Could not compile on FreeBSD-i386 system

[wenheping]

Could not compile on FreeBSD-i386 system, while build well on amd64 system.

The error message say :
...
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for 'data.table' in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/wrkdirs/usr/ports/devel/R-cran-data.table/work/stage/usr/local/lib/R/library/00LOCK-data.table/00new/data.table/libs/datatable.so':
/wrkdirs/usr/ports/devel/R-cran-data.table/work/stage/usr/local/lib/R/library/00LOCK-data.table/00new/data.table/libs/datatable.so: Undefined symbol "__atomic_load"
Error: loading failed
Execution halted
ERROR: loading failed

• removing '/wrkdirs/usr/ports/devel/R-cran-data.table/work/stage/usr/local/lib/R/library/data.table'
  *** Error code 1

Thanks! Please remove the text above and include the two items below.

# Minimal reproducible example

# Output of sessionInfo()

[jangorecki]

Thanks for reporting. Could you provide full content of 00install.out? also please include your compiler and what is its version.

[wenheping]

I just test it with FreeBSD tool poudriere, I did not find 00install.out. I paste the whole build log below.
It failed on FreeBSD 11,12 and 13 i386 system, but all success on amd64 system.
On i386 system ,both failed when build with gcc9 or llvm8.

build started at Tue Aug 27 15:30:24 CST 2019
port directory: /usr/ports/devel/R-cran-data.table
package name: R-cran-data.table-1.11.8_2
building for: FreeBSD 13i386-ports 13.0-CURRENT FreeBSD 13.0-CURRENT i386
maintained by: tota@FreeBSD.org
Makefile ident: $FreeBSD: head/devel/R-cran-data.table/Makefile 507372 2019-07-26 20:46:53Z gerald $
Poudriere version: 3.3.2
Host OSVERSION: 1300021
Jail OSVERSION: 1300021
Job Id:

---Begin Environment---
SHELL=/bin/csh
UNAME_p=i386
UNAME_m=i386
OSVERSION=1300021
UNAME_v=FreeBSD 13.0-CURRENT
UNAME_r=13.0-CURRENT
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
HOME=/root
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin
LOCALBASE=/usr/local
USER=root
TRYBROKEN=yes
LIBEXECPREFIX=/usr/local/libexec/poudriere
POUDRIERE_VERSION=3.3.2
MASTERMNT=/usr/local/poudriere/data/.m/13i386-ports/ref
POUDRIERE_BUILD_TYPE=bulk
PACKAGE_BUILDING=yes
SAVED_TERM=xterm
PWD=/usr/local/poudriere/data/.m/13i386-ports/ref/.p
NO_WARNING_PKG_INSTALL_EOL=yes
P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS
MASTERNAME=13i386-ports
SCRIPTPREFIX=/usr/local/share/poudriere
OLDPWD=/usr/local/poudriere/data/.m/13i386-ports/ref/.p
SCRIPTPATH=/usr/local/share/poudriere/testport.sh
POUDRIEREPATH=/usr/local/bin/poudriere
---End Environment---

---Begin Poudriere Port Flags/Env---
PORT_FLAGS=
PKGENV=PACKAGES=/tmp/pkgs PKGREPOSITORY=/tmp/pkgs PKGLATESTREPOSITORY=/tmp/pkgs/Latest
FLAVOR=
DEPENDS_ARGS=
MAKE_ARGS=
---End Poudriere Port Flags/Env---

---Begin OPTIONS List---
---End OPTIONS List---

--MAINTAINER--
tota@FreeBSD.org
--End MAINTAINER--

--CONFIGURE_ARGS--

--End CONFIGURE_ARGS--

--CONFIGURE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/devel/R-cran-data.table/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/devel/R-cran-data.table/work HOME=/wrkdirs/usr/ports/devel/R-cran-data.table/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/devel/R-cran-data.table/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin SHELL=/bin/sh CONFIG_SHELL=/bin/sh
--End CONFIGURE_ENV--

