[package - head-amd64-default][biology/ncbi-cxx-toolkit] Failed for ncbi-cxx-toolkit-21.0.0_2 in configure
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Sat Jul 18 20:32:25 UTC 2020
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 at FreeBSD.org
Last committer: zeising at FreeBSD.org
Ident: $FreeBSD: head/biology/ncbi-cxx-toolkit/Makefile 516742 2019-11-04 21:08:20Z zeising $
Log URL: http://beefy18.nyi.freebsd.org/data/head-amd64-default/p542461_s363297/logs/ncbi-cxx-toolkit-21.0.0_2.log
Build URL: http://beefy18.nyi.freebsd.org/build.html?mastername=head-amd64-default&build=p542461_s363297
Log:
=>> Building biology/ncbi-cxx-toolkit
build started at Sat Jul 18 20:32:08 UTC 2020
port directory: /usr/ports/biology/ncbi-cxx-toolkit
package name: ncbi-cxx-toolkit-21.0.0_2
building for: FreeBSD head-amd64-default-job-04 13.0-CURRENT FreeBSD 13.0-CURRENT 1300101 amd64
maintained by: yuri at FreeBSD.org
Makefile ident: $FreeBSD: head/biology/ncbi-cxx-toolkit/Makefile 516742 2019-11-04 21:08:20Z zeising $
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=======================<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-1.14.6.txz
[head-amd64-default-job-04] Installing pkg-1.14.6...
[head-amd64-default-job-04] Extracting pkg-1.14.6: .......... done
===> 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 from /usr/ports/biology/ncbi-cxx-toolkit/files
===========================================================================
=======================<phase: build-depends >============================
===> ncbi-cxx-toolkit-21.0.0_2 depends on package: gmake>=4.3 - not found
===> Installing existing package /packages/All/gmake-4.3_2.txz
[head-amd64-default-job-04] Installing gmake-4.3_2...
[head-amd64-default-job-04] `-- Installing gettext-runtime-0.20.2...
[head-amd64-default-job-04] | `-- Installing indexinfo-0.3.1...
[head-amd64-default-job-04] | `-- Extracting indexinfo-0.3.1: .... done
[head-amd64-default-job-04] `-- Extracting gettext-runtime-0.20.2: .......... done
[head-amd64-default-job-04] Extracting gmake-4.3_2: .......... done
===> ncbi-cxx-toolkit-21.0.0_2 depends on package: gmake>=4.3 - found
===> Returning to build of ncbi-cxx-toolkit-21.0.0_2
<snip>
py37-gdbm databases/py-gdbm at py37
py37-sqlite3 databases/py-sqlite3 at py37
py37-tkinter x11-toolkits/py-tkinter at py37
===> ncbi-cxx-toolkit-21.0.0_2 depends on file: /usr/local/bin/python3.7 - found
===> Returning to build of ncbi-cxx-toolkit-21.0.0_2
===> ncbi-cxx-toolkit-21.0.0_2 depends on package: perl5>=5.30.r1<5.31 - not found
===> Installing existing package /packages/All/perl5-5.30.3.txz
[head-amd64-default-job-04] Installing perl5-5.30.3...
[head-amd64-default-job-04] Extracting perl5-5.30.3: .......... done
=====
Message from perl5-5.30.3:
--
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.
===> 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_2,1.txz
[head-amd64-default-job-04] Installing libX11-1.6.9_2,1...
[head-amd64-default-job-04] `-- Installing libxcb-1.13.1...
[head-amd64-default-job-04] | `-- Installing libXau-1.0.9...
[head-amd64-default-job-04] | `-- Extracting libXau-1.0.9: .......... done
[head-amd64-default-job-04] | `-- Installing libXdmcp-1.1.3...
[head-amd64-default-job-04] | | `-- Installing xorgproto-2020.1...
[head-amd64-default-job-04] | | `-- Extracting xorgproto-2020.1: .......... done
[head-amd64-default-job-04] | `-- Extracting libXdmcp-1.1.3: ......... done
[head-amd64-default-job-04] | `-- Installing libpthread-stubs-0.4...
