[package - 131powerpc64-quarterly][graphics/R-cran-rgdal] Failed for R-cran-rgdal-1.5.32_4 in stage
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Date: Mon, 15 May 2023 11:26:47 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: tota@FreeBSD.org Log URL: https://pkg-status.freebsd.org/foul1/data/131powerpc64-quarterly/4d1861680423/logs/R-cran-rgdal-1.5.32_4.log Build URL: https://pkg-status.freebsd.org/foul1/build.html?mastername=131powerpc64-quarterly&build=4d1861680423 Log: =>> Building graphics/R-cran-rgdal build started at Mon May 15 11:25:24 UTC 2023 port directory: /usr/ports/graphics/R-cran-rgdal package name: R-cran-rgdal-1.5.32_4 building for: FreeBSD 131powerpc64-quarterly-job-02 13.1-RELEASE FreeBSD 13.1-RELEASE powerpc maintained by: tota@FreeBSD.org Makefile ident: Poudriere version: 3.2.8-23-ga7f8d188 Host OSVERSION: 1400087 Jail OSVERSION: 1301000 Job Id: 02 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1301000 UNAME_v=FreeBSD 13.1-RELEASE UNAME_r=13.1-RELEASE 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 USER=root LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.8-23-ga7f8d188 MASTERMNT=/usr/local/poudriere/data/.m/131powerpc64-quarterly/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/131powerpc64-quarterly/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=131powerpc64-quarterly SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/131powerpc64-quarterly/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-- tota@FreeBSD.org --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- F77="gfortran12" F90="gfortran12" FC="gfortran12" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc12" F90FLAGS="-O -Wl,-rpath=/usr/local/lib/gcc12" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc12" PKG_CONFIG=pkgconf XDG_DATA_HOME=/wrkdirs/usr/ports/graphics/R-cran-rgdal/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/graphics/R-cran-rgdal/work XDG_CACHE_HOME=/wrkdirs/usr/ports/graphics/R-cran-rgdal/work/.cache HOME=/wrkdirs/usr/ports/graphics/R-cran-rgdal/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/graphics/R-cran-rgdal/work/.bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin PKG_CONFIG_LIBDIR=/wrkdirs/usr/ports/graphics/R-cran-rgdal/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-- F77="gfortran12" F90="gfortran12" FC="gfortran12" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc12" F90FLAGS="-O -Wl,-rpath=/usr/local/lib/gcc12" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc12" XDG_DATA_HOME=/wrkdirs/usr/ports/graphics/R-cran-rgdal/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/graphics/R-cran-rgdal/work 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PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=yes PACKAGE_BUILDING_FLAVORS=yes #### /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. 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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_921dbbb2=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: powerpc64-unknown-freebsd13.1 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: powerpc64-unknown-freebsd13.1 Thread model: posix InstalledDir: /usr/bin "/usr/bin/ld" "--eh-frame-hdr" "-dynamic-linker" "/libexec/ld-elf.so.1" "--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_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_53255a77=yes CC_OUTPUT_921dbbb2_911cfe02=yes CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=yes CC_OUTPUT_921dbbb2_af59ad06=yes CC_OUTPUT_921dbbb2_a15f3fcf=yes _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 13.0.0 (git@github.com:llvm/llvm-project.git llvmorg-13.0.0-0-gd7b669b3a303) Target: powerpc64-unknown-freebsd13.1 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=powerpc64 PPC_ABI=ELFv2 OPSYS=FreeBSD _OSRELEASE=13.1-RELEASE OSREL=13.1 OSVERSION=1301000 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=524288 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) 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 GPLv2+ accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> R-cran-rgdal-1.5.32_4 