[package - 103i386-default][science/R-cran-Epi] Failed for R-cran-Epi-2.16 in stage
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Tue Jul 4 07:45:22 UTC 2017
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 at FreeBSD.org
Last committer: tota at FreeBSD.org
Ident: $FreeBSD: head/science/R-cran-Epi/Makefile 444914 2017-07-03 06:01:18Z tota $
Log URL: http://beefy5.nyi.freebsd.org/data/103i386-default/444994/logs/R-cran-Epi-2.16.log
Build URL: http://beefy5.nyi.freebsd.org/build.html?mastername=103i386-default&build=444994
Log:
====>> Building science/R-cran-Epi
build started at Tue Jul 4 07:44:32 UTC 2017
port directory: /usr/ports/science/R-cran-Epi
building for: FreeBSD 103i386-default-job-23 10.3-RELEASE-p19 FreeBSD 10.3-RELEASE-p19 i386
maintained by: tota at FreeBSD.org
Makefile ident: $FreeBSD: head/science/R-cran-Epi/Makefile 444914 2017-07-03 06:01:18Z tota $
Poudriere version: 3.1.19-40-ga434dff0
Host OSVERSION: 1200033
Jail OSVERSION: 1003000
Job Id: 23
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POUDRIERE_BUILD_TYPE=bulk
PKGNAME=R-cran-Epi-2.16
OLDPWD=/
PWD=/usr/local/poudriere/data/.m/103i386-default/ref/.p/pool
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SCRIPTPREFIX=/usr/local/share/poudriere
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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/science/R-cran-Epi/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/R-cran-Epi/work HOME=/wrkdirs/usr/ports/science/R-cran-Epi/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/science/R-cran-Epi/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/R-cran-Epi/work HOME=/wrkdirs/usr/ports/science/R-cran-Epi/work TMPDIR="/tmp" NO_PIE=yes WITHOUT_DEBUG_FILES=yes WITHOUT_KERNEL_SYMBOLS=yes 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/gcc5 -L/usr/local/lib/gcc5 -B/usr/local/bin -f
stack-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/Epi
OSREL=10.3
PREFIX=%D
LOCALBASE=/usr/local
RESETPREFIX=/usr/local
PORTDOCS=""
PORTEXAMPLES=""
LIB32DIR=lib
DOCSDIR="share/doc/Epi"
EXAMPLESDIR="share/examples/Epi"
DATADIR="share/Epi"
WWWDIR="www/Epi"
ETCDIR="etc/Epi"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local
LOCALBASE=/usr/local
DATADIR=/usr/local/share/Epi
DOCSDIR=/usr/local/share/doc/Epi
EXAMPLESDIR=/usr/local/share/examples/Epi
WWWDIR=/usr/local/www/Epi
ETCDIR=/usr/local/etc/Epi
--End SUB_LIST--
---Begin make.conf---
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
PACKAGE_BUILDING=yes
MACHINE=i386
MACHINE_ARCH=i386
ARCH=${MACHINE_ARCH}
#### /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=i386
CONFIGURE_MAX_CMD_LEN=262144
OPSYS=FreeBSD
OSREL=10.3
OSVERSION=1003000
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=10.3-RELEASE-p19
#### 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) 524288
stack size (kbytes, -s) 65536
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
sbsize (bytes, -b) unlimited
pseudo-terminals (-p) unlimited
--End resource limits--
=======================<phase: check-sanity >============================
===> License GPLv2 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> R-cran-Epi-2.16 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.10.1.txz
[103i386-default-job-23] Installing pkg-1.10.1...
[103i386-default-job-23] Extracting pkg-1.10.1: .......... done
===> R-cran-Epi-2.16 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of R-cran-Epi-2.16
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv2 accepted by the user
=> Epi_2.16.tar.gz doesn't seem to exist in /portdistfiles/.
