D1.6\|1.7\|1.8\|1.6+\|1.7+\|1.8+
> POUDRIERE_BUILD_TYPE=3Dbulk
> PKGNAME=3Dncbi-blast+-2.2.30_2
> OSREL=3D9.3
> _OSRELEASE=3D9.3-RELEASE-p45
> PYTHONBASE=3D/usr/local
> OLDPWD=3D/
> _SMP_CPUS=3D24
> PWD=3D/usr/local/poudriere/data/.m/93amd64-default/ref/.p/pool
> HAVE_COMPAT_IA32_KERN=3DYES LINUX_OSRELEASE=3D2.6.32
> MASTERNAME=3D93amd64-default
> SCRIPTPREFIX=3D/usr/local/share/poudriere
> _JAVA_VENDOR_LIST_REGEXP=3Dopenjdk\|oracle\|sun
> USER=3Droot
> HOME=3D/root
> POUDRIERE_VERSION=3D3.1.14
> SCRIPTPATH=3D/usr/local/share/poudriere/bulk.sh
> CONFIGURE_MAX_CMD_LEN=3D262144
> LIBEXECPREFIX=3D/usr/local/libexec/poudriere
> LOCALBASE=3D/usr/local
> PACKAGE_BUILDING=3Dyes
> _JAVA_OS_LIST_REGEXP=3Dnative\|linux
> OSVERSION=3D903000
> ---End Environment---
>
> ---Begin OPTIONS List---
> ---End OPTIONS List---
>
> --CONFIGURE_ARGS--
> AR=3D"ar cr" --without-boost --prefix=3D/usr/local ${_LATE_CONFIGURE_AR=
GS}
> --End CONFIGURE_ARGS--
>
> --CONFIGURE_ENV--
> ncbi_cv_prog_amq_w=3Dno MAKE=3Dgmake ac_cv_path_PERL=3D/usr/local/bin/p=
erl ac_cv_path_PERL_PATH=3D/usr/local/bin/perl PYTHON=3D"/usr/local/bin/p=
ython2.7" XDG_DATA_HOME=3D/wrkdirs/usr/ports/biology/ncbi-blast+/work XD=
G_CONFIG_HOME=3D/wrkdirs/usr/ports/biology/ncbi-blast+/work HOME=3D/wrkd=
irs/usr/ports/biology/ncbi-blast+/work TMPDIR=3D"/tmp" SHELL=3D/bin/sh CO=
NFIG_SHELL=3D/bin/sh ADDR2LINE=3D"/usr/local/bin/addr2line" AR=3D"/usr/lo=
cal/bin/ar" AS=3D"/usr/local/bin/as" CPPFILT=3D"/usr/local/bin/c++filt" G=
PROF=3D"/usr/local/bin/gprof" LD=3D"/usr/local/bin/ld" NM=3D"/usr/local/b=
in/nm" OBJCOPY=3D"/usr/local/bin/objcopy" OBJDUMP=3D"/usr/local/bin/objdu=
mp" RANLIB=3D"/usr/local/bin/ranlib" READELF=3D"/usr/local/bin/readelf" S=
IZE=3D"/usr/local/bin/size" STRINGS=3D"/usr/local/bin/strings" CONFIG_SIT=
E=3D/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=3D262144
> --End CONFIGURE_ENV--
>
> --MAKE_ENV--
> XDG_DATA_HOME=3D/wrkdirs/usr/ports/biology/ncbi-blast+/work XDG_CONFIG=
_HOME=3D/wrkdirs/usr/ports/biology/ncbi-blast+/work HOME=3D/wrkdirs/usr/=
ports/biology/ncbi-blast+/work TMPDIR=3D"/tmp" NO_PIE=3Dyes WITHOUT_DEBUG=
_FILES=3Dyes WITHOUT_KERNEL_SYMBOLS=3Dyes SHELL=3D/bin/sh NO_LINT=3DYES A=
DDR2LINE=3D"/usr/local/bin/addr2line" AR=3D"/usr/local/bin/ar" AS=3D"/usr=
/local/bin/as" CPPFILT=3D"/usr/local/bin/c++filt" GPROF=3D"/usr/local/bin=
/gprof" LD=3D"/usr/local/bin/ld" NM=3D"/usr/local/bin/nm" OBJCOPY=3D"/usr=
