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Maintainer: [email protected] Last committer: [email protected] Ident: $FreeBSD: head/print/R-cran-knitr/Makefile 465156 2018-03-21 08:10:01Z tota $ Log URL: http://thunderx1.nyi.freebsd.org/data/111arm64-default/475217/logs/R-cran-knitr-1.20.log Build URL: http://thunderx1.nyi.freebsd.org/build.html?mastername=111arm64-default&build=475217 Log: =>> Building print/R-cran-knitr build started at Thu Jul 26 12:10:31 UTC 2018 port directory: /usr/ports/print/R-cran-knitr package name: R-cran-knitr-1.20 building for: FreeBSD 111arm64-default-job-14 11.1-RELEASE FreeBSD 11.1-RELEASE arm64 maintained by: [email protected] Makefile ident: $FreeBSD: head/print/R-cran-knitr/Makefile 465156 2018-03-21 08:10:01Z tota $ Poudriere version: 3.2.7-2-g1cf194be Host OSVERSION: 1200072 Jail OSVERSION: 1101001 Job Id: 14 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1101001 UNAME_v=FreeBSD 11.1-RELEASE UNAME_r=11.1-RELEASE 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 LIBEXECPREFIX=/usr/local/libexec/poudriere POUDRIERE_VERSION=3.2.7-2-g1cf194be MASTERMNT=/usr/local/poudriere/data/.m/111arm64-default/ref POUDRIERE_BUILD_TYPE=bulk PACKAGE_BUILDING=yes SAVED_TERM= PWD=/usr/local/poudriere/data/.m/111arm64-default/ref/.p/pool P_PORTS_FEATURES=FLAVORS SELECTED_OPTIONS MASTERNAME=111arm64-default SCRIPTPREFIX=/usr/local/share/poudriere OLDPWD=/usr/local/poudriere/data/.m/111arm64-default/ref/.p SCRIPTPATH=/usr/local/share/poudriere/bulk.sh POUDRIEREPATH=/usr/local/bin/poudriere ---End Environment--- ---Begin Poudriere Port Flags/Env--- PORT_FLAGS= PKGENV= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- [email protected] --End MAINTAINER-- --CONFIGURE_ARGS-- --End CONFIGURE_ARGS-- --CONFIGURE_ENV-- XDG_DATA_HOME=/wrkdirs/usr/ports/print/R-cran-knitr/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/print/R-cran-knitr/work HOME=/wrkdirs/usr/ports/print/R-cran-knitr/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/print/R-cran-knitr/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/print/R-cran-knitr/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/print/R-cran-knitr/work HOME=/wrkdirs/usr/ports/print/R-cran-knitr/work TMPDIR="/tmp" PATH=/wrkdirs/usr/ports/print/R-cran-knitr/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 PREFIX=/usr/local LOCALBASE=/usr/local CC="cc" CFLAGS="-O2 -pipe -fno-strict-aliasing" CPP="cpp" CPPFLAGS="" LDFLAGS="" 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-- PORTDOCS="" PORTEXAMPLES="" R_MOD_DIR=lib/R/library/knitr OSREL=11.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local LIB32DIR=lib DOCSDIR="share/doc/knitr" EXAMPLESDIR="share/examples/knitr" DATADIR="share/knitr" WWWDIR="www/knitr" ETCDIR="etc/knitr" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/knitr DOCSDIR=/usr/local/share/doc/knitr EXAMPLESDIR=/usr/local/share/examples/knitr WWWDIR=/usr/local/www/knitr ETCDIR=/usr/local/etc/knitr --End SUB_LIST-- ---Begin make.conf--- USE_PACKAGE_DEPENDS=yes BATCH=yes WRKDIRPREFIX=/wrkdirs 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. 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 # stable/10 includes src.conf too late but make.conf is in sys.mk .if ${.CURDIR:M/poudriere/jails/10*/usr/src/usr.bin/xlint*} # Disable build of llib now that head no longer has lint(1) LINT= true .endif #### /usr/ports/Mk/Scripts/ports_env.sh #### _CCVERSION_921dbbb2=FreeBSD clang version 4.0.0 (tags/RELEASE_400/final 297347) (based on LLVM 4.0.0) Target: aarch64-unknown-freebsd11.1 Thread model: posix InstalledDir: /usr/bin _ALTCCVERSION_921dbbb2=none _CXXINTERNAL_acaad9ca=FreeBSD clang version 4.0.0 (tags/RELEASE_400/final 297347) (based on LLVM 4.0.0) Target: aarch64-unknown-freebsd11.1 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=error: invalid value 'c++17' in '-std=c++17' CC_OUTPUT_921dbbb2_b2657cc3=yes CC_OUTPUT_921dbbb2_380987f7=yes CC_OUTPUT_921dbbb2_160933ec=yes CC_OUTPUT_921dbbb2_fb62803b=error: invalid value 'gnu++17' in '-std=gnu++17' _OBJC_CCVERSION_921dbbb2=FreeBSD clang version 4.0.0 (tags/RELEASE_400/final 297347) (based on LLVM 4.0.0) Target: aarch64-unknown-freebsd11.1 Thread model: posix InstalledDir: /usr/bin _OBJC_ALTCCVERSION_921dbbb2=none ARCH=aarch64 OPSYS=FreeBSD _OSRELEASE=11.1-RELEASE OSREL=11.1 OSVERSION=1101001 PYTHONBASE=/usr/local CONFIGURE_MAX_CMD_LEN=262144 HAVE_PORTS_ENV=1 #### Misc Poudriere #### GID=0 UID=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-- =======================<phase: check-sanity >============================ ===> License GPLv2+ accepted by the user =========================================================================== =======================<phase: pkg-depends >============================ ===> R-cran-knitr-1.20 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.5_1.txz [111arm64-default-job-14] Installing pkg-1.10.5_1... [111arm64-default-job-14] Extracting pkg-1.10.5_1: .......... done ===> R-cran-knitr-1.20 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of R-cran-knitr-1.20 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv2+ accepted by the user ===> Fetching all distfiles required by R-cran-knitr-1.20 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv2+ accepted by the user ===> Fetching all distfiles required by R-cran-knitr-1.20 for building => SHA256 Checksum OK for knitr_1.20.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv2+ accepted by the user ===> Fetching all distfiles required by R-cran-knitr-1.20 for building ===> Extracting for R-cran-knitr-1.20 => SHA256 Checksum OK for knitr_1.20.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for R-cran-knitr-1.20 =========================================================================== =======================<phase: build-depends >============================ ===> R-cran-knitr-1.20 depends on package: R-cran-evaluate>=0.10 - not found ===> Installing existing package /packages/All/R-cran-evaluate-0.11.txz [111arm64-default-job-14] Installing R-cran-evaluate-0.11... [111arm64-default-job-14] `-- Installing R-3.5.1... [111arm64-default-job-14] | `-- Installing cairo-1.14.8_1,2... [111arm64-default-job-14] | | `-- Installing dri2proto-2.8... [111arm64-default-job-14] | | `-- Extracting dri2proto-2.8: .... done [111arm64-default-job-14] | | `-- Installing fontconfig-2.12.6,1... [111arm64-default-job-14] | | `-- Installing expat-2.2.5... [111arm64-default-job-14] | | `-- Extracting expat-2.2.5: .......... done [111arm64-default-job-14] | | `-- Installing freetype2-2.9.1... [111arm64-default-job-14] | | `-- Extracting freetype2-2.9.1: .......... done [111arm64-default-job-14] | | `-- Extracting fontconfig-2.12.6,1: .......... done Running fc-cache to build fontconfig cache... /usr/local/share/fonts: skipping, no such directory <snip> [111arm64-default-job-14] | `-- Extracting R-cran-magrittr-1.5_1: .......... done [111arm64-default-job-14] | `-- Installing R-cran-stringi-1.2.3_1... [111arm64-default-job-14] | `-- Extracting R-cran-stringi-1.2.3_1: .......... done [111arm64-default-job-14] `-- Extracting R-cran-stringr-1.3.1: .......... done [111arm64-default-job-14] Extracting R-cran-evaluate-0.11: .......... done Message from freetype2-2.9.1: 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 perl5-5.26.2: 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 python27-2.7.15: =========================================================================== 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-3.38: ********************************* 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 gcc6-6.4.0_7: 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. Message from trousers-0.3.14_2: 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 libijs-0.35_5: ===> NOTICE: The libijs 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://www.freebsd.org/doc/en/articles/contributing/ports-contributing.html#maintain-port Message from ghostscript9-agpl-base-9.23_1: This package installs a script named dvipdf that depends on dvips. If you want to use this script you need to install print/tex-dvipsk. 