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.19.1_1.pkg [131powerpc64-quarterly-job-02] Installing pkg-1.19.1_1... [131powerpc64-quarterly-job-02] Extracting pkg-1.19.1_1: .......... done ===> R-cran-rgdal-1.5.32_4 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of R-cran-rgdal-1.5.32_4 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv2+ accepted by the user ===> Fetching all distfiles required by R-cran-rgdal-1.5.32_4 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv2+ accepted by the user ===> Fetching all distfiles required by R-cran-rgdal-1.5.32_4 for building => SHA256 Checksum OK for rgdal_1.5-32.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv2+ accepted by the user ===> Fetching all distfiles required by R-cran-rgdal-1.5.32_4 for building ===> Extracting for R-cran-rgdal-1.5.32_4 => SHA256 Checksum OK for rgdal_1.5-32.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for R-cran-rgdal-1.5.32_4 =========================================================================== =======================<phase: build-depends >============================ ===> R-cran-rgdal-1.5.32_4 depends on package: R-cran-sp>=1.1.0 - not found ===> Installing existing package /packages/All/R-cran-sp-1.6.0.pkg [131powerpc64-quarterly-job-02] Installing R-cran-sp-1.6.0... [131powerpc64-quarterly-job-02] `-- Installing R-4.2.3... [131powerpc64-quarterly-job-02] | `-- Installing cairo-1.17.4_2,3... [131powerpc64-quarterly-job-02] | | `-- Installing fontconfig-2.14.2,1... [131powerpc64-quarterly-job-02] | | `-- Installing expat-2.5.0... [131powerpc64-quarterly-job-02] | | `-- Extracting expat-2.5.0: .......... done [131powerpc64-quarterly-job-02] | | `-- Installing freetype2-2.12.1_2... [131powerpc64-quarterly-job-02] | | | `-- Installing brotli-1.0.9,1... [131powerpc64-quarterly-job-02] | | | `-- Extracting brotli-1.0.9,1: .......... done [131powerpc64-quarterly-job-02] | | | `-- Installing png-1.6.39... [131powerpc64-quarterly-job-02] | | | `-- Extracting png-1.6.39: .......... done [131powerpc64-quarterly-job-02] | | `-- Extracting freetype2-2.12.1_2: .......... done [131powerpc64-quarterly-job-02] | | `-- Extracting fontconfig-2.14.2,1: .......... done <snip> ===> NOTICE: The libthai port currently does not have a maintainer. As a result, it is more likely to have unresolved issues, not be up-to-date, or even be removed in the future. To volunteer to maintain this port, please create an issue at: https://bugs.freebsd.org/bugzilla More information about port maintainership is available at: https://docs.freebsd.org/en/articles/contributing/#ports-contributing ===== Message from dejavu-2.37_1: -- Make sure that the freetype module is loaded. If it is not, add the following line to the "Modules" section of your X Windows configuration file: Load "freetype" Add the following line to the "Files" section of X Windows configuration file: FontPath "/usr/local/share/fonts/dejavu/" Note: your X Windows configuration file is typically /etc/X11/XF86Config if you are using XFree86, and /etc/X11/xorg.conf if you are using X.Org. ===> R-cran-rgdal-1.5.32_4 depends on package: R-cran-sp>=1.1.0 - found ===> Returning to build of R-cran-rgdal-1.5.32_4 ===> R-cran-rgdal-1.5.32_4 depends on file: /usr/local/bin/R - found ===> R-cran-rgdal-1.5.32_4 depends on executable: gfortran12 - found ===> R-cran-rgdal-1.5.32_4 depends on package: pkgconf>=1.3.0_1 - not found ===> Installing existing package /packages/All/pkgconf-1.8.1,1.pkg [131powerpc64-quarterly-job-02] Installing pkgconf-1.8.1,1... [131powerpc64-quarterly-job-02] Extracting pkgconf-1.8.1,1: .......... done ===> R-cran-rgdal-1.5.32_4 depends on package: pkgconf>=1.3.0_1 - found ===> Returning to build of R-cran-rgdal-1.5.32_4 ===> R-cran-rgdal-1.5.32_4 depends on file: /usr/local/bin/as - found =========================================================================== =======================<phase: lib-depends >============================ ===> R-cran-rgdal-1.5.32_4 depends on shared library: libgdal.so - not found ===> Installing existing package /packages/All/gdal-3.6.2_3.pkg [131powerpc64-quarterly-job-02] Installing gdal-3.6.2_3... [131powerpc64-quarterly-job-02] `-- Installing freexl-1.0.6... [131powerpc64-quarterly-job-02] `-- Extracting freexl-1.0.6: .......... done [131powerpc64-quarterly-job-02] `-- Installing geos-3.11.1... [131powerpc64-quarterly-job-02] `-- Extracting geos-3.11.1: .......... done [131powerpc64-quarterly-job-02] `-- Installing giflib-5.2.1... [131powerpc64-quarterly-job-02] `-- Extracting giflib-5.2.1: .......... done [131powerpc64-quarterly-job-02] `-- Installing hdf5-1.12.2_1,1... [131powerpc64-quarterly-job-02] | `-- Installing libaec-1.0.6... [131powerpc64-quarterly-job-02] | `-- Extracting libaec-1.0.6: .......... done [131powerpc64-quarterly-job-02] `-- Extracting hdf5-1.12.2_1,1: .......... done [131powerpc64-quarterly-job-02] `-- Installing json-c-0.16... [131powerpc64-quarterly-job-02] `-- Extracting json-c-0.16: .......... done [131powerpc64-quarterly-job-02] `-- Installing libgeotiff-1.7.1_3... [131powerpc64-quarterly-job-02] | `-- Installing proj-9.2.0,1... [131powerpc64-quarterly-job-02] | | `-- Installing sqlite3-3.41.2,1... [131powerpc64-quarterly-job-02] | | `-- Installing libedit-3.1.20221030,1... [131powerpc64-quarterly-job-02] | | `-- Extracting libedit-3.1.20221030,1: .......... done [131powerpc64-quarterly-job-02] | | `-- Extracting sqlite3-3.41.2,1: .......... done [131powerpc64-quarterly-job-02] | `-- Extracting proj-9.2.0,1: .......... done [131powerpc64-quarterly-job-02] `-- Extracting libgeotiff-1.7.1_3: .......... done [131powerpc64-quarterly-job-02] `-- Installing libkml-1.3.0_25... [131powerpc64-quarterly-job-02] | `-- Installing boost-libs-1.81.0... [131powerpc64-quarterly-job-02] | `-- Extracting boost-libs-1.81.0: .......... done [131powerpc64-quarterly-job-02] | `-- Installing minizip-1.2.11... [131powerpc64-quarterly-job-02] | `-- Extracting minizip-1.2.11: .......... done [131powerpc64-quarterly-job-02] | `-- Installing uriparser-0.9.6... [131powerpc64-quarterly-job-02] | `-- Extracting uriparser-0.9.6: .......... done [131powerpc64-quarterly-job-02] `-- Extracting libkml-1.3.0_25: .......... done [131powerpc64-quarterly-job-02] `-- Installing netcdf-4.9.0_2... [131powerpc64-quarterly-job-02] `-- Extracting netcdf-4.9.0_2: .......... done [131powerpc64-quarterly-job-02] `-- Installing poppler-23.03.0... [131powerpc64-quarterly-job-02] | `-- Installing nspr-4.35... [131powerpc64-quarterly-job-02] | `-- Extracting nspr-4.35: .......... done [131powerpc64-quarterly-job-02] | `-- Installing nss-3.89... [131powerpc64-quarterly-job-02] | `-- Extracting nss-3.89: .......... done [131powerpc64-quarterly-job-02] `-- Extracting poppler-23.03.0: .......... done [131powerpc64-quarterly-job-02] `-- Installing postgresql13-client-13.10... [131powerpc64-quarterly-job-02] `-- Extracting postgresql13-client-13.10: .......... done [131powerpc64-quarterly-job-02] `-- Installing qhull-8.0.2_1,1... [131powerpc64-quarterly-job-02] `-- Extracting qhull-8.0.2_1,1: .......... done [131powerpc64-quarterly-job-02] `-- Installing sfcgal-1.4.1_3... [131powerpc64-quarterly-job-02] `-- Extracting sfcgal-1.4.1_3: .......... done [131powerpc64-quarterly-job-02] `-- Installing shapelib-1.5.0... [131powerpc64-quarterly-job-02] `-- Extracting shapelib-1.5.0: .......... done [131powerpc64-quarterly-job-02] `-- Installing spatialite-5.0.1_5... [131powerpc64-quarterly-job-02] | `-- Installing librttopo-1.1.0... [131powerpc64-quarterly-job-02] | `-- Extracting librttopo-1.1.0: .......... done [131powerpc64-quarterly-job-02] `-- Extracting spatialite-5.0.1_5: .......... done [131powerpc64-quarterly-job-02] `-- Installing webp-1.3.0... [131powerpc64-quarterly-job-02] `-- Extracting webp-1.3.0: .......... done [131powerpc64-quarterly-job-02] `-- Installing xerces-c3-3.2.4... [131powerpc64-quarterly-job-02] `-- Extracting xerces-c3-3.2.4: .......... done [131powerpc64-quarterly-job-02] Extracting gdal-3.6.2_3: .......... done ===== Message from boost-libs-1.81.0: -- You have built the Boost library with thread support. Don't forget to add -pthread to your linker options