[package - main-i386-default][science/dssp] Failed for dssp-4.4.2_1 in configure
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Date: Sun, 15 Sep 2024 13:57:39 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/beefy17/data/main-i386-default/p14728ba1fb78_s50982d26e45/logs/dssp-4.4.2_1.log
Build URL: https://pkg-status.freebsd.org/beefy17/build.html?mastername=main-i386-default&build=p14728ba1fb78_s50982d26e45
Log:
=>> Building science/dssp
build started at Sun Sep 15 13:57:27 UTC 2024
port directory: /usr/ports/science/dssp
package name: dssp-4.4.2_1
building for: FreeBSD main-i386-default-job-04 15.0-CURRENT FreeBSD 15.0-CURRENT 1500023 i386
maintained by: yuri@FreeBSD.org
Makefile datestamp: -rw-r--r-- 1 root wheel 646 Aug 1 01:01 /usr/ports/science/dssp/Makefile
Ports top last git commit: 14728ba1fb7
Ports top unclean checkout: no
Port dir last git commit: b4d3bbb5d13
Port dir unclean checkout: no
Poudriere version: poudriere-git-3.4.2
Host OSVERSION: 1500023
Jail OSVERSION: 1500023
Job Id: 04
---Begin Environment---
SHELL=/bin/sh
BLOCKSIZE=K
MAIL=/var/mail/root
MM_CHARSET=UTF-8
LANG=C.UTF-8
OSVERSION=1500023
STATUS=1
HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
MAKE_OBJDIR_CHECK_WRITABLE=0
UNAME_m=i386
UNAME_p=i386
UNAME_r=15.0-CURRENT
LOCALBASE=/usr/local
UNAME_v=FreeBSD 15.0-CURRENT 1500023
USER=root
POUDRIERE_NAME=poudriere-git
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.4.2
MASTERMNT=/usr/local/poudriere/data/.m/main-i386-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-i386-default/04/.p
OUTPUT_REDIRECTED_STDOUT=3
P_PORTS_FEATURES=FLAVORS SUBPACKAGES SELECTED_OPTIONS
MASTERNAME=main-i386-default
SCRIPTPREFIX=/usr/local/share/poudriere
SCRIPTNAME=bulk.sh
OLDPWD=/usr/local/poudriere/data/.m/main-i386-default/ref/.p/pool
POUDRIERE_PKGNAME=poudriere-git-3.4.2
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=" -fstack-protector-strong " 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="i
nstall -m 444"
--End MAKE_ENV--
--PLIST_SUB--
CMAKE_BUILD_TYPE="release" OSREL=15.0 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---
# 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
USE_PACKAGE_DEPENDS=yes
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}
#### ####
# 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) 524288
stack size (kbytes, -s) 65536
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
--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-4.4.2_1 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.21.3.pkg
[main-i386-default-job-04] Installing pkg-1.21.3...
[main-i386-default-job-04] Extracting pkg-1.21.3: .......... done
===> dssp-4.4.2_1 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of dssp-4.4.2_1
===========================================================================
=======================<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-4.4.2_1 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-4.4.2_1 for building
=> SHA256 Checksum OK for PDB-REDO-dssp-v4.4.2_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-4.4.2_1 for building
===> Extracting for dssp-4.4.2_1
=> SHA256 Checksum OK for PDB-REDO-dssp-v4.4.2_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-4.4.2_1
===========================================================================
=======================<phase: build-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> dssp-4.4.2_1 depends on package: libmcfp>0 - not found
===> Installing existing package /packages/All/libmcfp-1.3.3.pkg
[main-i386-default-job-04] Installing libmcfp-1.3.3...
[main-i386-default-job-04] Extracting libmcfp-1.3.3: .......... done
===> dssp-4.4.2_1 depends on package: libmcfp>0 - found
===> Returning to build of dssp-4.4.2_1
===> dssp-4.4.2_1 depends on executable: mrc - not found
===> Installing existing package /packages/All/mrc-1.3.13.pkg
[main-i386-default-job-04] Installing mrc-1.3.13...
[main-i386-default-job-04] Extracting mrc-1.3.13: ...... done
===> dssp-4.4.2_1 depends on executable: mrc - found
===> Returning to build of dssp-4.4.2_1
===> dssp-4.4.2_1 depends on file: /usr/local/bin/cmake - not found
===> Installing existing package /packages/All/cmake-core-3.30.3_1.pkg
[main-i386-default-job-04] Installing cmake-core-3.30.3_1...
[main-i386-default-job-04] `-- Installing expat-2.6.2...
[main-i386-default-job-04] `-- Extracting expat-2.6.2: .......... done
[main-i386-default-job-04] `-- Installing jsoncpp-1.9.6_1...
[main-i386-default-job-04] `-- Extracting jsoncpp-1.9.6_1: .......... done
[main-i386-default-job-04] `-- Installing libuv-1.48.0...
[main-i386-default-job-04] `-- Extracting libuv-1.48.0: .......... done
[main-i386-default-job-04] `-- Installing rhash-1.4.4_1...
