From owner-freebsd-pkg-fallout@freebsd.org Wed Aug 23 15:08:32 2017 Return-Path: Delivered-To: freebsd-pkg-fallout@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 18382DE9489 for ; Wed, 23 Aug 2017 15:08:32 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from mailman.ysv.freebsd.org (unknown [127.0.1.3]) by mx1.freebsd.org (Postfix) with ESMTP id 053A873F13 for ; Wed, 23 Aug 2017 15:08:32 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: by mailman.ysv.freebsd.org (Postfix) id 0189BDE9487; Wed, 23 Aug 2017 15:08:32 +0000 (UTC) Delivered-To: pkg-fallout@mailman.ysv.freebsd.org Received: from mx1.freebsd.org (mx1.freebsd.org [IPv6:2001:1900:2254:206a::19:1]) by mailman.ysv.freebsd.org (Postfix) with ESMTP id 00EB0DE9486 for ; Wed, 23 Aug 2017 15:08:32 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from thunderx1.nyi.freebsd.org (thunderx1.nyi.freebsd.org [IPv6:2610:1c1:1:6082::16:fb]) (using TLSv1.2 with cipher ECDHE-RSA-AES256-GCM-SHA384 (256/256 bits)) (Client did not present a certificate) by mx1.freebsd.org (Postfix) with ESMTPS id C5A2C73F11 for ; Wed, 23 Aug 2017 15:08:31 +0000 (UTC) (envelope-from pkg-fallout@FreeBSD.org) Received: from thunderx1.nyi.freebsd.org (localhost [127.0.0.1]) by thunderx1.nyi.freebsd.org (8.15.2/8.15.2) with ESMTP id v7NF8UxU040559 for ; Wed, 23 Aug 2017 15:08:30 GMT (envelope-from pkg-fallout@FreeBSD.org) Received: (from root@localhost) by thunderx1.nyi.freebsd.org (8.15.2/8.15.2/Submit) id v7NF8UZK040554; Wed, 23 Aug 2017 15:08:30 GMT (envelope-from pkg-fallout@FreeBSD.org) Date: Wed, 23 Aug 2017 15:08:30 GMT From: pkg-fallout@FreeBSD.org Message-Id: <201708231508.v7NF8UZK040554@thunderx1.nyi.freebsd.org> To: pkg-fallout@FreeBSD.org Subject: [package - 110arm64-default][math/R-cran-irlba] Failed for R-cran-irlba-2.2.1 in stage X-BeenThere: freebsd-pkg-fallout@freebsd.org X-Mailman-Version: 2.1.23 Precedence: list List-Id: Fallout logs from package building List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , X-List-Received-Date: Wed, 23 Aug 2017 15:08:32 -0000 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 Last committer: tota@FreeBSD.org Ident: $FreeBSD: head/math/R-cran-irlba/Makefile 441209 2017-05-19 05:11:36Z tota $ Log URL: http://thunderx1.nyi.freebsd.org/data/110arm64-default/448504/logs/R-cran-irlba-2.2.1.log Build URL: http://thunderx1.nyi.freebsd.org/build.html?mastername=110arm64-default&build=448504 Log: ====>> Building math/R-cran-irlba build started at Wed Aug 23 15:06:19 UTC 2017 port directory: /usr/ports/math/R-cran-irlba building for: FreeBSD 110arm64-default-job-04 11.0-RELEASE-p1 FreeBSD 11.0-RELEASE-p1 arm64 maintained by: tota@FreeBSD.org Makefile ident: $FreeBSD: head/math/R-cran-irlba/Makefile 441209 2017-05-19 05:11:36Z tota $ Poudriere version: 3.1.19-61-ga8829ba9 Host OSVERSION: 1200040 Jail OSVERSION: 1100122 Job Id: 04 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1100122 UNAME_v=FreeBSD 11.0-RELEASE-p1 UNAME_r=11.0-RELEASE-p1 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/110arm64-default/ref PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk PKGNAME=R-cran-irlba-2.2.1 OLDPWD=/ PWD=/usr/local/poudriere/data/.m/110arm64-default/ref/.p/pool MASTERNAME=110arm64-default SCRIPTPREFIX=/usr/local/share/poudriere USER=root HOME=/root POUDRIERE_VERSION=3.1.19-61-ga8829ba9 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="gfortran5" FC="gfortran5" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc5" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc5" XDG_DATA_HOME=/wrkdirs/usr/ports/math/R-cran-irlba/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/math/R-cran-irlba/work HOME=/wrkdirs/usr/ports/math/R-cran-irlba/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh --End CONFIGURE_ENV-- --MAKE_ENV-- F77="gfortran5" FC="gfortran5" FFLAGS="-O -Wl,-rpath=/usr/local/lib/gcc5" FCFLAGS="-Wl,-rpath=/usr/local/lib/gcc5" XDG_DATA_HOME=/wrkdirs/usr/ports/math/R-cran-irlba/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/math/R-cran-irlba/work HOME=/wrkdirs/usr/ports/math/R-cran-irlba/work TMPDIR="/tmp" 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 -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS=" -Wl,-rpath=/usr/local/lib/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin" LIBS="" CXX="c++" CXXFLAGS="-O2 - pipe -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/irlba OSREL=11.0 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib DOCSDIR="share/doc/irlba" EXAMPLESDIR="share/examples/irlba" DATADIR="share/irlba" WWWDIR="www/irlba" ETCDIR="etc/irlba" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/irlba DOCSDIR=/usr/local/share/doc/irlba EXAMPLESDIR=/usr/local/share/examples/irlba WWWDIR=/usr/local/www/irlba ETCDIR=/usr/local/etc/irlba --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=aarch64 CONFIGURE_MAX_CMD_LEN=262144 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|1.6\+|1.7\+|1.8\+ _OSRELEASE=11.0-RELEASE-p1 #### 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) 1048576 stack size (kbytes, -s) 1048576 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-- =================================================== ===> License GPLv3 accepted by the user =========================================================================== =================================================== ===> R-cran-irlba-2.2.1 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.1.txz [110arm64-default-job-04] Installing pkg-1.10.1... [110arm64-default-job-04] Extracting pkg-1.10.1: .......... done ===> R-cran-irlba-2.2.1 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of R-cran-irlba-2.2.1 =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by R-cran-irlba-2.2.1 for building =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by R-cran-irlba-2.2.1 for building => SHA256 Checksum OK for irlba_2.2.1.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> License GPLv3 accepted by the user ===> Fetching all distfiles required by R-cran-irlba-2.2.1 for building ===> Extracting for R-cran-irlba-2.2.1 => SHA256 Checksum OK for irlba_2.2.1.tar.gz. =========================================================================== =================================================== =========================================================================== =================================================== ===> Patching for R-cran-irlba-2.2.1 =========================================================================== =================================================== ===> R-cran-irlba-2.2.1 depends on file: /usr/local/bin/R - not found ===> Installing existing package /packages/All/R-3.4.1_4.txz [110arm64-default-job-04] Installing R-3.4.1_4... [110arm64-default-job-04] `-- Installing cairo-1.14.8_1,2... [110arm64-default-job-04] | `-- Installing dri2proto-2.8... [110arm64-default-job-04] | `-- Extracting dri2proto-2.8: .... done [110arm64-default-job-04] | `-- Installing fontconfig-2.12.1,1... [110arm64-default-job-04] | | `-- Installing expat-2.2.1... [110arm64-default-job-04] | | `-- Extracting expat-2.2.1: .......... done [110arm64-default-job-04] | | `-- Installing freetype2-2.8... [110arm64-default-job-04] | | `-- Extracting freetype2-2.8: .......... done [110arm64-default-job-04] | `-- 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 [110arm64-default-job-04] | `-- Installing gettext-runtime-0.19.8.1_1... [110arm64-default-job-04] | | `-- Installing indexinfo-0.2.6... [110arm64-default-job-04] | | `-- Extracting indexinfo-0.2.6: .... done [110arm64-default-job-04] | `-- Extracting