--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/devel/R-cran-data.table/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/devel/R-cran-data.table/work HOME=/wrkdirs/usr/ports/devel/R-cran-data.table/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/devel/R-cran-data.table/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin NO_PIE=yes 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/local/bin/objcopy" OBJDUMP="/usr/local/bin/objdump" RANLIB="/usr/local/bin/ranlib" READELF="/usr/local/bin/readelf" SIZE="/usr/local/bin/size" STRINGS="/usr/local/bin/strings" PREFIX=/usr/local LOCALBASE=/usr/local CC="gcc9" CFLAGS="-O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -fno-strict-aliasing " CPP="cpp9" CPPFLAGS="" LDFLAGS=" -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -L/usr/local/lib/gcc9 " LIBS="" CXX="g++9" CXXFLAGS="-O2 -pipe -fstack-protector-strong -Wl,-rpath=/usr/local/lib/gcc9 -Wl,-rpath=/usr/local/lib/gcc9 " 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--
R_MOD_DIR=lib/R/library/data.table OSREL=13.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/data.table" EXAMPLESDIR="share/examples/data.table" DATADIR="share/data.table" WWWDIR="www/data.table" ETCDIR="etc/data.table"
--End PLIST_SUB--

--SUB_LIST--
PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/data.table DOCSDIR=/usr/local/share/doc/data.table EXAMPLESDIR=/usr/local/share/examples/data.table WWWDIR=/usr/local/www/data.table ETCDIR=/usr/local/etc/data.table
--End SUB_LIST--

---Begin make.conf---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
FORCE_PACKAGE=yes
PACKAGE_BUILDING=yes
PACKAGE_BUILDING_FLAVORS=yes
MACHINE=i386
MACHINE_ARCH=i386
ARCH=${MACHINE_ARCH}
WITH_CCACHE_BUILD=yes
CCACHE_DIR=/root/.ccache

/usr/ports/Mk/Scripts/ports_env.sh

_CCVERSION_921dbbb2=FreeBSD clang version 8.0.0 (tags/RELEASE_800/final 356365) (based on LLVM 8.0.0) Target: i386-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin
_ALTCCVERSION_921dbbb2=none
_CXXINTERNAL_acaad9ca=FreeBSD clang version 8.0.0 (tags/RELEASE_800/final 356365) (based on LLVM 8.0.0) Target: i386-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--hash-style=both" "--enable-new-dtags" "-m" "elf_i386_fbsd" "-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_921dbbb2_58173849=yes
CC_OUTPUT_921dbbb2_9bdba57c=yes
CC_OUTPUT_921dbbb2_6a4fe7f5=yes
CC_OUTPUT_921dbbb2_6bcac02b=yes
CC_OUTPUT_921dbbb2_67d20829=yes
CC_OUTPUT_921dbbb2_bfa62e83=yes
CC_OUTPUT_921dbbb2_f0b4d593=yes
CC_OUTPUT_921dbbb2_308abb44=yes
CC_OUTPUT_921dbbb2_f00456e5=yes
CC_OUTPUT_921dbbb2_65ad290d=yes
CC_OUTPUT_921dbbb2_f2776b26=yes
CC_OUTPUT_921dbbb2_b2657cc3=yes
CC_OUTPUT_921dbbb2_380987f7=yes
CC_OUTPUT_921dbbb2_160933ec=yes
CC_OUTPUT_921dbbb2_fb62803b=yes
_OBJC_CCVERSION_921dbbb2=FreeBSD clang version 8.0.0 (tags/RELEASE_800/final 356365) (based on LLVM 8.0.0) Target: i386-unknown-freebsd13.0 Thread model: posix InstalledDir: /usr/bin
_OBJC_ALTCCVERSION_921dbbb2=none
ARCH=i386
OPSYS=FreeBSD
_OSRELEASE=13.0-CURRENT
OSREL=13.0
OSVERSION=1300021
PYTHONBASE=/usr/local
_SMP_CPUS=2
CONFIGURE_MAX_CMD_LEN=262144
HAVE_PORTS_ENV=1

