[package - main-amd64-default][science/dssp] Failed for dssp-4.5.8 in configure
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Date: Thu, 11 Jun 2026 01:45:08 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/beefy24/data/main-amd64-default/p138cf1688788_s64b053f879a/logs/dssp-4.5.8.log
Build URL: https://pkg-status.freebsd.org/beefy24/build.html?mastername=main-amd64-default&build=p138cf1688788_s64b053f879a
Log:
=>> Building science/dssp
build started at Thu Jun 11 01:44:56 UTC 2026
port directory: /usr/ports/science/dssp
package name: dssp-4.5.8
building for: FreeBSD main-amd64-default-job-13 16.0-CURRENT FreeBSD 16.0-CURRENT 1600018 amd64
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 756 Mar 24 01:01 /usr/ports/science/dssp/Makefile
Ports top last git commit: 138cf1688788ba93cbd00a35be679a88fe1fb9e4
Ports top unclean checkout: no
Port dir last git commit: d63020f72bc68010d0df3a0dcc4449d08a008659
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.8
Host OSVERSION: 1600018
Jail OSVERSION: 1600018
Job Id: 13
---Begin Environment---
SHELL=/bin/sh
OSVERSION=1600018
UNAME_v=FreeBSD 16.0-CURRENT 1600018
UNAME_r=16.0-CURRENT
BLOCKSIZE=K
MAIL=/var/mail/root
MM_CHARSET=UTF-8
LANG=C.UTF-8
STATUS=1
HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
MAKE_OBJDIR_CHECK_WRITABLE=0
LOCALBASE=/usr/local
USER=root
POUDRIERE_NAME=poudriere-git
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.4.8
MASTERMNT=/usr/local/poudriere/data/.m/main-amd64-default/ref
LC_COLLATE=C
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
OUTPUT_REDIRECTED_STDERR=4
OUTPUT_REDIRECTED=1
PWD=/usr/local/poudriere/data/.m/main-amd64-default/13/.p
OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS
MASTERNAME=main-amd64-default
SCRIPTPREFIX=/usr/local/share/poudriere
SCRIPTNAME=bulk.sh
OLDPWD=/usr/local/poudriere/data/.m/main-amd64-default/ref/.p/pool
POUDRIERE_PKGNAME=poudriere-git-3.4.8
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
POUDRIEREPATH=/usr/local/bin/poudriere
---End Environment---
---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=
FLAVOR=
MAKE_ARGS=
---End Poudriere Port Flags/Env---
---Begin OPTIONS List---
---End OPTIONS List---
--MAINTAINER--
yuri@FreeBSD.org
--End MAINTAINER--
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/science/dssp/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/dssp/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/dssp/work/.cache HOME=/wrkdirs/usr/ports/science/dssp/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/dssp/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/dssp/work/.pkgconfig:/usr/local/libdata/pkgconfig:/usr/local/share/pkgconfig:/usr/libdata/pkgconfig SHELL=/bin/sh CONFIG_SHELL=/bin/sh
--End CONFIGURE_ENV--
--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/science/dssp/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/dssp/work XDG_CACHE_HOME=/wrkdirs/usr/ports/science/dssp/work/.cache HOME=/wrkdirs/usr/ports/science/dssp/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/science/dssp/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/science/dssp/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 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="cpp" CPPFLAGS="" LDFLAGS=" " LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " 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"
--End MAKE_ENV--
--PLIST_SUB--
CMAKE_BUILD_TYPE="release" OSREL=16.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/dssp" EXAMPLESDIR="share/examples/dssp" DATADIR="share/dssp" WWWDIR="www/dssp" ETCDIR="etc/dssp"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/dssp DOCSDIR=/usr/local/share/doc/dssp EXAMPLESDIR=/usr/local/share/examples/dssp WWWDIR=/usr/local/www/dssp ETCDIR=/usr/local/etc/dssp
--End SUB_LIST--
---Begin make.conf---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
#### ####
# 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 3 jobs
MAKE_JOBS_NUMBER=3
#### Misc Poudriere ####
.include "/etc/make.conf.ports_env"
GID=0
UID=0
---End make.conf---
--Resource limits--
cpu time (seconds, -t) unlimited
file size (512-blocks, -f) unlimited
data seg size (kbytes, -d) 33554432
stack size (kbytes, -s) 524288
core file size (512-blocks, -c) unlimited
max memory size (kbytes, -m) unlimited
locked memory (kbytes, -l) unlimited
max user processes (-u) 89999
open files (-n) 8192
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
pipebuf (kbytes, -y) unlimited
virtual machines (-V) unlimited
--End resource limits--
=======================<phase: check-sanity >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD2CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> dssp-4.5.8 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-2.7.5.pkg
[main-amd64-default-job-13] Installing pkg-2.7.5...
