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Date:      Sun, 5 Apr 2020 04:51:48 GMT
From:      pkg-fallout@FreeBSD.org
To:        yuri@FreeBSD.org
Cc:        pkg-fallout@FreeBSD.org
Subject:   [package - head-i386-default][biology/ncbi-cxx-toolkit] Failed for ncbi-cxx-toolkit-21.0.0_2 in configure
Message-ID:  <202004050451.0354pmB4020574@beefy17.nyi.freebsd.org>

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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:     yuri@FreeBSD.org
Last committer: zeising@FreeBSD.org
Ident:          $FreeBSD: head/biology/ncbi-cxx-toolkit/Makefile 516742 2019-11-04 21:08:20Z zeising $
Log URL:        http://beefy17.nyi.freebsd.org/data/head-i386-default/p530538_s359627/logs/ncbi-cxx-toolkit-21.0.0_2.log
Build URL:      http://beefy17.nyi.freebsd.org/build.html?mastername=head-i386-default&build=p530538_s359627
Log:

=>> Building biology/ncbi-cxx-toolkit
build started at Sun Apr  5 04:51:28 UTC 2020
port directory: /usr/ports/biology/ncbi-cxx-toolkit
package name: ncbi-cxx-toolkit-21.0.0_2
building for: FreeBSD head-i386-default-job-09 13.0-CURRENT FreeBSD 13.0-CURRENT 1300088 i386
maintained by: yuri@FreeBSD.org
Makefile ident:      $FreeBSD: head/biology/ncbi-cxx-toolkit/Makefile 516742 2019-11-04 21:08:20Z zeising $
Poudriere version: 3.2.8-5-gc81843e5
Host OSVERSION: 1300076
Jail OSVERSION: 1300088
Job Id: 09




!!! Jail is newer than host. (Jail: 1300088, Host: 1300076) !!!
!!! This is not supported. !!!
!!! Host kernel must be same or newer than jail. !!!
!!! Expect build failures. !!!



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MAKE_ARGS=
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---Begin OPTIONS List---
---End OPTIONS List---

--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--

--CONFIGURE_ARGS--
--without-debug --with-dll --without-static --x-libraries=/usr/local/lib --x-includes=/usr/local/include --prefix=/usr/local ${_LATE_CONFIGURE_ARGS}
--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
MAKE=gmake ac_cv_path_PERL=/usr/local/bin/perl ac_cv_path_PERL_PATH=/usr/local/bin/perl  PERL_USE_UNSAFE_INC=1 PYTHON="/usr/local/bin/python3.7" XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work  HOME=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh CONFIG_SITE=/usr/ports/Templates/config.site lt_cv_sys_max_cmd_len=524288
--End CONFIGURE_ENV--

--MAKE_ENV--
PERL_USE_UNSAFE_INC=1 OPENSSLBASE=/usr OPENSSLDIR=/etc/ssl OPENSSLINC=/usr/include OPENSSLLIB=/usr/lib XDG_DATA_HOME=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work  HOME=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local  LOCALBASE=/usr/local  CC="cc" CFLAGS="-O2 -pipe  -fstack-protector-strong -fno-strict-aliasing "  CPP="cpp" CPPFLAGS=""  LDFLAGS="  -fstack-protector-strong " LIBS=""  CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing  "  MANPREFIX="/usr/local" BSD_INSTALL_PROGRAM="install  -s -m 555"  BSD_INSTALL_LIB="install  -s -m 0644"  BSD_INSTALL_SCRIPT="install  -m 555"  BSD_INSTALL_DATA="install  -m 0644"  BSD_INSTALL_MAN="install  -m 444"
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--End PLIST_SUB--

