[package - main-armv6-default][science/dssp] Failed for dssp-4.0.5 in build
- Go to: [ bottom of page ] [ top of archives ] [ this month ]
Date: Fri, 25 Nov 2022 21:56:26 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/beefy8/data/main-armv6-default/p62230210f012_sc36de97088/logs/dssp-4.0.5.log
Build URL: https://pkg-status.freebsd.org/beefy8/build.html?mastername=main-armv6-default&build=p62230210f012_sc36de97088
Log:
=>> Building science/dssp
build started at Fri Nov 25 21:55:38 UTC 2022
port directory: /usr/ports/science/dssp
package name: dssp-4.0.5
building for: FreeBSD main-armv6-default-job-09 14.0-CURRENT FreeBSD 14.0-CURRENT 1400073 arm
maintained by: yuri@FreeBSD.org
Makefile ident:
Poudriere version: 3.2.8-23-ga7f8d188
Host OSVERSION: 1400073
Jail OSVERSION: 1400073
Job Id: 09
---Begin Environment---
SHELL=/bin/sh
UNAME_p=armv6
UNAME_m=arm
ABI_FILE=/usr/lib/crt1.o
OSVERSION=1400073
UNAME_v=FreeBSD 14.0-CURRENT 1400073
UNAME_r=14.0-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
LOCALBASE=/usr/local
QEMU_EMULATING=1
USER=root
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.2.8-23-ga7f8d188
MASTERMNT=/usr/local/poudriere/data/.m/main-armv6-default/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=
PWD=/usr/local/poudriere/data/.m/main-armv6-default/ref/.p/pool
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=main-armv6-default
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/main-armv6-default/ref/.p
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
POUDRIEREPATH=/usr/local/bin/poudriere
---End Environment---
---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=
FLAVOR=
DEPENDS_ARGS=
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="/nxb-bin/usr/bin/cc" CFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " CPP="/nxb-bin/usr/bin/cpp" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong " LIBS="" CXX="/nxb-bin/usr/bin/c++" CXXFLAGS="-O2 -pipe -fstack-protector-strong -fno-strict-aliasing " MANPREFIX="/usr/local" 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=14.0 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---
.sinclude "/etc/make.nxb.conf"
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
MACHINE=arm
MACHINE_ARCH=armv6
ARCH=${MACHINE_ARCH}
#### /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
# 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 2 jobs
MAKE_JOBS_NUMBER=2
#### /usr/ports/Mk/Scripts/ports_env.sh ####
_CCVERSION_9d218390=FreeBSD clang version 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc12386ae247c) Target: armv6-unknown-freebsd14.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin
_ALTCCVERSION_9d218390=none
_CXXINTERNAL_9c45a5b1=FreeBSD clang version 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc12386ae247c) Target: armv6-unknown-freebsd14.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin "/nxb-bin/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-o" "a.out" "/usr/lib/crt1.o" "/usr/lib/crti.o" "/usr/lib/crtbegin.o" "-L/usr/lib" "/dev/null" "-lc++" "-lm" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "-lc" "-lgcc" "--as-needed" "-lgcc_s" "--no-as-needed" "/usr/lib/crtend.o" "/usr/lib/crtn.o"
CC_OUTPUT_9d218390_58173849=yes
CC_OUTPUT_9d218390_9bdba57c=yes
CC_OUTPUT_9d218390_6a4fe7f5=yes
CC_OUTPUT_9d218390_6bcac02b=yes
CC_OUTPUT_9d218390_67d20829=yes
CC_OUTPUT_9d218390_bfa62e83=yes
CC_OUTPUT_9d218390_f0b4d593=yes
CC_OUTPUT_9d218390_308abb44=yes
CC_OUTPUT_9d218390_f00456e5=yes
CC_OUTPUT_9d218390_65ad290d=yes
CC_OUTPUT_9d218390_f2776b26=yes
CC_OUTPUT_9d218390_53255a77=yes
CC_OUTPUT_9d218390_911cfe02=yes
CC_OUTPUT_9d218390_b2657cc3=yes
CC_OUTPUT_9d218390_380987f7=yes
CC_OUTPUT_9d218390_160933ec=yes
CC_OUTPUT_9d218390_fb62803b=yes