/local/bin/objcopy" OBJDUMP=3D"/usr/local/bin/objdump" RANLIB=3D"/usr/loc=
al/bin/ranlib" READELF=3D"/usr/local/bin/readelf" SIZE=3D"/usr/local/bin/=
size" STRINGS=3D"/usr/local/bin/strings" PREFIX=3D/usr/local LOCALBASE=3D=
/usr/local LIBDIR=3D"/usr/lib" CC=3D"gcc48" CFLAGS=3D"-O2 -pipe -fstack=
-protector -Wl,-rpath=3D/usr/local/lib/gcc48 -fno-strict-aliasing" CPP=3D=
"cpp48" CPPFLAGS=3D"" LDFLAGS=3D" -fstack-protector -Wl,-rpath=3D/usr/lo=
cal/lib/gcc48 -L/usr/local/lib/gcc48" LIBS=3D"" CXX=3D"g++48" CXXFLAGS=3D=
"-O2 -pipe -fstack-protector -Wl,-rpath=3D/usr/
> local/lib/gcc48 -fno-strict-aliasing -Wl,-rpath=3D/usr/local/lib/gcc4=
8" MANPREFIX=3D"/usr/local" BSD_INSTALL_PROGRAM=3D"install -s -m 555" =
BSD_INSTALL_LIB=3D"install -s -m 444" BSD_INSTALL_SCRIPT=3D"install -m=
555" BSD_INSTALL_DATA=3D"install -m 0644" BSD_INSTALL_MAN=3D"install =
-m 444"
> --End MAKE_ENV--
>
> --PLIST_SUB--
> PYTHON_INCLUDEDIR=3Dinclude/python2.7
> PYTHON_LIBDIR=3Dlib/python2.7
> PYTHON_PLATFORM=3Dfreebsd9
> PYTHON_SITELIBDIR=3Dlib/python2.7/site-packages
> PYTHON_VER=3D2.7
> PYTHON_VERSION=3Dpython2.7
> OSREL=3D9.3
> PREFIX=3D%D
> LOCALBASE=3D/usr/local
> RESETPREFIX=3D/usr/local
> PORTDOCS=3D""
> PORTEXAMPLES=3D""
> LIB32DIR=3Dlib
> PERL_VERSION=3D5.20.3
> PERL_VER=3D5.20
> PERL5_MAN1=3Dlib/perl5/site_perl/man/man1
> PERL5_MAN3=3Dlib/perl5/site_perl/man/man3
> SITE_PERL=3Dlib/perl5/site_perl
> SITE_ARCH=3Dlib/perl5/site_perl/mach/5.20
> DOCSDIR=3D"share/doc/blast+"
> EXAMPLESDIR=3D"share/examples/blast+"
> DATADIR=3D"share/blast+"
> WWWDIR=3D"www/blast+"
> ETCDIR=3D"etc/blast+"
> --End PLIST_SUB--
>
> --SUB_LIST--
> PREFIX=3D/usr/local
> LOCALBASE=3D/usr/local
> DATADIR=3D/usr/local/share/blast+
> DOCSDIR=3D/usr/local/share/doc/blast+
> EXAMPLESDIR=3D/usr/local/share/examples/blast+
> WWWDIR=3D/usr/local/www/blast+
> ETCDIR=3D/usr/local/etc/blast+
> --End SUB_LIST--
>
> ---Begin make.conf---
> USE_PACKAGE_DEPENDS=3Dyes
> BATCH=3Dyes
> WRKDIRPREFIX=3D/wrkdirs
> PORTSDIR=3D/usr/ports
> PACKAGES=3D/packages
> DISTDIR=3D/distfiles
> #### /usr/local/etc/poudriere.d/make.conf ####
> # XXX: We really need this but cannot use it while 'make checksum' does=
not
> # try the next mirror on checksum failure. It currently retries the sa=
me
> # failed mirror and then fails rather then trying another. It *does*
> # try the next if the size is mismatched though.