=> Attempting to fetch https://cloud.r-project.org/src/contrib/Epi_2.16.tar.gz
Epi_2.16.tar.gz 0 B 0 Bps
===> Fetching all distfiles required by R-cran-Epi-2.16 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by R-cran-Epi-2.16 for building
=> SHA256 Checksum OK for Epi_2.16.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv2 accepted by the user
===> Fetching all distfiles required by R-cran-Epi-2.16 for building
===> Extracting for R-cran-Epi-2.16
=> SHA256 Checksum OK for Epi_2.16.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for R-cran-Epi-2.16
===========================================================================
=======================<phase: build-depends >============================
===> R-cran-Epi-2.16 depends on package: R-cran-cmprsk>0 - not found
===> Installing existing package /packages/All/R-cran-cmprsk-2.2.7_1.txz
[103i386-default-job-23] Installing R-cran-cmprsk-2.2.7_1...
[103i386-default-job-23] `-- Installing R-3.4.0_2...
[103i386-default-job-23] | `-- Installing cairo-1.14.8_1,2...
[103i386-default-job-23] | | `-- Installing dri2proto-2.8...
[103i386-default-job-23] | | `-- Extracting dri2proto-2.8: .... done
[103i386-default-job-23] | | `-- Installing fontconfig-2.12.1,1...
[103i386-default-job-23] | | `-- Installing expat-2.2.1...
[103i386-default-job-23] | | `-- Extracting expat-2.2.1: .......... done
[103i386-default-job-23] | | `-- Installing freetype2-2.8...
[103i386-default-job-23] | | `-- Extracting freetype2-2.8: .......... done
[103i386-default-job-23] | | `-- 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
[103i386-default-job-23] | | `-- Installing gettext-runtime-0.19.8.1_1...
[103i386-default-job-23] | | `-- Installing indexinfo-0.2.6...
[103i386-default-job-23] | | `-- Extracting indexinfo-0.2.6: .... done
[103i386-default-job-23] | | `-- Extracting gettext-runtime-0.19.8.1_1: .......... done
[103i386-default-job-23] | | `-- Installing glib-2.50.2_3,1...
[103i386-default-job-23] | | `-- Installing libffi-3.2.1...
[103i386-default-job-23] | | `-- Extracting libffi-3.2.1: .......... done
<snip>
[103i386-default-job-23] | | `-- Extracting font-util-1.3.1: .......... done
[103i386-default-job-23] | | `-- Extracting encodings-1.0.4_3,1: .......... done
[103i386-default-job-23] | | `-- Installing harfbuzz-1.4.6_1...
[103i386-default-job-23] | | `-- Installing graphite2-1.3.10...
[103i386-default-job-23] | | `-- Extracting graphite2-1.3.10: .......... done
[103i386-default-job-23] | | `-- Extracting harfbuzz-1.4.6_1: .......... done
[103i386-default-job-23] | | `-- Installing libXft-2.3.2_1...
[103i386-default-job-23] | | `-- Extracting libXft-2.3.2_1: ......... done
[103i386-default-job-23] | | `-- Installing xorg-fonts-truetype-7.7_1...
[103i386-default-job-23] | | `-- Installing dejavu-2.37...
[103i386-default-job-23] | | | `-- Installing mkfontdir-1.0.7...
[103i386-default-job-23] | | | `-- Installing mkfontscale-1.1.2...
[103i386-default-job-23] | | | | `-- Installing libfontenc-1.1.3_1...
[103i386-default-job-23] | | | | `-- Extracting libfontenc-1.1.3_1: ......... done
[103i386-default-job-23] | | | `-- Extracting mkfontscale-1.1.2: .. done
[103i386-default-job-23] | | | `-- Extracting mkfontdir-1.0.7: .. done
[103i386-default-job-23] | | `-- Extracting dejavu-2.37: .......... done
[103i386-default-job-23] | | `-- Installing font-bh-ttf-1.0.3_3...
[103i386-default-job-23] | | `-- Extracting font-bh-ttf-1.0.3_3: .......... done
[103i386-default-job-23] | | `-- Installing font-misc-ethiopic-1.0.3_3...
[103i386-default-job-23] | | `-- Extracting font-misc-ethiopic-1.0.3_3: ... done
[103i386-default-job-23] | | `-- Installing font-misc-meltho-1.0.3_3...
[103i386-default-job-23] | | `-- Extracting font-misc-meltho-1.0.3_3: .......... done
[103i386-default-job-23] | `-- Extracting pango-1.40.6: .......... done
[103i386-default-job-23] | `-- Installing tcl86-8.6.6_2...