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. ===> R-cran-knitr-1.20 depends on package: R-cran-evaluate>=0.10 - found ===> Returning to build of R-cran-knitr-1.20 ===> R-cran-knitr-1.20 depends on package: R-cran-highr>0 - not found ===> Installing existing package /packages/All/R-cran-highr-0.7.txz [111arm64-default-job-14] Installing R-cran-highr-0.7... [111arm64-default-job-14] Extracting R-cran-highr-0.7: .......... done ===> R-cran-knitr-1.20 depends on package: R-cran-highr>0 - found ===> Returning to build of R-cran-knitr-1.20 ===> R-cran-knitr-1.20 depends on package: R-cran-markdown>0 - not found ===> Installing existing package /packages/All/R-cran-markdown-0.8_2.txz [111arm64-default-job-14] Installing R-cran-markdown-0.8_2... [111arm64-default-job-14] `-- Installing R-cran-mime-0.5_1... [111arm64-default-job-14] `-- Extracting R-cran-mime-0.5_1: .......... done [111arm64-default-job-14] Extracting R-cran-markdown-0.8_2: .......... done ===> R-cran-knitr-1.20 depends on package: R-cran-markdown>0 - found ===> Returning to build of R-cran-knitr-1.20 ===> R-cran-knitr-1.20 depends on package: R-cran-stringr>=0.6 - found ===> R-cran-knitr-1.20 depends on package: R-cran-yaml>0 - not found ===> Installing existing package /packages/All/R-cran-yaml-2.1.19.txz [111arm64-default-job-14] Installing R-cran-yaml-2.1.19... [111arm64-default-job-14] Extracting R-cran-yaml-2.1.19: .......... done ===> R-cran-knitr-1.20 depends on package: R-cran-yaml>0 - found ===> Returning to build of R-cran-knitr-1.20 ===> R-cran-knitr-1.20 depends on file: /usr/local/bin/R - found =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for R-cran-knitr-1.20 =========================================================================== =======================<phase: build >============================ =========================================================================== =======================<phase: run-depends >============================ ===> R-cran-knitr-1.20 depends on package: R-cran-evaluate>=0.10 - found ===> R-cran-knitr-1.20 depends on package: R-cran-highr>0 - found ===> R-cran-knitr-1.20 depends on package: R-cran-markdown>0 - found ===> R-cran-knitr-1.20 depends on package: R-cran-stringr>=0.6 - found ===> R-cran-knitr-1.20 depends on package: R-cran-yaml>0 - found ===> R-cran-knitr-1.20 depends on file: /usr/local/bin/R - found =========================================================================== =======================<phase: stage >============================ ===> Staging for R-cran-knitr-1.20 ===> Generating temporary packing list * installing *source* package 'knitr' ... ** package 'knitr' successfully unpacked and MD5 sums checked ** R ** demo ** inst *** caught segfault *** address 0x0, cause 'memory not mapped' Traceback: 1: grep(pattern, x, invert = TRUE, value = TRUE, ...) 2: filtergrep(e, i_files, perl = TRUE, ignore.case = TRUE) 3: do_install_source(pkg_name, instdir, pkg, desc) 4: do_install(pkg) 5: tools:::.install_packages() An irrecoverable exception occurred. R is aborting now ... Segmentation fault (core dumped) *** Error code 139 Stop. make: stopped in /usr/ports/print/R-cran-knitr _______________________________________________ [email protected] mailing list https://lists.freebsd.org/mailman/listinfo/freebsd-pkg-fallout To unsubscribe, send any mail to "[email protected]"