> #MASTER_SITE_FREEBSD=3Dyes
> DISABLE_MAKE_JOBS=3Dpoudriere
> ---End make.conf---
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D<p=
hase: check-sanity >=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> =3D=3D=3D> License PD accepted by the user
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D<p=
hase: pkg-depends >=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> =3D=3D=3D> ncbi-blast+-2.2.30_2 depends on file: /usr/local/sbin/pkg =
- not found
> =3D=3D=3D> Installing existing package /packages/All/pkg-1.8.7_1.txz
> [93amd64-default-job-14] Installing pkg-1.8.7_1...
> [93amd64-default-job-14] Extracting pkg-1.8.7_1: .......... done
> =3D=3D=3D> ncbi-blast+-2.2.30_2 depends on file: /usr/local/sbin/pkg =
- found
> =3D=3D=3D> Returning to build of ncbi-blast+-2.2.30_2
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D<p=
hase: fetch-depends >=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D<p=
hase: fetch >=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> =3D=3D=3D> License PD accepted by the user
> =3D=3D=3D> Fetching all distfiles required by ncbi-blast+-2.2.30_2 for =
building
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D<p=
hase: checksum >=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> =3D=3D=3D> License PD accepted by the user
> =3D=3D=3D> Fetching all distfiles required by ncbi-blast+-2.2.30_2 for =
building
> =3D> SHA256 Checksum OK for ncbi-blast-2.2.30+-src.tar.gz.
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D<p=
hase: extract-depends>=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D<p=
hase: extract >=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> =3D=3D=3D> License PD accepted by the user
> =3D=3D=3D> Fetching all distfiles required by ncbi-blast+-2.2.30_2 for =
building
> =3D=3D=3D> Extracting for ncbi-blast+-2.2.30_2
> =3D> SHA256 Checksum OK for ncbi-blast-2.2.30+-src.tar.gz.
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D<p=
hase: patch-depends >=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D<p=
hase: patch >=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> =3D=3D=3D> Patching for ncbi-blast+-2.2.30_2
> =3D=3D=3D> Applying FreeBSD patches for ncbi-blast+-2.2.30_2
> /usr/bin/sed -i.bak -e 's|-D_THREAD_SAFE|-D_THREAD_SAFE -D__RUNETYPE_I=
NTERNAL|' -e '/--infodir=3DDIR/d' -e '/--mandir=3DDIR/d' /wrkdirs/usr/=
ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++/src/build-syste=
m/configure
> /usr/bin/sed -i.bak -e 's|@prefix@|/wrkdirs/usr/ports/biology/ncbi-blas=
t+/work/stage@prefix@|g' /wrkdirs/usr/ports/biology/ncbi-blast+/work/ncb=
i-blast-2.2.30+-src/c++/src/build-system/Makefile.in.top
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D<p=
hase: build-depends >=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> =3D=3D=3D> ncbi-blast+-2.2.30_2 depends on executable: gmake - not fo=
und
> =3D=3D=3D> Installing existing package /packages/All/gmake-4.2.1_1.tx=
z
> [93amd64-default-job-14] Installing gmake-4.2.1_1...
> [93amd64-default-job-14] `-- Installing indexinfo-0.2.4...
> [93amd64-default-job-14] `-- Extracting indexinfo-0.2.4: .... done
> [93amd64-default-job-14] `-- Installing libiconv-1.14_9...
> [93amd64-default-job-14] `-- Extracting libiconv-1.14_9: .......... don=
e
> [93amd64-default-job-14] `-- Installing gettext-runtime-0.19.8.1...
> [93amd64-default-job-14] `-- Extracting gettext-runtime-0.19.8.1: .....=
=2E.... done
> [93amd64-default-job-14] Extracting gmake-4.2.1_1: .......... done
> =3D=3D=3D> ncbi-blast+-2.2.30_2 depends on executable: gmake - found
> =3D=3D=3D> Returning to build of ncbi-blast+-2.2.30_2
> =3D=3D=3D> ncbi-blast+-2.2.30_2 depends on file: /usr/local/bin/pytho=
n2.7 - not found
> =3D=3D=3D> Installing existing package /packages/All/python27-2.7.12.=
txz
> [93amd64-default-job-14] Installing python27-2.7.12...
> [93amd64-default-job-14] `-- Installing libffi-3.2.1...