[main-i386-default-job-04] | `-- Installing gettext-runtime-0.22.5...
[main-i386-default-job-04] | | `-- Installing indexinfo-0.3.1...
[main-i386-default-job-04] | | `-- Extracting indexinfo-0.3.1: .... done
[main-i386-default-job-04] | `-- Extracting gettext-runtime-0.22.5: .......... done
[main-i386-default-job-04] `-- Extracting rhash-1.4.4_1: .......... done
[main-i386-default-job-04] Extracting cmake-core-3.30.3_1: .......... done
===> dssp-4.4.2_1 depends on file: /usr/local/bin/cmake - found
===> Returning to build of dssp-4.4.2_1
===========================================================================
=======================<phase: lib-depends >============================
===== env: USE_PACKAGE_DEPENDS_ONLY=1 USER=root UID=0 GID=0
===> dssp-4.4.2_1 depends on shared library: libboost_iostreams.so - not found
===> Installing existing package /packages/All/boost-libs-1.84.0.pkg
[main-i386-default-job-04] Installing boost-libs-1.84.0...
[main-i386-default-job-04] `-- Installing icu-74.2_1,1...
[main-i386-default-job-04] `-- Extracting icu-74.2_1,1: .......... done
[main-i386-default-job-04] Extracting boost-libs-1.84.0: .......... done
=====
Message from boost-libs-1.84.0:
--
You have built the Boost library with thread support.
Don't forget to add -pthread to your linker options when
linking your code.
===> dssp-4.4.2_1 depends on shared library: libboost_iostreams.so - found (/usr/local/lib/libboost_iostreams.so)
===> Returning to build of dssp-4.4.2_1
===> dssp-4.4.2_1 depends on shared library: libcifpp.so - not found
===> Installing existing package /packages/All/libcifpp-7.0.5.pkg
[main-i386-default-job-04] Installing libcifpp-7.0.5...
[main-i386-default-job-04] `-- Installing bash-5.2.32...
[main-i386-default-job-04] | `-- Installing readline-8.2.13...
[main-i386-default-job-04] | `-- Extracting readline-8.2.13: .......... done
[main-i386-default-job-04] `-- Extracting bash-5.2.32: .......... done
[main-i386-default-job-04] Extracting libcifpp-7.0.5: .......... done
===> dssp-4.4.2_1 depends on shared library: libcifpp.so - found (/usr/local/lib/libcifpp.so)
===> Returning to build of dssp-4.4.2_1
===========================================================================
=======================<phase: configure >============================
===== env: NO_DEPENDS=yes USER=root UID=0 GID=0
===> Configuring for dssp-4.4.2_1
===> Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/science/dssp/work/.build
-- The CXX compiler identification is Clang 18.1.6
-- 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
CMake Warning (dev) at CMakeLists.txt:37 (include):
Policy CMP0145 is not set: The Dart and FindDart modules are removed. Run
"cmake --help-policy CMP0145" for policy details. Use the cmake_policy
command to set the policy and suppress this warning.
This warning is for project developers. Use -Wno-dev to suppress it.
CMake Warning (dev) at /usr/local/share/cmake/Modules/Dart.cmake:47 (message):
Policy CMP0145 is not set: The Dart and FindDart modules are removed. Run
"cmake --help-policy CMP0145" for policy details. Use the cmake_policy
command to set the policy and suppress this warning.
Call Stack (most recent call first):
CMakeLists.txt:37 (include)
This warning is for project developers. Use -Wno-dev to suppress it.
-- Looking for C++ include filesystem
-- Looking for C++ include filesystem - found
-- Performing Test CXX_FILESYSTEM_NO_LINK_NEEDED
-- Performing Test CXX_FILESYSTEM_NO_LINK_NEEDED - Success
-- 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
-- Found ZLIB: /usr/lib/libz.so (found version "1.3.1")
-- Configuring done (5.6s)
CMake Error at /usr/local/lib/cmake/cifpp/cifpp-targets.cmake:61 (set_target_properties):
The link interface of target "cifpp::cifpp" contains:
std::atomic
but the target was not found. Possible reasons include:
* There is a typo in the target name.
* A find_package call is missing for an IMPORTED target.
* An ALIAS target is missing.
Call Stack (most recent call first):
/usr/local/lib/cmake/cifpp/cifpp-config.cmake:27 (include)
CMakeLists.txt:108 (find_package)
-- Generating done (0.1s)
CMake Warning:
Manually-specified variables were not used by the project:
CMAKE_C_COMPILER
CMAKE_C_FLAGS
CMAKE_C_FLAGS_DEBUG
CMAKE_C_FLAGS_RELEASE
CMAKE_MODULE_LINKER_FLAGS
FETCHCONTENT_FULLY_DISCONNECTED
CMake Generate step failed. Build files cannot be regenerated correctly.
*** Error code 1
Stop.
make: stopped making "configure" in /usr/ports/science/dssp