Date: Tue, 17 Oct 2017 10:21:49 GMT From: pkg-fallout@FreeBSD.org To: tota@FreeBSD.org Cc: pkg-fallout@FreeBSD.org Subject: [package - 110amd64-default][math/R-cran-minqa] Failed for R-cran-minqa-1.2.4_1 in stage Message-ID: <201710171021.v9HALnMq001301@beefy9.nyi.freebsd.org>
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Maintainer: tota@FreeBSD.org Last committer: dbn@FreeBSD.org Ident: $FreeBSD: head/math/R-cran-minqa/Makefile 443845 2017-06-18 18:09:16Z dbn $ Log URL: http://beefy9.nyi.freebsd.org/data/110amd64-default/452255/logs/R-cran-minqa-1.2.4_1.log Build URL: http://beefy9.nyi.freebsd.org/build.html?mastername=110amd64-default&build=452255 Log: ====>> Building math/R-cran-minqa build started at Tue Oct 17 10:15:45 UTC 2017 port directory: /usr/ports/math/R-cran-minqa building for: FreeBSD 110amd64-default-job-15 11.0-RELEASE-p12 FreeBSD 11.0-RELEASE-p12 amd64 maintained by: tota@FreeBSD.org Makefile ident: $FreeBSD: head/math/R-cran-minqa/Makefile 443845 2017-06-18 18:09:16Z dbn $ Poudriere version: 3.1.21 Host OSVERSION: 1200042 Jail OSVERSION: 1100122 Job Id: 15 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1100122 UNAME_v=FreeBSD 11.0-RELEASE-p12 UNAME_r=11.0-RELEASE-p12 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/110amd64-default/ref PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk PKGNAME=R-cran-minqa-1.2.4_1 OLDPWD=/ PWD=/usr/local/poudriere/data/.m/110amd64-default/ref/.p/pool MASTERNAME=110amd64-default SCRIPTPREFIX=/usr/local/share/poudriere USER=root HOME=/root POUDRIERE_VERSION=3.1.21 SCRIPTPATH=/usr/local/share/poudriere/bulk.sh LIBEXECPREFIX=/usr/local/libexec/poudriere LOCALBASE=/usr/local POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- F77="gfortran6" FC="gfortran6" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc6" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc6" XDG_DATA_HOME=/wrkdirs/usr/ports/math/R-cran-minqa/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/math/R-cran-minqa/work HOME=/wrkdirs/usr/ports/math/R-cran-minqa/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/math/R-cran-minqa/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-- F77="gfortran6" FC="gfortran6" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc6" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc6" XDG_DATA_HOME=/wrkdirs/usr/ports/math/R-cran-minqa/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/math/R-cran-minqa/work HOME=/wrkdirs/usr/ports/math/R-cran-minqa/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/math/R-cran-minqa/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 LIBDIR="/usr/lib" CC="cc" CFLAGS="-O2 -pipe -fstack-protector -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc6 -L/usr/local/lib/gcc6 -B/usr/local/bin -fstack-protector" LIBS="" CXX="c++" CXXFLAGS="-O2 -pipe -fstack-protector -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-- R_MOD_DIR=lib/R/library/minqa OSREL=11.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib DOCSDIR="share/doc/minqa" EXAMPLESDIR="share/examples/minqa" DATADIR="share/minqa" WWWDIR="www/minqa" ETCDIR="etc/minqa" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/minqa DOCSDIR=/usr/local/share/doc/minqa EXAMPLESDIR=/usr/local/share/examples/minqa WWWDIR=/usr/local/www/minqa ETCDIR=/usr/local/etc/minqa --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs PORTSDIR=/usr/ports PACKAGES=/packages DISTDIR=/distfiles PACKAGE_BUILDING=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. 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 #### ARCH=amd64 CONFIGURE_MAX_CMD_LEN=262144 HAVE_COMPAT_IA32_KERN=YES OPSYS=FreeBSD OSREL=11.0 OSVERSION=1100122 PYTHONBASE=/usr/local UID=0 _JAVA_OS_LIST_REGEXP=native|linux _JAVA_VENDOR_LIST_REGEXP=openjdk|oracle|sun _JAVA_VERSION_LIST_REGEXP=1.6|1.7|1.8|1.9|1.6\+|1.7\+|1.8\+|1.9\+ _OSRELEASE=11.0-RELEASE-p12 #### Misc Poudriere #### GID=0 DISABLE_MAKE_JOBS=poudriere ---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-minqa-1.2.4_1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.1.txz [110amd64-default-job-15] Installing pkg-1.10.1... [110amd64-default-job-15] Extracting pkg-1.10.1: .......... done ===> R-cran-minqa-1.2.4_1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of R-cran-minqa-1.2.4_1 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by R-cran-minqa-1.2.4_1 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by R-cran-minqa-1.2.4_1 for building => SHA256 Checksum OK for minqa_1.2.4.