[package - 130releng-armv7-quarterly][biology/ncbi-blast+] Failed for ncbi-blast+-2.12.0 in configure
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Date: Wed, 15 Sep 2021 09:52:10 UTC
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: jwb@FreeBSD.org
Log URL: http://beefy12.nyi.freebsd.org/data/130releng-armv7-quarterly/5744604f85d8/logs/ncbi-blast+-2.12.0.log
Build URL: http://beefy12.nyi.freebsd.org/build.html?mastername=130releng-armv7-quarterly&build=5744604f85d8
Log:
=>> Building biology/ncbi-blast+
build started at Wed Sep 15 09:51:17 UTC 2021
port directory: /usr/ports/biology/ncbi-blast+
package name: ncbi-blast+-2.12.0
building for: FreeBSD 130releng-armv7-quarterly-job-08 13.0-RELEASE-p4 FreeBSD 13.0-RELEASE-p4 1300139 arm
maintained by: jwb@FreeBSD.org
Makefile ident:
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AR="ar cr" --without-boost --libdir=/usr/local/lib/ncbi-tools++ --prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
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=======================<phase: check-sanity >============================
===> License PD accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> ncbi-blast+-2.12.0 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.16.3.txz
[130releng-armv7-quarterly-job-08] Installing pkg-1.16.3...
[130releng-armv7-quarterly-job-08] Extracting pkg-1.16.3: .......... done
===> ncbi-blast+-2.12.0 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of ncbi-blast+-2.12.0
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License PD accepted by the user
===> Fetching all distfiles required by ncbi-blast+-2.12.0 for building
===========================================================================
=======================<phase: checksum >============================
===> License PD accepted by the user
===> Fetching all distfiles required by ncbi-blast+-2.12.0 for building
=> SHA256 Checksum OK for ncbi-blast-2.12.0+-src.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License PD accepted by the user
===> Fetching all distfiles required by ncbi-blast+-2.12.0 for building
===> Extracting for ncbi-blast+-2.12.0
=> SHA256 Checksum OK for ncbi-blast-2.12.0+-src.tar.gz.
===========================================================================
<snip>
[130releng-armv7-quarterly-job-08] `-- Installing libidn2-2.3.1...
[130releng-armv7-quarterly-job-08] | `-- Installing libunistring-0.9.10_1...
[130releng-armv7-quarterly-job-08] | `-- Extracting libunistring-0.9.10_1: .......... done
[130releng-armv7-quarterly-job-08] `-- Extracting libidn2-2.3.1: .......... done
[130releng-armv7-quarterly-job-08] `-- Installing libtasn1-4.17.0...
[130releng-armv7-quarterly-job-08] `-- Extracting libtasn1-4.17.0: .......... done
[130releng-armv7-quarterly-job-08] `-- Installing nettle-3.7.3...
[130releng-armv7-quarterly-job-08] `-- Extracting nettle-3.7.3: .......... done
[130releng-armv7-quarterly-job-08] `-- Installing p11-kit-0.24.0...
[130releng-armv7-quarterly-job-08] | `-- Installing glib-2.66.8,2...
[130releng-armv7-quarterly-job-08] | | `-- Installing libiconv-1.16...
[130releng-armv7-quarterly-job-08] | | `-- Extracting libiconv-1.16: .......... done
[130releng-armv7-quarterly-job-08] | | `-- Installing libxml2-2.9.12...
[130releng-armv7-quarterly-job-08] | | `-- Extracting libxml2-2.9.12: .......... done
[130releng-armv7-quarterly-job-08] | `-- Extracting glib-2.66.8,2: .......... done
No schema files found: doing nothing.
[130releng-armv7-quarterly-job-08] `-- Extracting p11-kit-0.24.0: .......... done
[130releng-armv7-quarterly-job-08] `-- Installing trousers-0.3.14_3...
[130releng-armv7-quarterly-job-08] | `-- Installing tpm-emulator-0.7.4_2...
===> Creating groups.
Creating group '_tss' with gid '601'.
===> Creating users
Creating user '_tss' with uid '601'.
[130releng-armv7-quarterly-job-08] | `-- Extracting tpm-emulator-0.7.4_2: ......... done
===> Creating groups.
Using existing group '_tss'.
===> Creating users
Using existing user '_tss'.
[130releng-armv7-quarterly-job-08] `-- Extracting trousers-0.3.14_3: .......... done
[130releng-armv7-quarterly-job-08] Extracting gnutls-3.6.15: .......... done
=====
Message from ca_root_nss-3.63:
--
FreeBSD does not, and can not warrant that the certification authorities
whose certificates are included in this package have in any way been
audited for trustworthiness or RFC 3647 compliance.
