[package - 133i386-default][science/dssp] Failed for dssp-4.4.2_1 in configure

From: <pkg-fallout_at_FreeBSD.org>
Date: Wed, 18 Sep 2024 17:12:11 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/beefy15/data/133i386-default/0047206c1c4f/logs/dssp-4.4.2_1.log
Build URL:      https://pkg-status.freebsd.org/beefy15/build.html?mastername=133i386-default&build=0047206c1c4f
Log:

=>> Building science/dssp
build started at Wed Sep 18 17:11:43 UTC 2024
port directory: /usr/ports/science/dssp
package name: dssp-4.4.2_1
building for: FreeBSD 133i386-default-job-10 13.3-RELEASE-p6 FreeBSD 13.3-RELEASE-p6 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: 0047206c1c4
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: 1303001
Job Id: 10

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---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=13.3 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
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--
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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
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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
[133i386-default-job-10] Installing pkg-1.21.3...
[133i386-default-job-10] 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
[133i386-default-job-10] Installing libmcfp-1.3.3...
[133i386-default-job-10] 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
[133i386-default-job-10] Installing mrc-1.3.13...
[133i386-default-job-10] 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
[133i386-default-job-10] Installing cmake-core-3.30.3_1...
[133i386-default-job-10] `-- Installing expat-2.6.3...
[133i386-default-job-10] `-- Extracting expat-2.6.3: .......... done
[133i386-default-job-10] `-- Installing jsoncpp-1.9.6_1...
[133i386-default-job-10] `-- Extracting jsoncpp-1.9.6_1: .......... done
[133i386-default-job-10] `-- Installing libuv-1.48.0...
[133i386-default-job-10] `-- Extracting libuv-1.48.0: .......... done
[133i386-default-job-10] `-- Installing rhash-1.4.4_1...
[133i386-default-job-10] |   `-- Installing gettext-runtime-0.22.5...
[133i386-default-job-10] |   | `-- Installing indexinfo-0.3.1...
[133i386-default-job-10] |   | `-- Extracting indexinfo-0.3.1: .... done
[133i386-default-job-10] |   `-- Extracting gettext-runtime-0.22.5: .......... done
[133i386-default-job-10] `-- Extracting rhash-1.4.4_1: .......... done
[133i386-default-job-10] 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
[133i386-default-job-10] Installing boost-libs-1.84.0...
[133i386-default-job-10] `-- Installing icu-74.2_1,1...
[133i386-default-job-10] `-- Extracting icu-74.2_1,1: .......... done
[133i386-default-job-10] 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
[133i386-default-job-10] Installing libcifpp-7.0.5...
[133i386-default-job-10] `-- Installing bash-5.2.32...
[133i386-default-job-10] |   `-- Installing readline-8.2.13...
[133i386-default-job-10] |   `-- Extracting readline-8.2.13: .......... done
[133i386-default-job-10] `-- Extracting bash-5.2.32: .......... done
[133i386-default-job-10] 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 17.0.6
-- 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 (4.6s)
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 (0.0s)
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 in /usr/ports/science/dssp