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by R-cran-minqa-1.2.4_1 for building ===> Extracting for R-cran-minqa-1.2.4_1 => SHA256 Checksum OK for minqa_1.2.4.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for R-cran-minqa-1.2.4_1 =========================================================================== =======================<phase: build-depends >============================ ===> R-cran-minqa-1.2.4_1 depends on file: /usr/local/bin/R - not found ===> Installing existing package /packages/All/R-3.4.2.txz [110amd64-default-job-15] Installing R-3.4.2... [110amd64-default-job-15] `-- Installing cairo-1.14.8_1,2... [110amd64-default-job-15] | `-- Installing dri2proto-2.8... [110amd64-default-job-15] | `-- Extracting dri2proto-2.8: .... done [110amd64-default-job-15] | `-- Installing fontconfig-2.12.1,1... [110amd64-default-job-15] | | `-- Installing expat-2.2.1... [110amd64-default-job-15] | | `-- Extracting expat-2.2.1: .......... done [110amd64-default-job-15] | | `-- Installing freetype2-2.8... [110amd64-default-job-15] | | `-- Extracting freetype2-2.8: .......... done [110amd64-default-job-15] | `-- Extracting fontconfig-2.12.1,1: .......... 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 [110amd64-default-job-15] | `-- Installing gettext-runtime-0.19.8.1_1... [110amd64-default-job-15] | | `-- Installing indexinfo-0.2.6... [110amd64-default-job-15] | | `-- Extracting indexinfo-0.2.6: .... done [110amd64-default-job-15] | `-- Extracting gettext-runtime-0.19.8.1_1: .......... done [110amd64-default-job-15] | `-- Installing glib-2.50.2_6,1... [110amd64-default-job-15] | | `-- Installing libffi-3.2.1_1... [110amd64-default-job-15] | | `-- Extracting libffi-3.2.1_1: .......... done [110amd64-default-job-15] | | `-- Installing libiconv-1.14_11... [110amd64-default-job-15] | | `-- Extracting libiconv-1.14_11: .......... done [110amd64-default-job-15] | | `-- Installing pcre-8.40_1... [110amd64-default-job-15] | | `-- Extracting pcre-8.40_1: .......... done [110amd64-default-job-15] | | `-- Installing perl5-5.24.3... [110amd64-default-job-15] | | `-- Extracting perl5-5.24.3: .......... done <snip> tkinter x11-toolkits/py-tkinter =========================================================================== Message from ca_root_nss-3.32.1: ********************************* WARNING ********************************* FreeBSD does not, and can not warrant that the certification authorities whose certificates are included in this package have in any way been audited for trustworthiness or RFC 3647 compliance. Assessment and verification of trust is the complete responsibility of the system administrator. *********************************** NOTE ********************************** This package installs symlinks to support root certificates discovery by default for software that uses OpenSSL. This enables SSL Certificate Verification by client software without manual intervention. If you prefer to do this manually, replace the following symlinks with either an empty file or your site-local certificate bundle. * /etc/ssl/cert.pem * /usr/local/etc/ssl/cert.pem * /usr/local/openssl/cert.pem *************************************************************************** Message from trousers-0.3.14_1: To run tcsd automatically, add the following line to /etc/rc.conf: tcsd_enable="YES" You might want to edit /usr/local/etc/tcsd.conf to reflect your setup. If you want to use tcsd with software TPM emulator, use the following configuration in /etc/rc.conf: tcsd_enable="YES" tcsd_mode="emulator" tpmd_enable="YES" To use TPM, add your_account to '_tss' group like following: # pw groupmod _tss -m your_account Message from ghostscript9-agpl-base-9.16_5: Note: in order to use the script "dvipdf", dvips must be installed. This program is provided by another package print/tex-dvipsk. FAPIfontmap and FAPIcidfmap in /usr/local/share/ghostscript/9.16/Resource/Init have to be configured if you want to use FAPI feature. Message from dejavu-2.37: 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. Message from R-3.4.2: ======================================================================== On 11.1 and later, there is a problem downloading R packages when R is built with gfortran. Use either of these workarounds until a permanent solution is found. 