[package - main-amd64-default][biology/viennarna] Failed for viennarna-2.6.3 in configure
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Date: Sat, 09 Sep 2023 01:25:55 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: yuri@FreeBSD.org
Log URL: https://pkg-status.freebsd.org/beefy18/data/main-amd64-default/peb032111a352_s9c80d66ec1/logs/viennarna-2.6.3.log
Build URL: https://pkg-status.freebsd.org/beefy18/build.html?mastername=main-amd64-default&build=peb032111a352_s9c80d66ec1
Log:
=>> Building biology/viennarna
build started at Sat Sep 9 01:25:05 UTC 2023
port directory: /usr/ports/biology/viennarna
package name: viennarna-2.6.3
building for: FreeBSD main-amd64-default-job-11 15.0-CURRENT FreeBSD 15.0-CURRENT 1500000 amd64
maintained by: yuri@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1500000
Jail OSVERSION: 1500000
Job Id: 11
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---Begin OPTIONS List---
===> The following configuration options are available for viennarna-2.6.3:
DOCS=on: Build and/or install documentation
EXAMPLES=on: Build and/or install examples
===> Use 'make config' to modify these settings
---End OPTIONS List---
--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--
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--MAKE_ENV--
F77="gfortran12" F90="gfortran12" FC="gfortran12" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc12" F90FLAGS="-O -Wl,-rpath=/usr/local/lib/gcc12" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc12" PERL_USE_UNSAFE_INC=1 XDG_DATA_HOME=/wrkdirs/usr/ports/biology/viennarna/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/biology/viennarna/work XDG_CACHE_HOME=/wrkdirs/usr/ports/biology/viennarna/work/.cache HOME=/wrkdirs/usr/ports/biology/viennarna/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/biology/viennarna/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/biology/viennarna/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig MK_DEBUG_FILES=no MK_KERNEL_SYMBOLS=no SHELL=/bin/sh NO_LINT=YES ADDR2LINE="/usr/local/bin/addr2line" AR="/usr/local/bin/ar" AS="/usr/local/bin/as" CPPFILT="/usr/local/bin/c++filt" GPROF="/usr/local/bin/gprof" LD="/usr/local/bin/ld" NM="/usr/local/bin/nm" OBJCOPY="/usr
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--End MAKE_ENV--
--PLIST_SUB--
PORTDOCS="" PORTEXAMPLES="" OSREL=15.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib PERL_VERSION=5.34.1 PERL_VER=5.34 PERL5_MAN1=lib/perl5/site_perl/man/man1 PERL5_MAN3=lib/perl5/site_perl/man/man3 SITE_PERL=lib/perl5/site_perl SITE_ARCH=lib/perl5/site_perl/mach/5.34 DOCSDIR="share/doc/ViennaRNA" EXAMPLESDIR="share/examples/ViennaRNA" DATADIR="share/viennarna" WWWDIR="www/viennarna" ETCDIR="etc/viennarna"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/viennarna DOCSDIR=/usr/local/share/doc/ViennaRNA EXAMPLESDIR=/usr/local/share/examples/ViennaRNA WWWDIR=/usr/local/www/viennarna ETCDIR=/usr/local/etc/viennarna
--End SUB_LIST--
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#### /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
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# Build ALLOW_MAKE_JOBS_PACKAGES with 2 jobs
MAKE_JOBS_NUMBER=2
#### /usr/ports/Mk/Scripts/ports_env.sh ####
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core file size (512-blocks, -c) unlimited
max memory size (kbytes, -m) unlimited
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--End resource limits--
=======================<phase: check-sanity >============================
===> License ViennaRNALicense accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> viennarna-2.6.3 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.20.6.pkg
[main-amd64-default-job-11] Installing pkg-1.20.6...