CC_OUTPUT_9d218390_af59ad06=yes
CC_OUTPUT_9d218390_a15f3fcf=yes
_OBJC_CCVERSION_9d218390=FreeBSD clang version 14.0.5 (https://github.com/llvm/llvm-project.git llvmorg-14.0.5-0-gc12386ae247c) Target: armv6-unknown-freebsd14.0-gnueabihf Thread model: posix InstalledDir: /nxb-bin/usr/bin
_OBJC_ALTCCVERSION_9d218390=none
ARCH=armv6
OPSYS=FreeBSD
_OSRELEASE=14.0-CURRENT
OSREL=14.0
OSVERSION=1400073
PYTHONBASE=/usr/local
CONFIGURE_MAX_CMD_LEN=524288
HAVE_PORTS_ENV=1
#### Misc Poudriere ####
GID=0
UID=0
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
---Begin make.nxb.conf---
CC=/nxb-bin/usr/bin/cc
CPP=/nxb-bin/usr/bin/cpp
CXX=/nxb-bin/usr/bin/c++
NM=/nxb-bin/usr/bin/nm
LD=/nxb-bin/usr/bin/ld
OBJCOPY=/nxb-bin/usr/bin/objcopy
SIZE=/nxb-bin/usr/bin/size
STRIPBIN=/nxb-bin/usr/bin/strip
SED=/nxb-bin/usr/bin/sed
RANLIB=/nxb-bin/usr/bin/ranlib
YACC=/nxb-bin/usr/bin/yacc
MAKE=/nxb-bin/usr/bin/make
STRINGS=/nxb-bin/usr/bin/strings
AWK=/nxb-bin/usr/bin/awk
FLEX=/nxb-bin/usr/bin/flex
---End make.nxb.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) 1024
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 >============================
===> License BSD2CLAUSE accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> dssp-4.0.5 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.18.4.pkg
[main-armv6-default-job-09] Installing pkg-1.18.4...
[main-armv6-default-job-09] Extracting pkg-1.18.4: .......... done
===> dssp-4.0.5 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of dssp-4.0.5
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by dssp-4.0.5 for building
===========================================================================
=======================<phase: checksum >============================
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by dssp-4.0.5 for building
=> SHA256 Checksum OK for PDB-REDO-dssp-v4.0.5_GH0.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License BSD2CLAUSE accepted by the user
===> Fetching all distfiles required by dssp-4.0.5 for building
===> Extracting for dssp-4.0.5
=> SHA256 Checksum OK for PDB-REDO-dssp-v4.0.5_GH0.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for dssp-4.0.5
===========================================================================
=======================<phase: build-depends >============================
===> dssp-4.0.5 depends on executable: mrc - not found
===> Installing existing package /packages/All/mrc-1.3.4.7.pkg
[main-armv6-default-job-09] Installing mrc-1.3.4.7...
[main-armv6-default-job-09] `-- Installing boost-libs-1.80.0_1...
[main-armv6-default-job-09] | `-- Installing icu-72.1,1...
[main-armv6-default-job-09] | `-- Extracting icu-72.1,1: .......... done
[main-armv6-default-job-09] `-- Extracting boost-libs-1.80.0_1: .......... done
[main-armv6-default-job-09] Extracting mrc-1.3.4.7: ......... done
=====
Message from boost-libs-1.80.0_1:
--
You have built the Boost library with thread support.
Don't forget to add -pthread to your linker options when
linking your code.
===> dssp-4.0.5 depends on executable: mrc - found
===> Returning to build of dssp-4.0.5
===> dssp-4.0.5 depends on file: /usr/local/bin/cmake - not found
===> Installing existing package /packages/All/cmake-core-3.24.3_2.pkg
[main-armv6-default-job-09] Installing cmake-core-3.24.3_2...
[main-armv6-default-job-09] `-- Installing expat-2.5.0...
[main-armv6-default-job-09] `-- Extracting expat-2.5.0: .......... done
[main-armv6-default-job-09] `-- Installing jsoncpp-1.9.5...
[main-armv6-default-job-09] `-- Extracting jsoncpp-1.9.5: .......... done
[main-armv6-default-job-09] `-- Installing libuv-1.44.2...
[main-armv6-default-job-09] `-- Extracting libuv-1.44.2: .......... done
[main-armv6-default-job-09] `-- Installing rhash-1.4.3...