> [93amd64-default-job-14] `-- Extracting libffi-3.2.1: .......... done
> [93amd64-default-job-14] Extracting python27-2.7.12: .......... done
> Message from python27-2.7.12:
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D
>
> Note that some standard Python modules are provided as separate ports
> as they require additional dependencies. They are available as:
>
> bsddb databases/py-bsddb
> gdbm databases/py-gdbm
> sqlite3 databases/py-sqlite3
> tkinter x11-toolkits/py-tkinter
>
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D
> =3D=3D=3D> ncbi-blast+-2.2.30_2 depends on file: /usr/local/bin/pytho=
n2.7 - found
> =3D=3D=3D> Returning to build of ncbi-blast+-2.2.30_2
> =3D=3D=3D> ncbi-blast+-2.2.30_2 depends on executable: gcc48 - not fo=
und
> =3D=3D=3D> Installing existing package /packages/All/gcc-4.8.5_2.txz
> [93amd64-default-job-14] Installing gcc-4.8.5_2...
> [93amd64-default-job-14] `-- Installing mpc-1.0.3...
> [93amd64-default-job-14] | `-- Installing gmp-5.1.3_3...
> [93amd64-default-job-14] | `-- Extracting gmp-5.1.3_3: .......... don=
e
> [93amd64-default-job-14] | `-- Installing mpfr-3.1.4...
> [93amd64-default-job-14] | `-- Extracting mpfr-3.1.4: .......... done=
> [93amd64-default-job-14] `-- Extracting mpc-1.0.3: ...... done
> [93amd64-default-job-14] `-- Installing gcc-ecj-4.5...
> [93amd64-default-job-14] `-- Extracting gcc-ecj-4.5: . done
> [93amd64-default-job-14] `-- Installing binutils-2.27,1...
> [93amd64-default-job-14] `-- Extracting binutils-2.27,1: .......... don=
e
> [93amd64-default-job-14] Extracting gcc-4.8.5_2: .......... done
> Message from gcc-4.8.5_2:
> To ensure binaries built with this toolchain find appropriate versions
> of the necessary run-time libraries, you may want to link using
>
> -Wl,-rpath=3D/usr/local/lib/gcc48
>
> For ports leveraging USE_GCC, USES=3Dcompiler, or USES=3Dfortran this h=
appens
> transparently.
> =3D=3D=3D> ncbi-blast+-2.2.30_2 depends on executable: gcc48 - found
> =3D=3D=3D> Returning to build of ncbi-blast+-2.2.30_2
> =3D=3D=3D> ncbi-blast+-2.2.30_2 depends on file: /usr/local/bin/as - =
found
> =3D=3D=3D> ncbi-blast+-2.2.30_2 depends on package: perl5>=3D5.20<5.2=
1 - not found
> =3D=3D=3D> Installing existing package /packages/All/perl5-5.20.3_15.=
txz
> [93amd64-default-job-14] Installing perl5-5.20.3_15...
> [93amd64-default-job-14] Extracting perl5-5.20.3_15: .......... done
> Message from perl5-5.20.3_15:
> The /usr/bin/perl symlink has been removed starting with Perl 5.20.
> For shebangs, you should either use:
>
> #!/usr/local/bin/perl
>
> or
>
> #!/usr/bin/env perl
>
> The first one will only work if you have a /usr/local/bin/perl,
> the second will work as long as perl is in PATH.
> =3D=3D=3D> ncbi-blast+-2.2.30_2 depends on package: perl5>=3D5.20<5.2=
1 - found
> =3D=3D=3D> Returning to build of ncbi-blast+-2.2.30_2
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D<p=
hase: lib-depends >=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> =3D=3D=3D> ncbi-blast+-2.2.30_2 depends on shared library: libpcre.so=
- not found
> =3D=3D=3D> Installing existing package /packages/All/pcre-8.39.txz
> [93amd64-default-job-14] Installing pcre-8.39...