Assessment and verification of trust is the complete responsibility of the
system administrator.
This package installs symlinks to support root certificates discovery by
default for software that uses OpenSSL.
This enables SSL Certificate Verification by client software without manual
intervention.
If you prefer to do this manually, replace the following symlinks with
either an empty file or your site-local certificate bundle.
* /etc/ssl/cert.pem
* /usr/local/etc/ssl/cert.pem
* /usr/local/openssl/cert.pem
=====
Message from trousers-0.3.14_3:
--
To run tcsd automatically, add the following line to /etc/rc.conf:
tcsd_enable="YES"
You might want to edit /usr/local/etc/tcsd.conf to reflect your setup.
If you want to use tcsd with software TPM emulator, use the following
configuration in /etc/rc.conf:
tcsd_enable="YES"
tcsd_mode="emulator"
tpmd_enable="YES"
To use TPM, add your_account to '_tss' group like following:
# pw groupmod _tss -m your_account
===> ncbi-blast+-2.12.0 depends on shared library: libgnutls.so - found (/usr/local/lib/libgnutls.so)
===> Returning to build of ncbi-blast+-2.12.0
===> ncbi-blast+-2.12.0 depends on shared library: libtspi.so - found (/usr/local/lib/libtspi.so)
===> ncbi-blast+-2.12.0 depends on shared library: libgmp.so - found (/usr/local/lib/libgmp.so)
===> ncbi-blast+-2.12.0 depends on shared library: libidn2.so - found (/usr/local/lib/libidn2.so)
===> ncbi-blast+-2.12.0 depends on shared library: libnettle.so - found (/usr/local/lib/libnettle.so)
===> ncbi-blast+-2.12.0 depends on shared library: libhogweed.so - found (/usr/local/lib/libhogweed.so)
===> ncbi-blast+-2.12.0 depends on shared library: libtasn1.so - found (/usr/local/lib/libtasn1.so)
===> ncbi-blast+-2.12.0 depends on shared library: libp11-kit.so - found (/usr/local/lib/libp11-kit.so)
===> ncbi-blast+-2.12.0 depends on shared library: libgcrypt.so - not found
===> Installing existing package /packages/All/libgcrypt-1.9.3.txz
[130releng-armv7-quarterly-job-08] Installing libgcrypt-1.9.3...
[130releng-armv7-quarterly-job-08] `-- Installing libgpg-error-1.42...
[130releng-armv7-quarterly-job-08] `-- Extracting libgpg-error-1.42: .......... done
[130releng-armv7-quarterly-job-08] Extracting libgcrypt-1.9.3: .......... done
===> ncbi-blast+-2.12.0 depends on shared library: libgcrypt.so - found (/usr/local/lib/libgcrypt.so)
===> Returning to build of ncbi-blast+-2.12.0
===> ncbi-blast+-2.12.0 depends on shared library: libgpg-error.so - found (/usr/local/lib/libgpg-error.so)
===> ncbi-blast+-2.12.0 depends on shared library: libsqlite3.so - not found
===> Installing existing package /packages/All/sqlite3-3.35.5_3,1.txz
[130releng-armv7-quarterly-job-08] Installing sqlite3-3.35.5_3,1...
[130releng-armv7-quarterly-job-08] `-- Installing libedit-3.1.20210216,1...
[130releng-armv7-quarterly-job-08] `-- Extracting libedit-3.1.20210216,1: .......... done
[130releng-armv7-quarterly-job-08] Extracting sqlite3-3.35.5_3,1: .......... done
===> ncbi-blast+-2.12.0 depends on shared library: libsqlite3.so - found (/usr/local/lib/libsqlite3.so)
===> Returning to build of ncbi-blast+-2.12.0
===> ncbi-blast+-2.12.0 depends on shared library: libuv.so - not found
===> Installing existing package /packages/All/libuv-1.41.0.txz
[130releng-armv7-quarterly-job-08] Installing libuv-1.41.0...
[130releng-armv7-quarterly-job-08] Extracting libuv-1.41.0: .......... done
===> ncbi-blast+-2.12.0 depends on shared library: libuv.so - found (/usr/local/lib/libuv.so)
===> Returning to build of ncbi-blast+-2.12.0
===> ncbi-blast+-2.12.0 depends on shared library: libnghttp2.so - not found
===> Installing existing package /packages/All/libnghttp2-1.43.0.txz
[130releng-armv7-quarterly-job-08] Installing libnghttp2-1.43.0...