[head-amd64-default-job-04] | `-- Extracting libpthread-stubs-0.4: .... done
[head-amd64-default-job-04] | `-- Installing libxml2-2.9.10...
[head-amd64-default-job-04] | `-- Extracting libxml2-2.9.10: .......... done
[head-amd64-default-job-04] `-- Extracting libxcb-1.13.1: .......... done
[head-amd64-default-job-04] Extracting libX11-1.6.9_2,1: .......... done
===> 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-amd64-default-job-04] Installing libXpm-3.5.13...
[head-amd64-default-job-04] `-- Installing libXext-1.3.4,1...
[head-amd64-default-job-04] `-- Extracting libXext-1.3.4,1: .......... done
[head-amd64-default-job-04] `-- Installing libXt-1.2.0,1...
[head-amd64-default-job-04] | `-- Installing libICE-1.0.10,1...
[head-amd64-default-job-04] | `-- Extracting libICE-1.0.10,1: .......... done
[head-amd64-default-job-04] | `-- Installing libSM-1.2.3,1...
[head-amd64-default-job-04] | `-- Extracting libSM-1.2.3,1: .......... done
[head-amd64-default-job-04] `-- Extracting libXt-1.2.0,1: .......... done
[head-amd64-default-job-04] Extracting libXpm-3.5.13: .......... done
===> 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-8.44.txz
[head-amd64-default-job-04] Installing pcre-8.44...
[head-amd64-default-job-04] Extracting pcre-8.44: .......... done
===> 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-5.7.31.txz
[head-amd64-default-job-04] Installing mysql57-client-5.7.31...
[head-amd64-default-job-04] `-- Installing curl-7.71.1...
[head-amd64-default-job-04] | `-- Installing ca_root_nss-3.54...
[head-amd64-default-job-04] | `-- Extracting ca_root_nss-3.54: ........ done
[head-amd64-default-job-04] | `-- Installing libnghttp2-1.41.0...
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[head-amd64-default-job-04] `-- Extracting curl-7.71.1: .......... done
[head-amd64-default-job-04] `-- Installing cyrus-sasl-2.1.27_1...
*** Added group `cyrus' (id 60)
*** Added user `cyrus' (id 60)
[head-amd64-default-job-04] `-- Extracting cyrus-sasl-2.1.27_1: .......... done
[head-amd64-default-job-04] `-- Installing groff-1.22.4_3...
[head-amd64-default-job-04] | `-- Installing psutils-1.17_5...
[head-amd64-default-job-04] | | `-- Installing libpaper-1.1.24.4...
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[head-amd64-default-job-04] | `-- Extracting psutils-1.17_5: .......... done
[head-amd64-default-job-04] | `-- Installing uchardet-0.0.7...
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[head-amd64-default-job-04] `-- Extracting groff-1.22.4_3: .......... done
[head-amd64-default-job-04] `-- Installing libedit-3.1.20191231,1...
[head-amd64-default-job-04] `-- Extracting libedit-3.1.20191231,1: .......... done
[head-amd64-default-job-04] `-- Installing libevent-2.1.11_1...
[head-amd64-default-job-04] `-- Extracting libevent-2.1.11_1: .......... done
[head-amd64-default-job-04] `-- Installing liblz4-1.9.2_1,1...
[head-amd64-default-job-04] `-- Extracting liblz4-1.9.2_1,1: .......... done
[head-amd64-default-job-04] `-- Installing protobuf-3.12.3,1...
[head-amd64-default-job-04] `-- Extracting protobuf-3.12.3,1: .......... done
[head-amd64-default-job-04] Extracting mysql57-client-5.7.31: .......... done
=====
Message from ca_root_nss-3.54:
--
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-5.7.31:
--
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... amd64-portbld-freebsd13.0
checking host system type... amd64-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 10.0.1
===> Script "configure" failed unexpectedly.
Please report the problem to yuri at 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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