[main-amd64-default-job-11] Extracting pkg-1.20.6: .......... done
===> viennarna-2.6.3 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of viennarna-2.6.3
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License ViennaRNALicense accepted by the user
===> Fetching all distfiles required by viennarna-2.6.3 for building
===========================================================================
=======================<phase: checksum >============================
===> License ViennaRNALicense accepted by the user
===> Fetching all distfiles required by viennarna-2.6.3 for building
=> SHA256 Checksum OK for ViennaRNA-2.6.3.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License ViennaRNALicense accepted by the user
===> Fetching all distfiles required by viennarna-2.6.3 for building
===> Extracting for viennarna-2.6.3
=> SHA256 Checksum OK for ViennaRNA-2.6.3.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for viennarna-2.6.3
===> Applying FreeBSD patches for viennarna-2.6.3 from /usr/ports/biology/viennarna/files
===========================================================================
=======================<phase: build-depends >============================
===> viennarna-2.6.3 depends on executable: bash - not found
===> Installing existing package /packages/All/bash-5.2.15.pkg
[main-amd64-default-job-11] Installing bash-5.2.15...
[main-amd64-default-job-11] `-- Installing gettext-runtime-0.22_1...
[main-amd64-default-job-11] | `-- Installing indexinfo-0.3.1...
[main-amd64-default-job-11] | `-- Extracting indexinfo-0.3.1: .... done
[main-amd64-default-job-11] `-- Extracting gettext-runtime-0.22_1: .......... done
[main-amd64-default-job-11] `-- Installing readline-8.2.1...
[main-amd64-default-job-11] `-- Extracting readline-8.2.1: .......... done
[main-amd64-default-job-11] Extracting bash-5.2.15: .......... done
<snip>
checking how to run the C preprocessor... cpp
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checking whether gmake sets $(MAKE)... (cached) yes
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checking if the linker (/usr/local/bin/ld) is GNU ld... yes
checking for BSD- or MS-compatible name lister (nm)... /usr/local/bin/nm
checking the name lister (/usr/local/bin/nm) interface... BSD nm
checking the maximum length of command line arguments... (cached) 524288
checking how to convert amd64-portbld-freebsd15.0 file names to amd64-portbld-freebsd15.0 format... func_convert_file_noop
checking how to convert amd64-portbld-freebsd15.0 file names to toolchain format... func_convert_file_noop
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checking for ranlib... /usr/local/bin/ranlib
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checking how to truncate binary pipes... /bin/dd bs=4096 count=1
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checking if mt is a manifest tool... no
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checking if cc supports -fno-rtti -fno-exceptions... yes
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checking if cc PIC flag -fPIC -DPIC works... yes
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checking whether the cc linker (/usr/local/bin/ld) supports shared libraries... yes
checking whether -lc should be explicitly linked in... no
checking dynamic linker characteristics... freebsd15.0 ld.so
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checking whether stripping libraries is possible... yes
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checking whether to build shared libraries... yes
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checking how to run the C++ preprocessor... c++ -E
checking for ld used by c++... /usr/local/bin/ld
checking if the linker (/usr/local/bin/ld) is GNU ld... yes
checking whether the c++ linker (/usr/local/bin/ld) supports shared libraries... yes
checking for c++ option to produce PIC... -fPIC -DPIC
checking if c++ PIC flag -fPIC -DPIC works... yes
checking if c++ static flag -static works... yes
checking if c++ supports -c -o file.o... yes
checking if c++ supports -c -o file.o... (cached) yes
checking whether the c++ linker (/usr/local/bin/ld) supports shared libraries... yes
checking dynamic linker characteristics... freebsd15.0 ld.so
checking how to hardcode library paths into programs... immediate
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./configure: line 19136: #include: command not found
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checking for inline... inline
checking for pdflatex... no
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checking pkg-config is at least version 0.9.0... yes
checking for C compiler vendor... clang
checking for perl... (cached) /usr/local/bin/perl
checking whether C compiler accepts -fno-strict-aliasing... yes
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configure: WARNING: Unknown target host, deactivating LTO support
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configure: WARNING: Could not find pdflatex!
configure: WARNING: deactivating automatic (re)generation of tutorial!
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configure: WARNING: Could not find pdflatex!
configure: WARNING: deactivating automatic (re)generation of CLA!
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configure: WARNING: check not found -- will not build C-library Unit tests
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checking for ./src/ViennaRNA/static/misc/rna_mod_dihydrouridine_parameters.hex... yes
sed: No error: 0
checking whether c++ supports C++17 features with -std=c++17... ./configure: line 29553: ${+y}: bad substitution
===> Script "configure" failed unexpectedly.
Please report the problem to yuri@FreeBSD.org [maintainer] and attach the
"/wrkdirs/usr/ports/biology/viennarna/work/ViennaRNA-2.6.3/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/viennarna