Misc Poudriere

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) 12186
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 MPL20 accepted by the user

=======================<phase: pkg-depends >============================
===> R-cran-data.table-1.11.8_2 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.11.1.txz
[13i386-ports] Installing pkg-1.11.1...
[13i386-ports] Extracting pkg-1.11.1: .......... done
===> R-cran-data.table-1.11.8_2 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of R-cran-data.table-1.11.8_2

=======================<phase: fetch-depends >============================

=======================<phase: fetch >============================
===> License MPL20 accepted by the user
===> R-cran-data.table-1.11.8_2 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by R-cran-data.table-1.11.8_2 for building

=======================<phase: checksum >============================
===> License MPL20 accepted by the user
===> R-cran-data.table-1.11.8_2 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by R-cran-data.table-1.11.8_2 for building
=> SHA256 Checksum OK for data.table_1.11.8.tar.gz.

=======================<phase: extract-depends>============================

=======================<phase: extract >============================
===> License MPL20 accepted by the user
===> R-cran-data.table-1.11.8_2 depends on file: /usr/local/sbin/pkg - found
===> Fetching all distfiles required by R-cran-data.table-1.11.8_2 for building
===> Extracting for R-cran-data.table-1.11.8_2
=> SHA256 Checksum OK for data.table_1.11.8.tar.gz.

=======================<phase: patch-depends >============================

=======================<phase: patch >============================
===> Patching for R-cran-data.table-1.11.8_2