[130releng-armv7-quarterly-job-08] Extracting libnghttp2-1.43.0: .......... done
===> ncbi-blast+-2.12.0 depends on shared library: libnghttp2.so - found (/usr/local/lib/libnghttp2.so)
===> Returning to build of ncbi-blast+-2.12.0
===> ncbi-blast+-2.12.0 depends on shared library: libgrpc.so - not found
===> Installing existing package /packages/All/grpc-1.38.1_1,2.txz
[130releng-armv7-quarterly-job-08] Installing grpc-1.38.1_1,2...
[130releng-armv7-quarterly-job-08] `-- Installing abseil-20210324.2...
[130releng-armv7-quarterly-job-08] `-- Extracting abseil-20210324.2: .......... done
[130releng-armv7-quarterly-job-08] `-- Installing benchmark-1.5.5...
[130releng-armv7-quarterly-job-08] `-- Extracting benchmark-1.5.5: .......... done
[130releng-armv7-quarterly-job-08] `-- Installing c-ares-1.17.1...
[130releng-armv7-quarterly-job-08] `-- Extracting c-ares-1.17.1: .......... done
[130releng-armv7-quarterly-job-08] `-- Installing gflags-2.2.2_2...
[130releng-armv7-quarterly-job-08] `-- Extracting gflags-2.2.2_2: .......... done
[130releng-armv7-quarterly-job-08] `-- Installing protobuf-3.14.0,1...
[130releng-armv7-quarterly-job-08] `-- Extracting protobuf-3.14.0,1: .......... done
[130releng-armv7-quarterly-job-08] `-- Installing re2-20210601...
[130releng-armv7-quarterly-job-08] `-- Extracting re2-20210601: .......... done
[130releng-armv7-quarterly-job-08] Extracting grpc-1.38.1_1,2: .......... done
===> ncbi-blast+-2.12.0 depends on shared library: libgrpc.so - found (/usr/local/lib/libgrpc.so)
===> Returning to build of ncbi-blast+-2.12.0
===========================================================================
=======================<phase: configure >============================
===> Configuring for ncbi-blast+-2.12.0
configure: loading site script /usr/ports/Templates/config.site
configure: creating cache config.cache
checking TeamCity build number... none
checking Subversion revision... unknown
checking NCBI stable components' version... unknown
checking build system type... armv7-portbld-freebsd13.0
checking host system type... armv7-portbld-freebsd13.0
checking for a BSD-compatible install... /usr/bin/install -c
checking for gcc... /nxb-bin/usr/bin/cc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether /nxb-bin/usr/bin/cc accepts -g... yes
checking for /nxb-bin/usr/bin/cc option to accept ISO C89... none needed
checking how to run the C preprocessor... /nxb-bin/usr/bin/cpp
checking for armv7-portbld-freebsd13.0-gcc... no
checking for gcc... no
checking for armv7-portbld-freebsd13.0-cc... no
checking for cc... cc
checking whether we are using the GNU C compiler... yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking how to run the C preprocessor... cc -E
checking whether we are using the GNU C++ compiler... yes
checking whether /nxb-bin/usr/bin/c++ accepts -g... yes
adjusted C compiler: /nxb-bin/usr/bin/cc
adjusted C++ compiler: /nxb-bin/usr/bin/c++
checking for grep that handles long lines and -e... (cached) /usr/bin/grep
checking for egrep... (cached) /usr/bin/egrep
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checking for sys/stat.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for memory.h... (cached) yes
checking for strings.h... (cached) yes
checking for inttypes.h... (cached) yes
checking for stdint.h... (cached) yes
checking for unistd.h... (cached) yes
checking for minix/config.h... (cached) no
checking whether it is safe to define __EXTENSIONS__... yes
checking whether /nxb-bin/usr/bin/cc has an option to export all symbols... no
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checking whether /nxb-bin/usr/bin/cc has an option to link in whole static archives... no
checking whether /nxb-bin/usr/bin/c++ supports -stdlib=libc++... no
checking whether _LIBCPP_VERSION is declared... yes
checking how to enable C++ '14 features in /nxb-bin/usr/bin/c++ ... no
configure: error: Please upgrade to a compiler supporting C++ '14, such as GCC 5 or newer.
===> Script "configure" failed unexpectedly.
Please report the problem to jwb@FreeBSD.org [maintainer] and attach the
"/wrkdirs/usr/ports/biology/ncbi-blast+/work/ncbi-blast-2.12.0+-src/c++/config.log"
including the output of the failure of your make command. Also, it might be
a good idea to provide an overview of all packages installed on your system
(e.g. a /usr/local/sbin/pkg-static info -g -Ea).
*** Error code 1
Stop.
make: stopped in /usr/ports/biology/ncbi-blast+