when linking your code. ===== Message from postgresql13-client-13.10: -- The PostgreSQL port has a collection of "side orders": postgresql-docs For all of the html documentation p5-Pg A perl5 API for client access to PostgreSQL databases. postgresql-tcltk If you want tcl/tk client support. postgresql-jdbc For Java JDBC support. postgresql-odbc For client access from unix applications using ODBC as access method. Not needed to access unix PostgreSQL servers from Win32 using ODBC. See below. ruby-postgres, py-psycopg2 For client access to PostgreSQL databases using the ruby & python languages. postgresql-plperl, postgresql-pltcl & postgresql-plruby For using perl5, tcl & ruby as procedural languages. postgresql-contrib Lots of contributed utilities, postgresql functions and datatypes. There you find pg_standby, pgcrypto and many other cool things. etc... ===> R-cran-rgdal-1.5.32_4 depends on shared library: libgdal.so - found (/usr/local/lib/libgdal.so) ===> Returning to build of R-cran-rgdal-1.5.32_4 ===> R-cran-rgdal-1.5.32_4 depends on shared library: libproj.so - found (/usr/local/lib/libproj.so) =========================================================================== =======================<phase: configure >============================ ===> Configuring for R-cran-rgdal-1.5.32_4 =========================================================================== =======================<phase: build >============================ =========================================================================== =======================<phase: run-depends >============================ ===> R-cran-rgdal-1.5.32_4 depends on package: R-cran-sp>=1.1.0 - found ===> R-cran-rgdal-1.5.32_4 depends on file: /usr/local/bin/R - found ===> R-cran-rgdal-1.5.32_4 depends on executable: gfortran12 - found =========================================================================== =======================<phase: stage >============================ ===> Staging for R-cran-rgdal-1.5.32_4 ===> Generating temporary packing list * installing *source* package 'rgdal' ... ** package 'rgdal' successfully unpacked and MD5 sums checked ** using staged installation configure: R_HOME: /usr/local/lib/R configure: CC: cc configure: CXX: c++ configure: CFLAGS: -O2 -pipe -fstack-protector-strong -fno-strict-aliasing configure: CPPFLAGS: configure: CXXFLAGS: -O2 -pipe -fstack-protector-strong -fno-strict-aliasing configure: LDFLAGS: -Wl,-rpath=/usr/local/lib/gcc12 -L/usr/local/lib/gcc12 -B/usr/local/bin -fstack-protector-strong configure: LDFLAGS: -Wl,-rpath=/usr/local/lib/gcc12 -L/usr/local/lib/gcc12 -B/usr/local/bin -fstack-protector-strong configure: CXX11 is: c++, CXX11STD is: -std=gnu++11 configure: CXX is: c++ -std=gnu++11 configure: C++11 support available configure: rgdal: 1.5-32 checking for /usr/bin/svnversion... no configure: svn revision: 1176 checking for gdal-config... /usr/local/bin/gdal-config checking gdal-config usability... yes configure: GDAL: 3.6.2 checking GDAL version >= 1.11.4... yes checking GDAL version <= 2.5 or >= 3.0... yes checking GDAL: linking with --libs only... yes checking GDAL: gdal-config data directory readable... yes checking GDAL: /usr/local/share/gdal/stateplane.csv readable... yes configure: pkg-config proj exists, will use it configure: PROJ version: 9.2.0 configure: PROJ CPP flags: -DPROJ_H_API -I/usr/local/include configure: PROJ LIBS: -L/usr/local/lib -lproj checking PROJ header API:... yes checking whether the C++ compiler works... yes checking for C++ compiler default output file name... a.out checking for suffix of executables... checking whether we are cross compiling... Segmentation fault (core dumped) configure: error: in `/wrkdirs/usr/ports/graphics/R-cran-rgdal/work/rgdal': configure: error: cannot run C++ compiled programs. If you meant to cross compile, use `--host'. See `config.log' for more details ERROR: configuration failed for package 'rgdal' * removing '/wrkdirs/usr/ports/graphics/R-cran-rgdal/work/stage/usr/local/lib/R/library/rgdal' *** Error code 1 Stop. make: stopped in /usr/ports/graphics/R-cran-rgdal