[103i386-default-job-23] | `-- Extracting tcl86-8.6.6_2: .......... done
[103i386-default-job-23] | `-- Installing tk86-8.6.6...
[103i386-default-job-23] | `-- Extracting tk86-8.6.6: .......... done
[103i386-default-job-23] `-- Extracting R-3.4.0_2: .......... done
[103i386-default-job-23] Extracting R-cran-cmprsk-2.2.7_1: .......... 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 perl5-5.24.1_1:
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_6:
===========================================================================
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-3.31:
********************************* 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.
===> R-cran-Epi-2.16 depends on package: R-cran-cmprsk>0 - found
===> Returning to build of R-cran-Epi-2.16
===> R-cran-Epi-2.16 depends on package: R-cran-etm>0 - not found
===> Installing existing package /packages/All/R-cran-etm-0.6.2_1.txz
[103i386-default-job-23] Installing R-cran-etm-0.6.2_1...
[103i386-default-job-23] Extracting R-cran-etm-0.6.2_1: .......... done
===> R-cran-Epi-2.16 depends on package: R-cran-etm>0 - found
===> Returning to build of R-cran-Epi-2.16
===> R-cran-Epi-2.16 depends on package: R-cran-plyr>0 - not found
===> Installing existing package /packages/All/R-cran-plyr-1.8.4_1.txz
[103i386-default-job-23] Installing R-cran-plyr-1.8.4_1...
[103i386-default-job-23] `-- Installing R-cran-Rcpp-0.12.11...
[103i386-default-job-23] `-- Extracting R-cran-Rcpp-0.12.11: .......... done
[103i386-default-job-23] Extracting R-cran-plyr-1.8.4_1: .......... done
===> R-cran-Epi-2.16 depends on package: R-cran-plyr>0 - found
===> Returning to build of R-cran-Epi-2.16
===> R-cran-Epi-2.16 depends on package: R-cran-numDeriv>0 - not found
===> Installing existing package /packages/All/R-cran-numDeriv-2016.8.1.txz
[103i386-default-job-23] Installing R-cran-numDeriv-2016.8.1...
[103i386-default-job-23] Extracting R-cran-numDeriv-2016.8.1: .......... done
===> R-cran-Epi-2.16 depends on package: R-cran-numDeriv>0 - found
===> Returning to build of R-cran-Epi-2.16
===> R-cran-Epi-2.16 depends on package: R-cran-data.table>0 - not found
===> Installing existing package /packages/All/R-cran-data.table-1.10.4.txz
[103i386-default-job-23] Installing R-cran-data.table-1.10.4...
[103i386-default-job-23] Extracting R-cran-data.table-1.10.4: .......... done
===> R-cran-Epi-2.16 depends on package: R-cran-data.table>0 - found
===> Returning to build of R-cran-Epi-2.16
===> R-cran-Epi-2.16 depends on file: /usr/local/bin/R - found
===> R-cran-Epi-2.16 depends on executable: gfortran5 - found
===> R-cran-Epi-2.16 depends on file: /usr/local/bin/as - found
===========================================================================
=======================<phase: lib-depends >============================
===========================================================================
=======================<phase: configure >============================
===> Configuring for R-cran-Epi-2.16
===========================================================================
=======================<phase: build >============================
===========================================================================
=======================<phase: run-depends >============================
===> R-cran-Epi-2.16 depends on package: R-cran-cmprsk>0 - found
===> R-cran-Epi-2.16 depends on package: R-cran-etm>0 - found
===> R-cran-Epi-2.16 depends on package: R-cran-plyr>0 - found
===> R-cran-Epi-2.16 depends on package: R-cran-numDeriv>0 - found
===> R-cran-Epi-2.16 depends on package: R-cran-data.table>0 - found
===> R-cran-Epi-2.16 depends on file: /usr/local/bin/R - found
===> R-cran-Epi-2.16 depends on executable: gfortran5 - found
===========================================================================
=======================<phase: stage >============================
===> Staging for R-cran-Epi-2.16
===> Generating temporary packing list
ERROR: dependency 'zoo' is not available for package 'Epi'
* removing '/wrkdirs/usr/ports/science/R-cran-Epi/work/stage/usr/local/lib/R/library/Epi'
*** Error code 1
Stop.
make: stopped in /usr/ports/science/R-cran-Epi
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