=======================<phase: build-depends >============================
===> R-cran-data.table-1.11.8_2 depends on file: /usr/local/bin/R - not found
===> Installing existing package /packages/All/R-3.6.1_1.txz
[13i386-ports] Installing R-3.6.1_1...
[13i386-ports] -- Installing cairo-1.16.0,2... [13i386-ports] | -- Installing fontconfig-2.12.6,1...
[13i386-ports] | | -- Installing expat-2.2.6_1... [13i386-ports] | | -- Extracting expat-2.2.6_1: .......... done
[13i386-ports] | | -- Installing freetype2-2.10.1... [13i386-ports] | | -- Extracting freetype2-2.10.1: .......... done
[13i386-ports] | -- Extracting fontconfig-2.12.6,1: .......... done Running fc-cache to build fontconfig cache... /usr/local/share/fonts: skipping, no such directory /usr/local/lib/X11/fonts: skipping, no such directory /var/db/fontconfig: cleaning cache directory fc-cache: succeeded [13i386-ports] | -- Installing gettext-runtime-0.20.1...
[13i386-ports] | | -- Installing indexinfo-0.3.1... [13i386-ports] | | -- Extracting indexinfo-0.3.1: .... done
[13i386-ports] | -- Extracting gettext-runtime-0.20.1: .......... done [13i386-ports] | -- Installing glib-2.56.3_6,1...
[13i386-ports] | | -- Installing libffi-3.2.1_3... [13i386-ports] | | -- Extracting libffi-3.2.1_3: .......... done
[13i386-ports] | | -- Installing libiconv-1.14_11... [13i386-ports] | | -- Extracting libiconv-1.14_11: .......... done
[13i386-ports] | | -- Installing libxml2-2.9.9... [13i386-ports] | | -- Extracting libxml2-2.9.9: .......... done
[13i386-ports] | | -- Installing pcre-8.43_2... [13i386-ports] | | -- Extracting pcre-8.43_2: .......... done
[13i386-ports] | | -- Installing python36-3.6.9... [13i386-ports] | | -- Installing readline-8.0.0...
[13i386-ports] | | -- Extracting readline-8.0.0: .......... done [13i386-ports] | | -- Extracting python36-3.6.9: .......... done
[13i386-ports] | -- Extracting glib-2.56.3_6,1: .......... done No schema files found: doing nothing. [13i386-ports] | -- Installing libX11-1.6.8,1...
[13i386-ports] | | -- Installing libXau-1.0.9... [13i386-ports] | | -- Extracting libXau-1.0.9: .......... done
[13i386-ports] | | -- Installing libXdmcp-1.1.3... [13i386-ports] | | -- Installing xorgproto-2019.1...
[13i386-ports] | | -- Extracting xorgproto-2019.1: .......... done [13i386-ports] | | -- Extracting libXdmcp-1.1.3: ......... done
[13i386-ports] | | -- Installing libxcb-1.13.1... [13i386-ports] | | -- Installing libpthread-stubs-0.4...
[13i386-ports] | | -- Extracting libpthread-stubs-0.4: .... done [13i386-ports] | | -- Extracting libxcb-1.13.1: .......... done
[13i386-ports] | -- Extracting libX11-1.6.8,1: .......... done [13i386-ports] | -- Installing libXext-1.3.4,1...
[13i386-ports] | -- Extracting libXext-1.3.4,1: .......... done [13i386-ports] | -- Installing libXrender-0.9.10_2...
[13i386-ports] | -- Extracting libXrender-0.9.10_2: .......... done [13i386-ports] | -- Installing mesa-libs-18.3.2_1...
[13i386-ports] | | -- Installing libXdamage-1.1.5... [13i386-ports] | | -- Installing libXfixes-5.0.3_2...
[13i386-ports] | | -- Extracting libXfixes-5.0.3_2: .......... done [13i386-ports] | | -- Extracting libXdamage-1.1.5: ......... done
[13i386-ports] | | -- Installing libXxf86vm-1.1.4_3... [13i386-ports] | | -- Extracting libXxf86vm-1.1.4_3: .......... done
[13i386-ports] | | -- Installing libdrm-2.4.99,1... [13i386-ports] | | -- Installing libpciaccess-0.16...