[main-amd64-default-job-13] Extracting pkg-2.7.5: .......... done
===> dssp-4.5.8 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of dssp-4.5.8
===========================================================================
=======================<phase: fetch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: fetch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by dssp-4.5.8 for building
===========================================================================
=======================<phase: checksum >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by dssp-4.5.8 for building
=> SHA256 Checksum OK for PDB-REDO-dssp-v4.5.8_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: extract >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by dssp-4.5.8 for building
===> Extracting for dssp-4.5.8
=> SHA256 Checksum OK for PDB-REDO-dssp-v4.5.8_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===========================================================================
=======================<phase: patch >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Patching for dssp-4.5.8
===> Applying FreeBSD patches for dssp-4.5.8 from /usr/ports/science/dssp/files
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> dssp-4.5.8 depends on package: libmcfp>0 - not found
===> Installing existing package /packages/All/libmcfp-2.0.2.pkg
[main-amd64-default-job-13] Installing libmcfp-2.0.2...
[main-amd64-default-job-13] Extracting libmcfp-2.0.2: .......... done
===> dssp-4.5.8 depends on package: libmcfp>0 - found
===> Returning to build of dssp-4.5.8
===> dssp-4.5.8 depends on executable: mrc - not found
===> Installing existing package /packages/All/mrc-1.3.17.pkg
[main-amd64-default-job-13] Installing mrc-1.3.17...
[main-amd64-default-job-13] Extracting mrc-1.3.17: ...... done
===> dssp-4.5.8 depends on executable: mrc - found
===> Returning to build of dssp-4.5.8
===> dssp-4.5.8 depends on file: /usr/local/bin/cmake - not found
===> Installing existing package /packages/All/cmake-core-3.31.12_1.pkg
[main-amd64-default-job-13] Installing cmake-core-3.31.12_1...
[main-amd64-default-job-13] `-- Installing expat-2.8.1...
[main-amd64-default-job-13] `-- Extracting expat-2.8.1: .......... done
[main-amd64-default-job-13] `-- Installing jsoncpp-1.9.6_1...
[main-amd64-default-job-13] `-- Extracting jsoncpp-1.9.6_1: .......... done
[main-amd64-default-job-13] `-- Installing libidn2-2.3.8...
[main-amd64-default-job-13] | `-- Installing indexinfo-0.3.1_1...
[main-amd64-default-job-13] | `-- Extracting indexinfo-0.3.1_1: .... done
[main-amd64-default-job-13] | `-- Installing libunistring-1.4.2...
[main-amd64-default-job-13] | `-- Extracting libunistring-1.4.2: .......... done
[main-amd64-default-job-13] `-- Extracting libidn2-2.3.8: .......... done
[main-amd64-default-job-13] `-- Installing libuv-1.52.1...
[main-amd64-default-job-13] `-- Extracting libuv-1.52.1: .......... done
[main-amd64-default-job-13] `-- Installing rhash-1.4.6...
[main-amd64-default-job-13] | `-- Installing gettext-runtime-1.0_1...