--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local  DATADIR=/usr/local/share/ncbi-cxx-toolkit DOCSDIR=/usr/local/share/doc/ncbi-cxx-toolkit EXAMPLESDIR=/usr/local/share/examples/ncbi-cxx-toolkit  WWWDIR=/usr/local/www/ncbi-cxx-toolkit ETCDIR=/usr/local/etc/ncbi-cxx-toolkit
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---Begin make.conf---
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BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
MACHINE=i386
MACHINE_ARCH=i386
ARCH=${MACHINE_ARCH}
#### /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 same
# failed mirror and then fails rather then trying another.  It *does*
# try the next if the size is mismatched though.
#MASTER_SITE_FREEBSD=yes
# Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs
MAKE_JOBS_NUMBER=2
#### /usr/ports/Mk/Scripts/ports_env.sh ####
_CCVERSION_921dbbb2=FreeBSD clang version 10.0.0 (git@github.com:llvm/llvm-project.git llvmorg-10.0.0-0-gd32170dbd5b) Target: i386-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin
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CC_OUTPUT_921dbbb2_58173849=yes
CC_OUTPUT_921dbbb2_9bdba57c=yes
CC_OUTPUT_921dbbb2_6a4fe7f5=yes
CC_OUTPUT_921dbbb2_6bcac02b=yes
CC_OUTPUT_921dbbb2_67d20829=yes
CC_OUTPUT_921dbbb2_bfa62e83=yes
CC_OUTPUT_921dbbb2_f0b4d593=yes
CC_OUTPUT_921dbbb2_308abb44=yes
CC_OUTPUT_921dbbb2_f00456e5=yes
CC_OUTPUT_921dbbb2_65ad290d=yes
CC_OUTPUT_921dbbb2_f2776b26=yes
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CC_OUTPUT_921dbbb2_380987f7=yes
CC_OUTPUT_921dbbb2_160933ec=yes
CC_OUTPUT_921dbbb2_fb62803b=yes
_OBJC_CCVERSION_921dbbb2=FreeBSD clang version 10.0.0 (git@github.com:llvm/llvm-project.git llvmorg-10.0.0-0-gd32170dbd5b) Target: i386-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin
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ARCH=i386
OPSYS=FreeBSD
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OSVERSION=1300088
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CONFIGURE_MAX_CMD_LEN=524288
HAVE_PORTS_ENV=1
#### Misc Poudriere ####
GID=0
UID=0
---End make.conf---
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cpu time               (seconds, -t)  unlimited
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data seg size           (kbytes, -d)  524288
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locked memory           (kbytes, -l)  unlimited
max user processes              (-u)  89999
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virtual mem size        (kbytes, -v)  unlimited
swap limit              (kbytes, -w)  unlimited
socket buffer size       (bytes, -b)  unlimited
pseudo-terminals                (-p)  unlimited
kqueues                         (-k)  unlimited
umtx shared locks               (-o)  unlimited
--End resource limits--
=======================<phase: check-sanity   >============================
===>  License PD accepted by the user
===========================================================================
=======================<phase: pkg-depends    >============================
===>   ncbi-cxx-toolkit-21.0.0_2 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.14.2.txz
[head-i386-default-job-09] Installing pkg-1.14.2...
[head-i386-default-job-09] Extracting pkg-1.14.2: .......... done
ldconfig: aout support is deprecated
===>   ncbi-cxx-toolkit-21.0.0_2 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of ncbi-cxx-toolkit-21.0.0_2
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===>  License PD accepted by the user
===> Fetching all distfiles required by ncbi-cxx-toolkit-21.0.0_2 for building
===========================================================================
=======================<phase: checksum       >============================
===>  License PD accepted by the user
===> Fetching all distfiles required by ncbi-cxx-toolkit-21.0.0_2 for building
=> SHA256 Checksum OK for ncbi_cxx--21_0_0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===>  License PD accepted by the user
===> Fetching all distfiles required by ncbi-cxx-toolkit-21.0.0_2 for building
===>  Extracting for ncbi-cxx-toolkit-21.0.0_2
=> SHA256 Checksum OK for ncbi_cxx--21_0_0.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for ncbi-cxx-toolkit-21.0.0_2
===>  Applying FreeBSD patches for ncbi-cxx-toolkit-21.0.0_2
===========================================================================
=======================<phase: build-depends  >============================
===>   ncbi-cxx-toolkit-21.0.0_2 depends on executable: gmake - not found
===>   Installing existing package /packages/All/gmake-4.2.1_3.txz
[head-i386-default-job-09] Installing gmake-4.2.1_3...
[head-i386-default-job-09] `-- Installing gettext-runtime-0.20.1...
[head-i386-default-job-09] |   `-- Installing indexinfo-0.3.1...
[head-i386-default-job-09] |   `-- Extracting indexinfo-0.3.1: .... done
<snip>