[13i386-ports] | | | -- Installing pciids-20190725... [13i386-ports] | | | -- Extracting pciids-20190725: ..... done
[13i386-ports] | | -- Extracting libpciaccess-0.16: ......... done [13i386-ports] | | -- Extracting libdrm-2.4.99,1: .......... done
[13i386-ports] | | -- Installing libunwind-20170615... [13i386-ports] | | -- Extracting libunwind-20170615: .......... done
[13i386-ports] | | -- Installing libxshmfence-1.3... [13i386-ports] | | -- Extracting libxshmfence-1.3: ......... done
[13i386-ports] | | -- Installing wayland-1.16.0_1... [13i386-ports] | | -- Installing libepoll-shim-0.0.20190311...
[13i386-ports] | | -- Extracting libepoll-shim-0.0.20190311: .......... done [13i386-ports] | | -- Extracting wayland-1.16.0_1: .......... done
[13i386-ports] | -- Extracting mesa-libs-18.3.2_1: .......... done [13i386-ports] | -- Installing pixman-0.38.4...
[13i386-ports] | -- Extracting pixman-0.38.4: .......... done [13i386-ports] | -- Installing png-1.6.37...
[13i386-ports] | -- Extracting png-1.6.37: .......... done [13i386-ports] -- Extracting cairo-1.16.0,2: .......... done
[13i386-ports] -- Installing curl-7.65.3... [13i386-ports] | -- Installing ca_root_nss-3.45...
[13i386-ports] | -- Extracting ca_root_nss-3.45: ........ done [13i386-ports] | -- Installing libnghttp2-1.39.2...
[13i386-ports] | -- Extracting libnghttp2-1.39.2: .......... done [13i386-ports] -- Extracting curl-7.65.3: .......... done
[13i386-ports] -- Installing gcc9-9.2.0... [13i386-ports] | -- Installing binutils-2.32_1,1...
[13i386-ports] | -- Extracting binutils-2.32_1,1: .......... done [13i386-ports] | -- Installing gmp-6.1.2_1...
[13i386-ports] | -- Extracting gmp-6.1.2_1: .......... done [13i386-ports] | -- Installing mpc-1.1.0_2...
[13i386-ports] | | -- Installing mpfr-4.0.2... [13i386-ports] | | -- Extracting mpfr-4.0.2: .......... done
[13i386-ports] | -- Extracting mpc-1.1.0_2: ......... done [13i386-ports] -- Extracting gcc9-9.2.0: .......... done
[13i386-ports] -- Installing ghostscript9-agpl-base-9.27_2... [13i386-ports] | -- Installing cups-2.2.12...
[13i386-ports] | | -- Installing avahi-app-0.7_2... [13i386-ports] | | -- Installing dbus-1.12.12...
[13i386-ports] | | | -- Installing libICE-1.0.10,1... [13i386-ports] | | | -- Extracting libICE-1.0.10,1: .......... done
[13i386-ports] | | | -- Installing libSM-1.2.3,1... [13i386-ports] | | | -- Extracting libSM-1.2.3,1: .......... done
===> Creating groups.
Creating group 'messagebus' with gid '556'.
===> Creating users
Creating user 'messagebus' with uid '556'.
[13i386-ports] | | -- Extracting dbus-1.12.12: ......... done [13i386-ports] | | -- Installing dbus-glib-0.110...
[13i386-ports] | | -- Extracting dbus-glib-0.110: .......... done [13i386-ports] | | -- Installing gdbm-1.18.1_1...
[13i386-ports] | | -- Extracting gdbm-1.18.1_1: .......... done [13i386-ports] | | -- Installing gnome_subr-1.0...
[13i386-ports] | | -- Extracting gnome_subr-1.0: .... done [13i386-ports] | | -- Installing gobject-introspection-1.56.1,1...
[13i386-ports] | | -- Extracting gobject-introspection-1.56.1,1: .......... done [13i386-ports] | | -- Installing libdaemon-0.14_1...
[13i386-ports] | | -- Extracting libdaemon-0.14_1: .......... done ===> Creating groups. Creating group 'avahi' with gid '558'. ===> Creating users Creating user 'avahi' with uid '558'. [13i386-ports] | | -- Extracting avahi-app-0.7_2: .......... done
[13i386-ports] | | -- Installing gnutls-3.6.9... [13i386-ports] | | -- Installing libidn2-2.2.0...