gettext-runtime-0.19.8.1_1: .......... done [110arm64-default-job-04] | `-- Installing glib-2.50.2_4,1... [110arm64-default-job-04] | | `-- Installing libffi-3.2.1... [110arm64-default-job-04] | | `-- Extracting libffi-3.2.1: .......... done [110arm64-default-job-04] | | `-- Installing libiconv-1.14_10... [110arm64-default-job-04] | | `-- Extracting libiconv-1.14_10: .......... done [110arm64-default-job-04] | | `-- Installing pcre-8.40_1... [110arm64-default-job-04] | | `-- Extracting pcre-8.40_1: .......... done [110arm64-default-job-04] | | `-- Installing perl5-5.24.2... [110arm64-default-job-04] | | `-- Extracting perl5-5.24.2: .......... done [110arm64-default-job-04] | | `-- Installing python27-2.7.13_7... [110arm64-default-job-04] | `-- Extracting libXt-1.1.5,1: .......... done [110arm64-default-job-04] `-- Extracting libXmu-1.1.2_3,1: .......... done [110arm64-default-job-04] `-- Installing pango-1.40.6... [110arm64-default-job-04] | `-- Installing encodings-1.0.4_3,1... [110arm64-default-job-04] | | `-- Installing font-util-1.3.1... [110arm64-default-job-04] | | `-- Extracting font-util-1.3.1: .......... done [110arm64-default-job-04] | `-- Extracting encodings-1.0.4_3,1: .......... done [110arm64-default-job-04] | `-- Installing harfbuzz-1.4.8... [110arm64-default-job-04] | | `-- Installing graphite2-1.3.10... [110arm64-default-job-04] | | `-- Extracting graphite2-1.3.10: .......... done [110arm64-default-job-04] | `-- Extracting harfbuzz-1.4.8: .......... done [110arm64-default-job-04] | `-- Installing libXft-2.3.2_1... [110arm64-default-job-04] | `-- Extracting libXft-2.3.2_1: ......... done [110arm64-default-job-04] | `-- Installing xorg-fonts-truetype-7.7_1... [110arm64-default-job-04] | | `-- Installing dejavu-2.37... [110arm64-default-job-04] | | `-- Installing mkfontdir-1.0.7... [110arm64-default-job-04] | | | `-- Installing mkfontscale-1.1.2... [110arm64-default-job-04] | | | `-- Installing libfontenc-1.1.3_1... [110arm64-default-job-04] | | | `-- Extracting libfontenc-1.1.3_1: ......... done [110arm64-default-job-04] | | | `-- Extracting mkfontscale-1.1.2: .. done [110arm64-default-job-04] | | `-- Extracting mkfontdir-1.0.7: .. done [110arm64-default-job-04] | | `-- Extracting dejavu-2.37: .......... done [110arm64-default-job-04] | | `-- Installing font-bh-ttf-1.0.3_3... [110arm64-default-job-04] | | `-- Extracting font-bh-ttf-1.0.3_3: .......... done [110arm64-default-job-04] | | `-- Installing font-misc-ethiopic-1.0.3_3... [110arm64-default-job-04] | | `-- Extracting font-misc-ethiopic-1.0.3_3: ... done [110arm64-default-job-04] | | `-- Installing font-misc-meltho-1.0.3_3... [110arm64-default-job-04] | | `-- Extracting font-misc-meltho-1.0.3_3: .......... done [110arm64-default-job-04] `-- Extracting pango-1.40.6: .......... done [110arm64-default-job-04] `-- Installing tcl86-8.6.7... [110arm64-default-job-04] `-- Extracting tcl86-8.6.7: .......... done [110arm64-default-job-04] `-- Installing tk86-8.6.7... [110arm64-default-job-04] `-- Extracting tk86-8.6.7: .......... done [110arm64-default-job-04] `-- Installing wget-1.19.1_1... [110arm64-default-job-04] `-- Extracting wget-1.19.1_1: .......... done [110arm64-default-job-04] Extracting R-3.4.1_4: .......... done Message from freetype2-2.8: The 2.7.x series now uses the new subpixel hinting mode (V40 port's option) as the default, emulating a modern version of ClearType. This change inevitably leads to different rendering results, and you might change port's options to adapt it to your taste (or use the new "FREETYPE_PROPERTIES" environment variable). The environment variable "FREETYPE_PROPERTIES" can be used to control the driver properties. Example: FREETYPE_PROPERTIES=truetype:interpreter-version=35 \ cff:no-stem-darkening=1 \ autofitter:warping=1 This allows to select, say, the subpixel hinting mode at runtime for a given application. The controllable properties are listed in the section "Controlling FreeType Modules" in the reference's table of contents (/usr/local/share/doc/freetype2/reference/ft2-toc.html, if documentation was installed). Message from perl5-5.24.2: The /usr/bin/perl symlink has been removed starting with Perl 5.20. For shebangs, you should either use: #!