> [93amd64-default-job-14] Extracting pcre-8.39: .......... done
> =3D=3D=3D> ncbi-blast+-2.2.30_2 depends on shared library: libpcre.so=
- found (/usr/local/lib/libpcre.so)
> =3D=3D=3D> Returning to build of ncbi-blast+-2.2.30_2
> =3D=3D=3D> ncbi-blast+-2.2.30_2 depends on shared library: libbz2.so =
- found (/usr/lib/libbz2.so)
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D
> =3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D<p=
hase: configure >=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=
=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D=3D
> =3D=3D=3D> Configuring for ncbi-blast+-2.2.30_2
> configure: loading site script /usr/ports/Templates/config.site
> configure: creating cache config.cache
> checking build system type... amd64-portbld-freebsd9.3
> checking host system type... amd64-portbld-freebsd9.3
> checking for a BSD-compatible install... /usr/bin/install -c
> checking for gcc... gcc48
> checking for C compiler default output file name... a.out
> checking whether the C compiler works... yes
> checking whether we are cross compiling... no
> checking for suffix of executables...
> checking for suffix of object files... o
> checking whether we are using the GNU C compiler... yes
> checking whether gcc48 accepts -g... yes
> checking for gcc48 option to accept ISO C89... none needed
> checking whether we are using the GNU C++ compiler... yes
> checking whether g++48 accepts -g... yes
> adjusted C compiler: /usr/local/bin/gcc48
> adjusted C++ compiler: /usr/local/bin/g++48
> Using built-in specs.
> COLLECT_GCC=3D/usr/local/bin/gcc48
> COLLECT_LTO_WRAPPER=3D/usr/local/libexec/gcc48/gcc/x86_64-portbld-freeb=
sd9.3/4.8.5/lto-wrapper
> Target: x86_64-portbld-freebsd9.3
> Configured with: /wrkdirs/usr/ports/lang/gcc/work/gcc-4.8.5/configure -=
-disable-bootstrap --disable-nls --enable-gnu-indirect-function --libdir=3D=
/usr/local/lib/gcc48 --libexecdir=3D/usr/local/libexec/gcc48 --program-su=
ffix=3D48 --with-as=3D/usr/local/bin/as --with-gmp=3D/usr/local --with-gx=
x-include-dir=3D/usr/local/lib/gcc48/include/c++/ --with-ld=3D/usr/local/=
bin/ld --with-libiconv-prefix=3D/usr/local --with-pkgversion=3D'FreeBSD P=
orts Collection' --with-system-zlib --with-ecj-jar=3D/usr/local/share/jav=
a/ecj-4.5.jar --enable-languages=3Dc,c++,objc,fortran,java --prefix=3D/us=
r/local --localstatedir=3D/var --mandir=3D/usr/local/man --infodir=3D/usr=
/local/info/gcc48 --build=3Dx86_64-portbld-freebsd9.3
> Thread model: posix
> gcc version 4.8.5 (FreeBSD Ports Collection)
> checking whether /usr/local/bin/gcc48 has an option to export all symb=
ols... -Wl,-export-dynamic
> checking whether /usr/local/bin/gcc48 supports -Wl,--{en,dis}able-new-=
dtags... yes
> checking whether _LIBCPP_VERSION is declared... no
> checking how to enable C++ '11 features in /usr/local/bin/g++48 ... -st=
d=3Dgnu++11
> checking how to enable C '11 or at least '99 features in /usr/local/bin=
/gcc48 ... -std=3Dgnu11 -fgnu89-inline
> checking whether ln -s works... yes
> checking for ranlib... /usr/local/bin/ranlib
> checking for ar... ar cr
> checking ranlib's effectiveness... neutral
> checking for strip... strip
> checking whether strip loses runtime type information... Segmentation f=
ault
> yes
> Do you still want to proceed (at your own risk)? [y/N]
> configure: error: Configuration has been canceled by user.
> =3D=3D=3D> Script "configure" failed unexpectedly.
> Please report the problem to bacon4000@gmail.com [maintainer] and attac=
h the
> "/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.2.30+-src/c++=
/config.log"
> including the output of the failure of your make command. Also, it migh=
t be
> a good idea to provide an overview of all packages installed on your sy=
stem
> (e.g. a /usr/local/sbin/pkg-static info -g -Ea).
> *** [do-configure] Error code 1
>
> Stop in /usr/ports/biology/ncbi-blast+.
--=20
Those who spend their lives in the shallows see their whole world in turm=
oil
every time the wind blows.
Those who explore the depths see only ripples at the surface of an otherw=
ise
serene world.
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?125e3373-730e-cdec-c5fc-506412c760cf>