[13i386-ports] | | | -- Installing libunistring-0.9.10_1... [13i386-ports] | | | -- Extracting libunistring-0.9.10_1: .......... done
[13i386-ports] | | -- Extracting libidn2-2.2.0: .......... done [13i386-ports] | | -- Installing libtasn1-4.14...
[13i386-ports] | | -- Extracting libtasn1-4.14: .......... done [13i386-ports] | | -- Installing nettle-3.5.1_1...
[13i386-ports] | | -- Extracting nettle-3.5.1_1: .......... done [13i386-ports] | | -- Installing p11-kit-0.23.16.1...
[13i386-ports] | | -- Extracting p11-kit-0.23.16.1: .......... done [13i386-ports] | | -- Installing trousers-0.3.14_2...
[13i386-ports] | | | -- Installing tpm-emulator-0.7.4_2... ===> Creating groups. Creating group '_tss' with gid '601'. ===> Creating users Creating user '_tss' with uid '601'. [13i386-ports] | | | -- Extracting tpm-emulator-0.7.4_2: ......... done
===> Creating groups.
Using existing group '_tss'.
===> Creating users
Using existing user '_tss'.
[13i386-ports] | | -- Extracting trousers-0.3.14_2: .......... done [13i386-ports] | | -- Extracting gnutls-3.6.9: .......... done
[13i386-ports] | | -- Installing libpaper-1.1.24.4... [13i386-ports] | | -- Extracting libpaper-1.1.24.4: .......... done
===> Creating groups.
Creating group 'cups' with gid '193'.
===> Creating users
Creating user 'cups' with uid '193'.
[13i386-ports] | -- Extracting cups-2.2.12: .......... done [13i386-ports] | -- Installing jbig2dec-0.16...
[13i386-ports] | -- Extracting jbig2dec-0.16: .......... done [13i386-ports] | -- Installing jpeg-turbo-2.0.2...
[13i386-ports] | -- Extracting jpeg-turbo-2.0.2: .......... done [13i386-ports] | -- Installing libidn-1.35...
[13i386-ports] | -- Extracting libidn-1.35: .......... done [13i386-ports] | -- Installing poppler-data-0.4.9...
[13i386-ports] | -- Extracting poppler-data-0.4.9: .......... done [13i386-ports] | -- Installing tiff-4.0.10_1...
[13i386-ports] | | -- Installing jbigkit-2.1_1... [13i386-ports] | | -- Extracting jbigkit-2.1_1: .......... done
[13i386-ports] | -- Extracting tiff-4.0.10_1: .......... done [13i386-ports] -- Extracting ghostscript9-agpl-base-9.27_2: .......... done
[13i386-ports] -- Installing gmake-4.2.1_3... [13i386-ports] -- Extracting gmake-4.2.1_3: .......... done
[13i386-ports] -- Installing icu-64.2,1... [13i386-ports] -- Extracting icu-64.2,1: .......... done
[13i386-ports] -- Installing libXScrnSaver-1.2.3_2... [13i386-ports] -- Extracting libXScrnSaver-1.2.3_2: .......... done
[13i386-ports] -- Installing libXmu-1.1.3,1... [13i386-ports] | -- Installing libXt-1.2.0,1...
[13i386-ports] | -- Extracting libXt-1.2.0,1: .......... done [13i386-ports] -- Extracting libXmu-1.1.3,1: .......... done
[13i386-ports] -- Installing pango-1.42.4_3... [13i386-ports] | -- Installing encodings-1.0.5,1...
[13i386-ports] | -- Extracting encodings-1.0.5,1: .......... done [13i386-ports] | -- Installing fribidi-0.19.7...
[13i386-ports] | -- Extracting fribidi-0.19.7: .......... done [13i386-ports] | -- Installing harfbuzz-2.6.1_1...
[13i386-ports] | | -- Installing graphite2-1.3.13_1... [13i386-ports] | | -- Extracting graphite2-1.3.13_1: .......... done
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===> R-cran-data.table-1.11.8_2 depends on file: /usr/local/bin/R - found
===> Returning to build of R-cran-data.table-1.11.8_2
===> R-cran-data.table-1.11.8_2 depends on executable: gcc9 - found
===> R-cran-data.table-1.11.8_2 depends on file: /usr/local/bin/as - found

