Date: Sun, 17 Dec 2017 01:22:42 GMT From: pkg-fallout@FreeBSD.org To: skreuzer@FreeBSD.org Cc: pkg-fallout@FreeBSD.org Subject: [package - 111amd64-quarterly][devel/R-cran-glmnet] Failed for R-cran-glmnet-1.8.5_7 in stage Message-ID: <201712170122.vBH1MgHM069490@beefy3.nyi.freebsd.org>
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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: skreuzer@FreeBSD.org Last committer: dbn@FreeBSD.org Ident: $FreeBSD: branches/2017Q4/devel/R-cran-glmnet/Makefile 443845 2017-06-18 18:09:16Z dbn $ Log URL: http://beefy3.nyi.freebsd.org/data/111amd64-quarterly/456459/logs/R-cran-glmnet-1.8.5_7.log Build URL: http://beefy3.nyi.freebsd.org/build.html?mastername=111amd64-quarterly&build=456459 Log: =>> Building devel/R-cran-glmnet build started at Sun Dec 17 01:21:17 UTC 2017 port directory: /usr/ports/devel/R-cran-glmnet package name: R-cran-glmnet-1.8.5_7 building for: FreeBSD 111amd64-quarterly-job-06 11.1-RELEASE-p6 FreeBSD 11.1-RELEASE-p6 amd64 maintained by: skreuzer@FreeBSD.org Makefile ident: $FreeBSD: branches/2017Q4/devel/R-cran-glmnet/Makefile 443845 2017-06-18 18:09:16Z dbn $ Poudriere version: 3.2.3-16-g77e43413 Host OSVERSION: 1200052 Jail OSVERSION: 1101001 Job Id: 06 ---Begin Environment--- SHELL=/bin/csh OSVERSION=1101001 UNAME_v=FreeBSD 11.1-RELEASE-p6 UNAME_r=11.1-RELEASE-p6 BLOCKSIZE=K MAIL=/var/mail/root STATUS=1 SAVED_TERM= MASTERMNT=/usr/local/poudriere/data/.m/111amd64-quarterly/ref PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/local/sbin:/usr/local/bin:/root/bin POUDRIERE_BUILD_TYPE=bulk OLDPWD=/usr/local/poudriere/data/.m/111amd64-quarterly/ref/.p P_PORTS_FEATURES=DEPENDS_ARGS SELECTED_OPTIONS PWD=/usr/local/poudriere/data/.m/111amd64-quarterly/ref/.p/pool MASTERNAME=111amd64-quarterly SCRIPTPREFIX=/usr/local/share/poudriere USER=root HOME=/root P_PYTHON_MAJOR_VER=2 POUDRIERE_VERSION=3.2.3-16-g77e43413 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= FLAVOR= DEPENDS_ARGS= MAKE_ARGS= ---End Poudriere Port Flags/Env--- ---Begin OPTIONS List--- ---End OPTIONS List--- --MAINTAINER-- skreuzer@FreeBSD.org --End MAINTAINER-- --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/devel/R-cran-glmnet/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/devel/R-cran-glmnet/work HOME=/wrkdirs/usr/ports/devel/R-cran-glmnet/work TMPDIR="/tmp" 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/devel/R-cran-glmnet/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/devel/R-cran-glmnet/work HOME=/wrkdirs/usr/ports/devel/R-cran-glmnet/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 -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-pro tector" 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/glmnet OSREL=11.1 PREFIX=%D LOCALBASE=/usr/local RESETPREFIX=/usr/local PORTDOCS="" PORTEXAMPLES="" LIB32DIR=lib DOCSDIR="share/doc/glmnet" EXAMPLESDIR="share/examples/glmnet" DATADIR="share/glmnet" WWWDIR="www/glmnet" ETCDIR="etc/glmnet" --End PLIST_SUB-- --SUB_LIST-- PREFIX=/usr/local LOCALBASE=/usr/local DATADIR=/usr/local/share/glmnet DOCSDIR=/usr/local/share/doc/glmnet EXAMPLESDIR=/usr/local/share/examples/glmnet WWWDIR=/usr/local/www/glmnet ETCDIR=/usr/local/etc/glmnet --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 #### /usr/ports/Mk/Scripts/ports_env.sh #### ARCH=amd64 CONFIGURE_MAX_CMD_LEN=262144 HAVE_COMPAT_IA32_KERN=YES OPSYS=FreeBSD OSREL=11.1 OSVERSION=1101001 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=11.1-RELEASE-p6 #### 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-glmnet-1.8.5_7 depends on file: /usr/local/sbin/pkg - not found ===> Installing existing package /packages/All/pkg-1.10.1.txz [111amd64-quarterly-job-06] Installing pkg-1.10.1... [111amd64-quarterly-job-06] Extracting pkg-1.10.1: .......... done ===> R-cran-glmnet-1.8.5_7 depends on file: /usr/local/sbin/pkg - found ===> Returning to build of R-cran-glmnet-1.8.5_7 =========================================================================== =======================<phase: fetch-depends >============================ =========================================================================== =======================<phase: fetch >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by R-cran-glmnet-1.8.5_7 for building =========================================================================== =======================<phase: checksum >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by R-cran-glmnet-1.8.5_7 for building => SHA256 Checksum OK for glmnet_1.8-5.tar.gz. =========================================================================== =======================<phase: extract-depends>============================ =========================================================================== =======================<phase: extract >============================ ===> License GPLv2 accepted by the user ===> Fetching all distfiles required by R-cran-glmnet-1.8.5_7 for building ===> Extracting for R-cran-glmnet-1.8.5_7 => SHA256 Checksum OK for glmnet_1.8-5.tar.gz. =========================================================================== =======================<phase: patch-depends >============================ =========================================================================== =======================<phase: patch >============================ ===> Patching for R-cran-glmnet-1.8.5_7 =========================================================================== =======================<phase: build-depends >============================ ===> R-cran-glmnet-1.8.5_7 depends on file: /usr/local/bin/R - not found ===> Installing existing package /packages/All/R-3.4.2.txz [111amd64-quarterly-job-06] Installing R-3.4.2... [111amd64-quarterly-job-06] `-- Installing cairo-1.14.8_1,2... [111amd64-quarterly-job-06] | `-- Installing dri2proto-2.8... [111amd64-quarterly-job-06] | `-- Extracting dri2proto-2.8: .... done [111amd64-quarterly-job-06] | `-- Installing fontconfig-2.12.1,1... [111amd64-quarterly-job-06] | | `-- Installing expat-2.2.1... [111amd64-quarterly-job-06] | | `-- Extracting expat-2.2.1: .......... done [111amd64-quarterly-job-06] | | `-- Installing freetype2-2.8... [111amd64-quarterly-job-06] | | `-- Extracting freetype2-2.8: .......... done [111amd64-quarterly-job-06] | `-- 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 [111amd64-quarterly-job-06] | `-- Installing gettext-runtime-0.19.8.1_1... [111amd64-quarterly-job-06] | | `-- Installing indexinfo-0.2.6... [111amd64-quarterly-job-06] | | `-- Extracting indexinfo-0.2.6: .... done [111amd64-quarterly-job-06] | `-- Extracting gettext-runtime-0.19.8.1_1: .......... done [111amd64-quarterly-job-06] | `-- Installing glib-2.50.2_6,1... [111amd64-quarterly-job-06] | | `-- Installing libffi-3.2.1_1... [111amd64-quarterly-job-06] | | `-- Extracting libffi-3.2.1_1: .......... done [111amd64-quarterly-job-06] | | `-- Installing libiconv-1.14_11... [111amd64-quarterly-job-06] | | `-- Extracting libiconv-1.14_11: .......... done [111amd64-quarterly-job-06] | | `-- Installing pcre-8.40_1... [111amd64-quarterly-job-06] | | `-- Extracting pcre-8.40_1: .......... done [111amd64-quarterly-job-06] | | `-- Installing perl5-5.24.3... [111amd64-quarterly-job-06] | | `-- Extracting perl5-5.24.3: .......... done [111amd64-quarterly-job-06] | | `-- Installing python27-2.7.14... [111amd64-quarterly-job-06] | | `-- Installing readline-7.0.3... [111amd64-quarterly-job-06] | | `-- Extracting readline-7.0.3: .......... done [111amd64-quarterly-job-06] | | `-- Extracting python27-2.7.14: .......... done [111amd64-quarterly-job-06] | `-- Extracting glib-2.50.2_6,1: .......... done No schema files found: doing nothing. [111amd64-quarterly-job-06] | `-- Installing glproto-1.4.17... [111amd64-quarterly-job-06] | `-- Extracting glproto-1.4.17: ...... done <snip> [111amd64-quarterly-job-06] | `-- Installing libXft-2.3.2_1... [111amd64-quarterly-job-06] | `-- Extracting libXft-2.3.2_1: ......... done [111amd64-quarterly-job-06] | `-- Installing xorg-fonts-truetype-7.7_1... [111amd64-quarterly-job-06] | | `-- Installing dejavu-2.37... [111amd64-quarterly-job-06] | | `-- Installing mkfontdir-1.0.7... [111amd64-quarterly-job-06] | | | `-- Installing mkfontscale-1.1.2... [111amd64-quarterly-job-06] | | | `-- Installing libfontenc-1.1.3_1... [111amd64-quarterly-job-06] | | | `-- Extracting libfontenc-1.1.3_1: ......... done [111amd64-quarterly-job-06] | | | `-- Extracting mkfontscale-1.1.2: .. done [111amd64-quarterly-job-06] | | `-- Extracting mkfontdir-1.0.7: .. done [111amd64-quarterly-job-06] | | `-- Extracting dejavu-2.37: .......... done [111amd64-quarterly-job-06] | | `-- Installing font-bh-ttf-1.0.3_3... [111amd64-quarterly-job-06] | | `-- Extracting font-bh-ttf-1.0.3_3: .......... done [111amd64-quarterly-job-06] | | `-- Installing font-misc-ethiopic-1.0.3_3... [111amd64-quarterly-job-06] | | `-- Extracting font-misc-ethiopic-1.0.3_3: ... done [111amd64-quarterly-job-06] | | `-- Installing font-misc-meltho-1.0.3_3... [111amd64-quarterly-job-06] | | `-- Extracting font-misc-meltho-1.0.3_3: .......... done [111amd64-quarterly-job-06] `-- Extracting pango-1.40.6: .......... done [111amd64-quarterly-job-06] `-- Installing tcl86-8.6.7... [111amd64-quarterly-job-06] `-- Extracting tcl86-8.6.7: .......... done [111amd64-quarterly-job-06] `-- Installing tk86-8.6.7... [111amd64-quarterly-job-06] `-- Extracting tk86-8.6.7: .......... done [111amd64-quarterly-job-06] Extracting R-3.4.2: .......... 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 perl5-5.24.3: 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 python27-2.7.14: =========================================================================== 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-3.34.1: ********************************* 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-glmnet-1.8.5_7 depends on file: /usr/local/bin/R - found ===> Returning to build of R-cran-glmnet-1.8.5_7 ===> R-cran-glmnet-1.8.5_7 depends on executable: gfortran6 - not found ===> Installing existing package /packages/All/gcc6-6.4.0_2.txz [111amd64-quarterly-job-06] Installing gcc6-6.4.0_2... [111amd64-quarterly-job-06] `-- Installing binutils-2.28,1... [111amd64-quarterly-job-06] `-- Extracting binutils-2.28,1: .......... done [111amd64-quarterly-job-06] `-- Installing gcc-ecj-4.5... [111amd64-quarterly-job-06] `-- Extracting gcc-ecj-4.5: . done [111amd64-quarterly-job-06] `-- Installing mpc-1.0.3... [111amd64-quarterly-job-06] | `-- Installing mpfr-3.1.6... [111amd64-quarterly-job-06] | `-- Extracting mpfr-3.1.6: .......... done [111amd64-quarterly-job-06] `-- Extracting mpc-1.0.3: ...... done [111amd64-quarterly-job-06] 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-glmnet-1.8.5_7 depends on executable: gfortran6 - found ===> Returning to build of R-cran-glmnet-1.8.5_7 ===> R-cran-glmnet-1.8.5_7 depends on file: /usr/local/bin/as - found =========================================================================== =======================<phase: lib-depends >============================ =========================================================================== =======================<phase: configure >============================ ===> Configuring for R-cran-glmnet-1.8.5_7 =========================================================================== =======================<phase: build >============================ =========================================================================== =======================<phase: run-depends >============================ ===> R-cran-glmnet-1.8.5_7 depends on file: /usr/local/bin/R - found ===> R-cran-glmnet-1.8.5_7 depends on executable: gfortran6 - found =========================================================================== =======================<phase: stage >============================ ===> Staging for R-cran-glmnet-1.8.5_7 ===> Generating temporary packing list * installing *source* package 'glmnet' ... ** package 'glmnet' successfully unpacked and MD5 sums checked This package requires a fortran 90 compiler. We assume that your fortran 90 environment is set up appropriately. Reference: Section on 'Using F95 code' in R-exts manual. R_HOME is /usr/local/lib/R Unsupported Fortran 90 compiler or Fortran 90 compilers unavailable! Stop! ERROR: configuration failed for package 'glmnet' * removing '/wrkdirs/usr/ports/devel/R-cran-glmnet/work/stage/usr/local/lib/R/library/glmnet' *** Error code 1 Stop. make: stopped in /usr/ports/devel/R-cran-glmnet
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