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.
===>   ncbi-cxx-toolkit-21.0.0_2 depends on package: perl5>=5.30.r1<5.31 - found
===>   Returning to build of ncbi-cxx-toolkit-21.0.0_2
===>   ncbi-cxx-toolkit-21.0.0_2 depends on file: /usr/local/libdata/pkgconfig/x11.pc - not found
===>   Installing existing package /packages/All/libX11-1.6.9,1.txz
[head-i386-default-job-09] Installing libX11-1.6.9,1...
[head-i386-default-job-09] `-- Installing libXau-1.0.9...
[head-i386-default-job-09] `-- Extracting libXau-1.0.9: .......... done
ldconfig: aout support is deprecated
[head-i386-default-job-09] `-- Installing libXdmcp-1.1.3...
[head-i386-default-job-09] |   `-- Installing xorgproto-2019.2...
[head-i386-default-job-09] |   `-- Extracting xorgproto-2019.2: .......... done
[head-i386-default-job-09] `-- Extracting libXdmcp-1.1.3: ......... done
ldconfig: aout support is deprecated
[head-i386-default-job-09] `-- Installing libxcb-1.13.1...
[head-i386-default-job-09] |   `-- Installing libpthread-stubs-0.4...
[head-i386-default-job-09] |   `-- Extracting libpthread-stubs-0.4: .... done
[head-i386-default-job-09] |   `-- Installing libxml2-2.9.10...
[head-i386-default-job-09] |   `-- Extracting libxml2-2.9.10: .......... done
ldconfig: aout support is deprecated
[head-i386-default-job-09] `-- Extracting libxcb-1.13.1: .......... done
ldconfig: aout support is deprecated
[head-i386-default-job-09] Extracting libX11-1.6.9,1: .......... done
ldconfig: aout support is deprecated
===>   ncbi-cxx-toolkit-21.0.0_2 depends on file: /usr/local/libdata/pkgconfig/x11.pc - found
===>   Returning to build of ncbi-cxx-toolkit-21.0.0_2
===>   ncbi-cxx-toolkit-21.0.0_2 depends on file: /usr/local/libdata/pkgconfig/xpm.pc - not found
===>   Installing existing package /packages/All/libXpm-3.5.13.txz
[head-i386-default-job-09] Installing libXpm-3.5.13...
[head-i386-default-job-09] `-- Installing libXext-1.3.4,1...
[head-i386-default-job-09] `-- Extracting libXext-1.3.4,1: .......... done
ldconfig: aout support is deprecated
[head-i386-default-job-09] `-- Installing libXt-1.2.0,1...
[head-i386-default-job-09] |   `-- Installing libICE-1.0.10,1...
[head-i386-default-job-09] |   `-- Extracting libICE-1.0.10,1: .......... done
ldconfig: aout support is deprecated
[head-i386-default-job-09] |   `-- Installing libSM-1.2.3,1...
[head-i386-default-job-09] |   `-- Extracting libSM-1.2.3,1: .......... done
ldconfig: aout support is deprecated
[head-i386-default-job-09] `-- Extracting libXt-1.2.0,1: .......... done
ldconfig: aout support is deprecated
[head-i386-default-job-09] Extracting libXpm-3.5.13: .......... done
ldconfig: aout support is deprecated
===>   ncbi-cxx-toolkit-21.0.0_2 depends on file: /usr/local/libdata/pkgconfig/xpm.pc - found
===>   Returning to build of ncbi-cxx-toolkit-21.0.0_2
===========================================================================
=======================<phase: lib-depends    >============================
===>   ncbi-cxx-toolkit-21.0.0_2 depends on shared library: libpcre.so - not found
===>   Installing existing package /packages/All/pcre-8.43_2.txz
[head-i386-default-job-09] Installing pcre-8.43_2...
[head-i386-default-job-09] Extracting pcre-8.43_2: .......... done
ldconfig: aout support is deprecated
===>   ncbi-cxx-toolkit-21.0.0_2 depends on shared library: libpcre.so - found (/usr/local/lib/libpcre.so)
===>   Returning to build of ncbi-cxx-toolkit-21.0.0_2
===>   ncbi-cxx-toolkit-21.0.0_2 depends on shared library: libmysqlclient.so.20 - not found
===>   Installing existing package /packages/All/mysql57-client-5.7.29_1.txz
[head-i386-default-job-09] Installing mysql57-client-5.7.29_1...
[head-i386-default-job-09] `-- Installing curl-7.69.1_1...
[head-i386-default-job-09] |   `-- Installing ca_root_nss-3.51...
[head-i386-default-job-09] |   `-- Extracting ca_root_nss-3.51: ........ done
[head-i386-default-job-09] |   `-- Installing libnghttp2-1.40.0...
[head-i386-default-job-09] |   `-- Extracting libnghttp2-1.40.0: .......... done
ldconfig: aout support is deprecated
[head-i386-default-job-09] `-- Extracting curl-7.69.1_1: .......... done
ldconfig: aout support is deprecated
[head-i386-default-job-09] `-- Installing cyrus-sasl-2.1.27_1...
*** Added group `cyrus' (id 60)
*** Added user `cyrus' (id 60)
[head-i386-default-job-09] `-- Extracting cyrus-sasl-2.1.27_1: .......... done
ldconfig: aout support is deprecated
[head-i386-default-job-09] `-- Installing groff-1.22.4_3...
[head-i386-default-job-09] |   `-- Installing psutils-1.17_5...
[head-i386-default-job-09] |   | `-- Installing libpaper-1.1.24.4...
[head-i386-default-job-09] |   | `-- Extracting libpaper-1.1.24.4: .......... done
ldconfig: aout support is deprecated
[head-i386-default-job-09] |   `-- Extracting psutils-1.17_5: .......... done
[head-i386-default-job-09] |   `-- Installing uchardet-0.0.6...
[head-i386-default-job-09] |   `-- Extracting uchardet-0.0.6: .......... done
ldconfig: aout support is deprecated
[head-i386-default-job-09] `-- Extracting groff-1.22.4_3: .......... done
[head-i386-default-job-09] `-- Installing libedit-3.1.20191231,1...
[head-i386-default-job-09] `-- Extracting libedit-3.1.20191231,1: .......... done
ldconfig: aout support is deprecated
[head-i386-default-job-09] `-- Installing libevent-2.1.11...
[head-i386-default-job-09] `-- Extracting libevent-2.1.11: .......... done
ldconfig: aout support is deprecated
[head-i386-default-job-09] `-- Installing liblz4-1.9.2_1,1...
[head-i386-default-job-09] `-- Extracting liblz4-1.9.2_1,1: .......... done
ldconfig: aout support is deprecated
[head-i386-default-job-09] `-- Installing protobuf-3.11.4,1...
[head-i386-default-job-09] `-- Extracting protobuf-3.11.4,1: .......... done
ldconfig: aout support is deprecated
[head-i386-default-job-09] Extracting mysql57-client-5.7.29_1: .......... done
ldconfig: aout support is deprecated
=====
Message from ca_root_nss-3.51:

--
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 cyrus-sasl-2.1.27_1:

--
You can use sasldb2 for authentication, to add users use:

	saslpasswd2 -c username

If you want to enable SMTP AUTH with the system Sendmail, read
Sendmail.README

NOTE: This port has been compiled with a default pwcheck_method of
      auxprop.  If you want to authenticate your user by /etc/passwd,
      PAM or LDAP, install ports/security/cyrus-sasl2-saslauthd and
      set sasl_pwcheck_method to saslauthd after installing the
      Cyrus-IMAPd 2.X port.  You should also check the
      /usr/local/lib/sasl2/*.conf files for the correct
      pwcheck_method.
      If you want to use GSSAPI mechanism, install
      ports/security/cyrus-sasl2-gssapi.
      If you want to use SRP mechanism, install
      ports/security/cyrus-sasl2-srp.
      If you want to use LDAP auxprop plugin, install
      ports/security/cyrus-sasl2-ldapdb.
=====
Message from groff-1.22.4_3:

--
In order to be able to use the html driver, you need to install the following
packages:
 - ghostscript
 - netpbm
=====
Message from mysql57-client-5.7.29_1:

--
This is the mysql CLIENT without the server.
for complete server and client, please install databases/mysql57-server
===>   ncbi-cxx-toolkit-21.0.0_2 depends on shared library: libmysqlclient.so.20 - found (/usr/local/lib/mysql/libmysqlclient.so.20)
===>   Returning to build of ncbi-cxx-toolkit-21.0.0_2
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for ncbi-cxx-toolkit-21.0.0_2
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... i386-portbld-freebsd13.0
checking host system type... i386-portbld-freebsd13.0
checking for a BSD-compatible install... /usr/bin/install -c
checking for gcc... cc
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 cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking how to run the C preprocessor... cpp
checking for gcc... no
checking for cc... cc
checking whether we are using the GNU C compiler... (cached) yes
checking whether cc accepts -g... yes
checking for cc option to accept ISO C89... none needed
checking how to run the C preprocessor... cc -E
checking whether we are using the GNU C++ compiler... yes
checking whether c++ accepts -g... yes
configure: error: Do not know how to parse GCC version number 10.0.0
===>  Script "configure" failed unexpectedly.
Please report the problem to yuri@FreeBSD.org [maintainer] and attach the
"/wrkdirs/usr/ports/biology/ncbi-cxx-toolkit/work/ncbi_cxx--21_0_0/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-cxx-toolkit



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