=======================<phase: lib-depends >============================

=>> Recording filesystem state for prebuild... done
=======================<phase: configure >============================
===> R-cran-data.table-1.11.8_2 depends on file: /usr/local/bin/R - found
===> R-cran-data.table-1.11.8_2 depends on executable: gcc9 - found
===> R-cran-data.table-1.11.8_2 depends on file: /usr/local/bin/as - found
===> Configuring for R-cran-data.table-1.11.8_2

=======================<phase: build >============================

=>> Checking for filesystem violations... done
=======================<phase: run-depends >============================
===> R-cran-data.table-1.11.8_2 depends on file: /usr/local/bin/R - found
===> R-cran-data.table-1.11.8_2 depends on executable: gcc9 - found

=>> Recording filesystem state for prestage... done
=======================<phase: stage >============================
===> Staging for R-cran-data.table-1.11.8_2
===> R-cran-data.table-1.11.8_2 depends on file: /usr/local/bin/R - found
===> R-cran-data.table-1.11.8_2 depends on executable: gcc9 - found
===> Generating temporary packing list

• installing source package 'data.table' ...
  ** package 'data.table' successfully unpacked and MD5 sums checked
  ** using staged installation
  ** libs
  gmake[1]: Entering directory '/wrkdirs/usr/ports/devel/R-cran-data.table/work/data.table/src'
  cc -I"/usr/local/lib/R/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c assign.c -o assign.o
  cc -I"/usr/local/lib/R/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c between.c -o between.o
  cc -I"/usr/local/lib/R/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c bmerge.c -o bmerge.o
  cc -I"/usr/local/lib/R/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c chmatch.c -o chmatch.o
  cc -I"/usr/local/lib/R/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c dogroups.c -o dogroups.o
  cc -I"/usr/local/lib/R/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c fastmean.c -o fastmean.o
  cc -I"/usr/local/lib/R/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c fcast.c -o fcast.o
  cc -I"/usr/local/lib/R/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c fmelt.c -o fmelt.o
  cc -I"/usr/local/lib/R/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c forder.c -o forder.o
  cc -I"/usr/local/lib/R/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c frank.c -o frank.o
  cc -I"/usr/local/lib/R/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c fread.c -o fread.o
  cc -I"/usr/local/lib/R/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c freadR.c -o freadR.o
  cc -I"/usr/local/lib/R/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c fsort.c -o fsort.o
  cc -I"/usr/local/lib/R/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c fwrite.c -o fwrite.o
  cc -I"/usr/local/lib/R/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c fwriteR.c -o fwriteR.o
  cc -I"/usr/local/lib/R/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c gsumm.c -o gsumm.o
  cc -I"/usr/local/lib/R/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c ijoin.c -o ijoin.o
  cc -I"/usr/local/lib/R/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c init.c -o init.o
  cc -I"/usr/local/lib/R/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c inrange.c -o inrange.o
  cc -I"/usr/local/lib/R/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c nqrecreateindices.c -o nqrecreateindices.o
  cc -I"/usr/local/lib/R/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c openmp-utils.c -o openmp-utils.o
  cc -I"/usr/local/lib/R/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c quickselect.c -o quickselect.o
  cc -I"/usr/local/lib/R/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c rbindlist.c -o rbindlist.o
  cc -I"/usr/local/lib/R/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c reorder.c -o reorder.o
  cc -I"/usr/local/lib/R/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c shift.c -o shift.o
  cc -I"/usr/local/lib/R/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c subset.c -o subset.o
  cc -I"/usr/local/lib/R/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c transpose.c -o transpose.o
  cc -I"/usr/local/lib/R/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c uniqlist.c -o uniqlist.o
  cc -I"/usr/local/lib/R/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c vecseq.c -o vecseq.o
  cc -I"/usr/local/lib/R/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c wrappers.c -o wrappers.o
  cc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -Wl,-rpath=/usr/local/lib/gcc9 -L/usr/local/lib/gcc9 -B/usr/local/bin -fstack-protector-strong -o data.table.so assign.o between.o bmerge.o chmatch.o dogroups.o fastmean.o fcast.o fmelt.o forder.o frank.o fread.o freadR.o fsort.o fwrite.o fwriteR.o gsumm.o ijoin.o init.o inrange.o nqrecreateindices.o openmp-utils.o quickselect.o rbindlist.o reorder.o shift.o subset.o transpose.o uniqlist.o vecseq.o wrappers.o -fopenmp -L/usr/local/lib/R/lib -lR
  mv data.table.so datatable.so
  if [ "" != "Windows_NT" ] && [ uname -s = 'Darwin' ]; then install_name_tool -id datatable.so datatable.so; fi
  gmake[1]: Leaving directory '/wrkdirs/usr/ports/devel/R-cran-data.table/work/data.table/src'
  installing to /wrkdirs/usr/ports/devel/R-cran-data.table/work/stage/usr/local/lib/R/library/00LOCK-data.table/00new/data.table/libs
  ** R
  ** inst
  ** tests
  ** byte-compile and prepare package for lazy loading
  ** help
  *** installing help indices
  ** building package indices
  ** installing vignettes
  ** testing if installed package can be loaded from temporary location
  Error: package or namespace load failed for 'data.table' in dyn.load(file, DLLpath = DLLpath, ...):
  unable to load shared object '/wrkdirs/usr/ports/devel/R-cran-data.table/work/stage/usr/local/lib/R/library/00LOCK-data.table/00new/data.table/libs/datatable.so':
  /wrkdirs/usr/ports/devel/R-cran-data.table/work/stage/usr/local/lib/R/library/00LOCK-data.table/00new/data.table/libs/datatable.so: Undefined symbol "__atomic_load"
  Error: loading failed
  Execution halted
  ERROR: loading failed
• removing '/wrkdirs/usr/ports/devel/R-cran-data.table/work/stage/usr/local/lib/R/library/data.table'
  *** Error code 1