/usr/local/bin/perl or #!/usr/bin/env perl The first one will only work if you have a /usr/local/bin/perl, the second will work as long as perl is in PATH. Message from python27-2.7.13_7: =========================================================================== Note that some standard Python modules are provided as separate ports as they require additional dependencies. They are available as: bsddb databases/py-bsddb gdbm databases/py-gdbm sqlite3 databases/py-sqlite3 tkinter x11-toolkits/py-tkinter =========================================================================== Message from ca_root_nss-3.32: ********************************* 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 gcc5-5.4.0_3: 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/gcc5 For ports leveraging USE_GCC, USES=compiler, or USES=fortran this happens transparently. 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-3.4.1_4: ======================================================================== On 11.1 and later, there is a problem downloading R packages when gfortran is chosen as the fortran compiler. Use either of these workarounds until a permanent solution is found. 1. If you are on an amd64 system, you can use flang as the fortran compiler. 2. If you choose gfortran as the fortran compiler, you can 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-irlba-2.2.1 depends on file: /usr/local/bin/R - found ===> Returning to build of R-cran-irlba-2.2.1 ===> R-cran-irlba-2.2.1 depends on executable: gfortran5 - found ===> R-cran-irlba-2.2.1 depends on file: /usr/local/bin/as - found =========================================================================== =================================================== =========================================================================== =================================================== ===> Configuring for R-cran-irlba-2.2.1 =========================================================================== =================================================== =========================================================================== =================================================== ===> R-cran-irlba-2.2.1 depends on file: /usr/local/bin/R - found ===> R-cran-irlba-2.2.1 depends on executable: gfortran5 - found =========================================================================== =================================================== ===> Staging for R-cran-irlba-2.2.1 ===> Generating temporary packing list * installing *source* package 'irlba' ... ** package 'irlba' successfully unpacked and MD5 sums checked ** libs gmake[1]: Entering directory '/wrkdirs/usr/ports/math/R-cran-irlba/work/irlba/src' /usr/local/bin/clang40 -I/usr/local/lib/R/include -DNDEBUG -I"/usr/local/lib/R/library/Matrix/include" -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include -fpic -O2 -pipe -DLIBICONV_PLUG -isystem /usr/local/include -fno-strict-aliasing -c irlb.c -o irlb.o /bin/sh: /usr/local/bin/clang40: not found gmake[1]: *** [/usr/local/lib/R/etc/Makeconf:159: irlb.o] Error 127 gmake[1]: Leaving directory '/wrkdirs/usr/ports/math/R-cran-irlba/work/irlba/src' ERROR: compilation failed for package 'irlba' * removing '/wrkdirs/usr/ports/math/R-cran-irlba/work/stage/usr/local/lib/R/library/irlba' *** Error code 1 Stop. make: stopped in /usr/ports/math/R-cran-irlba