[main-amd64-default-job-13] | `-- Extracting gettext-runtime-1.0_1: .......... done
[main-amd64-default-job-13] `-- Extracting rhash-1.4.6: .......... done
[main-amd64-default-job-13] Extracting cmake-core-3.31.12_1: .......... done
===> dssp-4.5.8 depends on file: /usr/local/bin/cmake - found
===> Returning to build of dssp-4.5.8
===========================================================================
=======================<phase: lib-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> dssp-4.5.8 depends on shared library: libboost_iostreams.so - not found
===> Installing existing package /packages/All/boost-libs-1.89.0_2.pkg
[main-amd64-default-job-13] Installing boost-libs-1.89.0_2...
[main-amd64-default-job-13] `-- Installing icu-76.1,1...
[main-amd64-default-job-13] `-- Extracting icu-76.1,1: .......... done
[main-amd64-default-job-13] `-- Installing zstd-1.5.7_2...
[main-amd64-default-job-13] | `-- Installing liblz4-1.10.0_2,1...
[main-amd64-default-job-13] | `-- Extracting liblz4-1.10.0_2,1: .......... done
[main-amd64-default-job-13] `-- Extracting zstd-1.5.7_2: .......... done
[main-amd64-default-job-13] Extracting boost-libs-1.89.0_2: .......... done
=====
Message from boost-libs-1.89.0_2:
--
You have built the Boost library with thread support.
Don't forget to add -pthread to your linker options when
linking your code.
===> dssp-4.5.8 depends on shared library: libboost_iostreams.so - found (/usr/local/lib/libboost_iostreams.so)
===> Returning to build of dssp-4.5.8
===> dssp-4.5.8 depends on shared library: libcifpp.so - not found
===> Installing existing package /packages/All/libcifpp-10.0.4.pkg
[main-amd64-default-job-13] Installing libcifpp-10.0.4...
[main-amd64-default-job-13] `-- Installing bash-5.3.15...
[main-amd64-default-job-13] `-- Extracting bash-5.3.15: .......... done
[main-amd64-default-job-13] `-- Installing pcre2-10.47_1...
[main-amd64-default-job-13] `-- Extracting pcre2-10.47_1: .......... done
[main-amd64-default-job-13] `-- Installing sqlite3-3.53.1,1...
[main-amd64-default-job-13] | `-- Installing libedit-3.1.20260512,1...
[main-amd64-default-job-13] | `-- Extracting libedit-3.1.20260512,1: .......... done
[main-amd64-default-job-13] `-- Extracting sqlite3-3.53.1,1: .......... done
[main-amd64-default-job-13] Extracting libcifpp-10.0.4: .......... done
===> dssp-4.5.8 depends on shared library: libcifpp.so - found (/usr/local/lib/libcifpp.so)
===> Returning to build of dssp-4.5.8
===========================================================================
=======================<phase: configure >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Configuring for dssp-4.5.8
===> Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/science/dssp/work/.build
-- The CXX compiler identification is Clang 21.1.8
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- Git hash not found
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD
-- Performing Test CMAKE_HAVE_LIBC_PTHREAD - Failed
-- Looking for pthread_create in pthreads
-- Looking for pthread_create in pthreads - not found
-- Looking for pthread_create in pthread
-- Looking for pthread_create in pthread - found
-- Found Threads: TRUE
CMake Error at /usr/local/lib/cmake/mcfp/mcfp-config.cmake:32 (INCLUDE):
INCLUDE could not find requested file:
/usr/local/lib/cmake/mcfp/mcfp-module-targets.cmake
Call Stack (most recent call first):
cmake/CPM.cmake:253 (find_package)
cmake/CPM.cmake:322 (cpm_find_package)
CMakeLists.txt:114 (CPMFindPackage)
-- CPM: Using local package mcfp@2.0.2
-- Git hash not found
-- Configuring incomplete, errors occurred!
*** Error code 1
Stop.
make: stopped making "configure" in /usr/ports/science/dssp