1. If you are on an amd64 system, use flang to build R. R is now built by default using flang on amd64. 2. If you use gfortran to build R, add options(download.file.method="wget") to ~/.Rprofile followed by a newline. Details: https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=221127 ======================================================================== ===> R-cran-minqa-1.2.4_1 depends on file: /usr/local/bin/R - found ===> Returning to build of R-cran-minqa-1.2.4_1 ===> R-cran-minqa-1.2.4_1 depends on executable: gfortran6 - not found ===> Installing existing package /packages/All/gcc6-6.4.0_2.txz [110amd64-default-job-15] Installing gcc6-6.4.0_2... [110amd64-default-job-15] `-- Installing binutils-2.28,1... [110amd64-default-job-15] `-- Extracting binutils-2.28,1: .......... done [110amd64-default-job-15] `-- Installing gcc-ecj-4.5... [110amd64-default-job-15] `-- Extracting gcc-ecj-4.5: . done [110amd64-default-job-15] `-- Installing mpc-1.0.3... [110amd64-default-job-15] | `-- Installing mpfr-3.1.6... [110amd64-default-job-15] | `-- Extracting mpfr-3.1.6: .......... done [110amd64-default-job-15] `-- Extracting mpc-1.0.3: ...... done [110amd64-default-job-15] Extracting gcc6-6.4.0_2: .......... done Message from gcc6-6.4.0_2: To ensure binaries built with this toolchain find appropriate versions of the necessary run-time libraries, you may want to link using -Wl,-rpath=/usr/local/lib/gcc6 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. ===> R-cran-minqa-1.2.4_1 depends on executable: gfortran6 - found ===> Returning to build of R-cran-minqa-1.2.4_1 ===> R-cran-minqa-1.2.4_1 depends on file: /usr/local/bin/as - found =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for R-cran-minqa-1.2.4_1 =========================================================================== =======================<phase: build >============================ =========================================================================== =======================<phase: run-depends >============================ ===> R-cran-minqa-1.2.4_1 depends on package: R-cran-Rcpp>=0.9.10 - not found ===> Installing existing package /packages/All/R-cran-Rcpp-0.12.13.txz [110amd64-default-job-15] Installing R-cran-Rcpp-0.12.13... [110amd64-default-job-15] Extracting R-cran-Rcpp-0.12.13: .......... done ===> R-cran-minqa-1.2.4_1 depends on package: R-cran-Rcpp>=0.9.10 - found ===> Returning to build of R-cran-minqa-1.2.4_1 ===> R-cran-minqa-1.2.4_1 depends on file: /usr/local/bin/R - found ===> R-cran-minqa-1.2.4_1 depends on executable: gfortran6 - found =========================================================================== =======================<phase: stage >============================ ===> Staging for R-cran-minqa-1.2.4_1 ===> Generating temporary packing list * installing *source* package 'minqa' ... ** package 'minqa' successfully unpacked and MD5 sums checked ** libs gmake[1]: Entering directory '/wrkdirs/usr/ports/math/R-cran-minqa/work/minqa/src' flang -fpic -O -c altmov.f -o altmov.o clang-4.0: warning: -lflang: 'linker' input unused [-Wunused-command-line-argument] clang-4.0: warning: -lflangmain: 'linker' input unused [-Wunused-command-line-argument] clang-4.0: warning: -lflangrti: 'linker' input unused [-Wunused-command-line-argument] clang-4.0: warning: -lompstub: 'linker' input unused [-Wunused-command-line-argument] clang-4.0: warning: -lexecinfo: 'linker' input unused [-Wunused-command-line-argument] clang-4.0: warning: argument unused during compilation: '-L/usr/local/flang/lib' [-Wunused-command-line-argument] flang -fpic -O -c bigden.f -o bigden.o clang-4.0: warning: -lflang: 'linker' input unused [-Wunused-command-line-argument] clang-4.0: warning: -lflangmain: 'linker' input unused [-Wunused-command-line-argument] clang-4.0: warning: -lflangrti: 'linker' input unused [-Wunused-command-line-argument] clang-4.0: warning: -lompstub: 'linker' input unused [-Wunused-command-line-argument] clang-4.0: warning: -lexecinfo: 'linker' input unused [-Wunused-command-line-argument] clang-4.0: warning: argument unused during compilation: '-L/usr/local/flang/lib' [-Wunused-command-line-argument] flang -fpic -O -c biglag.f -o biglag.o clang-4.0: warning: -lflang: 'linker' input unused [-Wunused-command-line-argument] clang-4.0: warning: -lflangmain: 'linker' input unused [-Wunused-command-line-argument] clang-4.0: warning: -lflangrti: 'linker' input unused [-Wunused-command-line-argument] clang-4.0: warning: -lompstub: 'linker' input unused [-Wunused-command-line-argument] clang-4.0: warning: -lexecinfo: 'linker' input unused [-Wunused-command-line-argument] clang-4.0: warning: argument unused during compilation: '-L/usr/local/flang/lib' [-Wunused-command-line-argument] flang -fpic -O -c bobyqa.f -o bobyqa.o clang-4.0: warning: -lflang: 'linker' input unused [-Wunused-command-line-argument] clang-4.0: warning: -lflangmain: 'linker' input unused [-Wunused-command-line-argument] clang-4.0: warning: -lflangrti: 'linker' input unused [-Wunused-command-line-argument] clang-4.0: warning: -lompstub: 'linker' input unused [-Wunused-command-line-argument] clang-4.0: warning: -lexecinfo: 'linker' input unused [-Wunused-command-line-argument] clang-4.0: warning: argument unused during compilation: '-L/usr/local/flang/lib' [-Wunused-command-line-argument] flang -fpic -O -c bobyqb.f -o bobyqb.o clang-4.0: warning: -lflang: 'linker' input unused [-Wunused-command-line-argument] clang-4.0: warning: -lflangmain: 'linker' input unused [-Wunused-command-line-argument] clang-4.0: warning: -lflangrti: 'linker' input unused [-Wunused-command-line-argument] clang-4.0: warning: -lompstub: 'linker' input unused [-Wunused-command-line-argument] clang-4.0: warning: -lexecinfo: 'linker' input unused [-Wunused-command-line-argument] clang-4.0: warning: argument unused during compilation: '-L/usr/local/flang/lib' [-Wunused-command-line-argument] flang -fpic -O -c lagmax.f -o lagmax.o clang-4.0: warning: -lflang: 'linker' input unused [-Wunused-command-line-argument] clang-4.0: warning: -lflangmain: 'linker' input unused [-Wunused-command-line-argument] clang-4.0: warning: -lflangrti: 'linker' input unused [-Wunused-command-line-argument] clang-4.0: warning: -lompstub: 'linker' input unused [-Wunused-command-line-argument] clang-4.0: warning: -lexecinfo: 'linker' input unused [-Wunused-command-line-argument] clang-4.0: warning: argument unused during compilation: '-L/usr/local/flang/lib' [-Wunused-command-line-argument] c++ -I/usr/local/lib/R/include -DNDEBUG -I"/usr/local/lib/R/library/Rcpp/include" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -fstack-protector -isystem /usr/local/include -fno-strict-aliasing -DLIBICONV_PLUG -isystem /usr/local/include -c minqa.cpp -o minqa.o c++: error: unable to execute command: Killed c++: error: clang frontend command failed due to signal (use -v to see invocation) FreeBSD clang version 3.8.0 (tags/RELEASE_380/final 262564) (based on LLVM 3.8.0) Target: x86_64-unknown-freebsd11.0 Thread model: posix InstalledDir: /usr/bin c++: note: diagnostic msg: PLEASE submit a bug report to https://bugs.freebsd.org/submit/ and include the crash backtrace, preprocessed source, and associated run script. c++: note: diagnostic msg: ******************** PLEASE ATTACH THE FOLLOWING FILES TO THE BUG REPORT: Preprocessed source(s) and associated run script(s) are located at: c++: note: diagnostic msg: /tmp/minqa-1be37b.cpp c++: note: diagnostic msg: /tmp/minqa-1be37b.sh c++: note: diagnostic msg: ******************** gmake[1]: *** [/usr/local/lib/R/etc/Makeconf:166: minqa.o] Error 254 gmake[1]: Leaving directory '/wrkdirs/usr/ports/math/R-cran-minqa/work/minqa/src' ERROR: compilation failed for package 'minqa' * removing '/wrkdirs/usr/ports/math/R-cran-minqa/work/stage/usr/local/lib/R/library/minqa' *** Error code 1 Stop. make: stopped in /usr/ports/math/R-cran-minqa
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