Stop.
make: stopped in /usr/ports/devel/R-cran-data.table
build of devel/R-cran-data.table | R-cran-data.table-1.11.8_2 ended at Tue Aug 27 15:32:10 CST 2019
build time: 00:01:46
!!! build failure encountered !!!

[jangorecki]

Please check if you still have problems trying to install recent stable release 1.12.2, and if possible 1.12.3 also

[wenheping]

1.12.2 has the same error.

[jangorecki]

you seems to be installing R-cran-data.table pkg, is it behaviour the same when just using install.packages from R session?
Additionally

cc -I"/usr/local/lib/R/include" -DNDEBUG -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fopenmp -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong -isystem /usr/local/include -fno-strict-aliasing -c assign.c -o assign.o

shouldn't this cc be a gcc if you are attempting to use gcc?

[wenheping]

The build still fails on FreeBSD-i386 system, even with 1.12.8 and use gcc compiler.
Success on amd64 system.

[jangorecki]

Could you provide output of R CMD INSTALL command or install.packages from R?

[MichaelChirico]

Is the failure for 1.12.8 the same? I see

Error: package or namespace load failed for 'data.table' in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/.../data.table/libs/datatable.so':
/.../data.table/libs/datatable.so: Undefined symbol "__atomic_load"

However, there is no __atomic_load in our source code, nor in /usr/include/ or the R source on my machine:

grep -r "__atomic_load" .
grep -r "__atomic_load" /usr/include/
grep -r "__atomic_load" ~/svn/R-devel/

[MichaelChirico]

However, I see this bug report:

https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=234976

Makes reference to #include <atomic>, which indeed matches our .so:

grep -r "include.*atomic" src
Binary file src/datatable.so matches

[MichaelChirico]

This Issue & fix look related but all I'm seeing so far is referencing C++

fish-shell/fish-shell#5865

fish-shell/fish-shell@45633f4

This one is with llvm, maybe something?

https://reviews.llvm.org/D47606

Another potentially related:

clangupc/clang-upc#49

[jangorecki]

@MichaelChirico haven't read all your links, but this symbol might have been generated by openmp library used by compiler. I think we need to start debugging by having install output of installation from source, not a binary package r-cran-data.table. @wenheping are you able to provide such output? so we can know if the problem is caused by package sources or binaries.

[wenheping]

Thank your reply. I have send a PR to unbreak the build of data.table on i386-FreeBSD system: https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=247631 Now it build. Regards, wen

…

________________________________ 发件人: Jan Gorecki <notifications@github.com> 发送时间: 2020年6月28日 6:53 收件人: Rdatatable/data.table <data.table@noreply.github.com> 抄送: wenheping <wen@FreeBSD.org>; Mention <mention@noreply.github.com> 主题: Re: [Rdatatable/data.table] Could not compile on FreeBSD-i386 system (#3789) @MichaelChirico<https://github.com/MichaelChirico> haven't read all your links, but this symbol might have been generated by openmp library used by compiler. I think we need to start debugging by having install output of installation from source, not a binary package r-cran-data.table. @wenheping<https://github.com/wenheping> are you able to provide such output? so we can know if the problem is caused by package sources or binaries. ― You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub<#3789 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AADZM7P5TQA4AS2TE72H3HLRYZZ6VANCNFSM4IPLCALQ>.

[jangorecki]

@wenheping Thanks, it seems that issue is resolved then. Be aware that dll file name will change in future version, to the more canonical R way. For details see #4442