[main-armv6-default-job-09] | `-- Installing gettext-runtime-0.21...
[main-armv6-default-job-09] | | `-- Installing indexinfo-0.3.1...
[main-armv6-default-job-09] | | `-- Extracting indexinfo-0.3.1: .... done
[main-armv6-default-job-09] | `-- Extracting gettext-runtime-0.21: .......... done
[main-armv6-default-job-09] `-- Extracting rhash-1.4.3: .......... done
[main-armv6-default-job-09] Extracting cmake-core-3.24.3_2: .......... done
===> dssp-4.0.5 depends on file: /usr/local/bin/cmake - found
===> Returning to build of dssp-4.0.5
===========================================================================
=======================<phase: lib-depends >============================
===> dssp-4.0.5 depends on shared library: libboost_iostreams.so - found (/usr/local/lib/libboost_iostreams.so)
===> dssp-4.0.5 depends on shared library: libcifpp.so - not found
===> Installing existing package /packages/All/libcifpp-5.0.3.1.pkg
[main-armv6-default-job-09] Installing libcifpp-5.0.3.1...
[main-armv6-default-job-09] `-- Installing bash-5.2.9_1...
[main-armv6-default-job-09] | `-- Installing readline-8.2.0...
[main-armv6-default-job-09] | `-- Extracting readline-8.2.0: .......... done
[main-armv6-default-job-09] `-- Extracting bash-5.2.9_1: .......... done
[main-armv6-default-job-09] Extracting libcifpp-5.0.3.1: .......... done
===> dssp-4.0.5 depends on shared library: libcifpp.so - found (/usr/local/lib/libcifpp.so)
===> Returning to build of dssp-4.0.5
===========================================================================
=======================<phase: configure >============================
===> Configuring for dssp-4.0.5
===> Performing out-of-source build
/bin/mkdir -p /wrkdirs/usr/ports/science/dssp/work/.build
-- The CXX compiler identification is Clang 14.0.5
-- Detecting CXX compiler ABI info
-- Detecting CXX compiler ABI info - done
-- Check for working CXX compiler: /nxb-bin/usr/bin/c++ - skipped
-- Detecting CXX compile features
-- Detecting CXX compile features - done
-- 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
-- Found Mrc: /usr/local/bin/mrc (found version "1.3.5")
Using resources compiled with
-- 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 "1.2.12")
-- Found Boost: /usr/local/include (found version "1.80.0") found components: date_time program_options
-- Configuring done
-- Generating done
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
CMAKE_SHARED_LINKER_FLAGS
FETCHCONTENT_FULLY_DISCONNECTED
-- Build files have been written to: /wrkdirs/usr/ports/science/dssp/work/.build
===========================================================================
=======================<phase: build >============================
===> Building for dssp-4.0.5
/usr/local/bin/cmake -S/wrkdirs/usr/ports/science/dssp/work/dssp-4.0.5 -B/wrkdirs/usr/ports/science/dssp/work/.build --check-build-system CMakeFiles/Makefile.cmake 0
/usr/local/bin/cmake -E cmake_progress_start /wrkdirs/usr/ports/science/dssp/work/.build/CMakeFiles /wrkdirs/usr/ports/science/dssp/work/.build//CMakeFiles/progress.marks
/nxb-bin/usr/bin/make -f CMakeFiles/Makefile2 all
/nxb-bin/usr/bin/make -f CMakeFiles/mkdssp.dir/build.make CMakeFiles/mkdssp.dir/depend
[-37%] Generating mkdssp_rsrc.obj, ALL
/usr/local/bin/mrc -o /wrkdirs/usr/ports/science/dssp/work/.build/mkdssp_rsrc.obj /usr/local/share/libcifpp/mmcif_pdbx_v50.dic
Error executing mrc: Could not open data file
*** Error code 1
Stop.
make[3]: stopped in /wrkdirs/usr/ports/science/dssp/work/.build
*** Error code 1
Stop.
make[2]: stopped in /wrkdirs/usr/ports/science/dssp/work/.build
*** Error code 1
Stop.
make[1]: stopped in /wrkdirs/usr/ports/science/dssp/work/.build
*** Error code 1
Stop.
make: stopped in /usr/ports/science/dssp