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Date:      Thu, 23 Nov 2017 13:41:01 GMT
From:      pkg-fallout@FreeBSD.org
To:        wen@FreeBSD.org
Cc:        pkg-fallout@FreeBSD.org
Subject:   [package - 103amd64-quarterly][math/R-cran-sm] Failed for R-cran-sm-2.2.5.4_2 in stage
Message-ID:  <201711231341.vANDf1GB028333@beefy2.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:     wen@FreeBSD.org
Last committer: dbn@FreeBSD.org
Ident:          $FreeBSD: branches/2017Q4/math/R-cran-sm/Makefile 443845 2017-06-18 18:09:16Z dbn $
Log URL:        http://beefy2.nyi.freebsd.org/data/103amd64-quarterly/454671/logs/R-cran-sm-2.2.5.4_2.log
Build URL:      http://beefy2.nyi.freebsd.org/build.html?mastername=103amd64-quarterly&build=454671
Log:

====>> Building math/R-cran-sm
build started at Thu Nov 23 13:39:26 UTC 2017
port directory: /usr/ports/math/R-cran-sm
building for: FreeBSD 103amd64-quarterly-job-01 10.3-RELEASE-p24 FreeBSD 10.3-RELEASE-p24 amd64
maintained by: wen@FreeBSD.org
Makefile ident:      $FreeBSD: branches/2017Q4/math/R-cran-sm/Makefile 443845 2017-06-18 18:09:16Z dbn $
Poudriere version: 3.1.22
Host OSVERSION: 1200052
Jail OSVERSION: 1003000
Job Id: 01

---Begin Environment---
SHELL=/bin/csh
OSVERSION=1003000
UNAME_v=FreeBSD 10.3-RELEASE-p24
UNAME_r=10.3-RELEASE-p24
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
SAVED_TERM=
MASTERMNT=/usr/local/poudriere/data/.m/103amd64-quarterly/ref
PATH=/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin
POUDRIERE_BUILD_TYPE=bulk
PKGNAME=R-cran-sm-2.2.5.4_2
OLDPWD=/
PWD=/usr/local/poudriere/data/.m/103amd64-quarterly/ref/.p/pool
MASTERNAME=103amd64-quarterly
SCRIPTPREFIX=/usr/local/share/poudriere
USER=root
HOME=/root
POUDRIERE_VERSION=3.1.22
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-sm/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/math/R-cran-sm/work  HOME=/wrkdirs/usr/ports/math/R-cran-sm/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/math/R-cran-sm/work  XDG_CONFIG_HOME=/wrkdirs/usr/ports/math/R-cran-sm/work  HOME=/wrkdirs/usr/ports/math/R-cran-sm/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/gcc6  -L/usr/local/lib/gcc6 -B/usr/local/bin -fstack-protec
 tor" 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/sm
OSREL=10.3
PREFIX=%D
LOCALBASE=/usr/local
RESETPREFIX=/usr/local
PORTDOCS=""
PORTEXAMPLES=""
LIB32DIR=lib
DOCSDIR="share/doc/sm"
EXAMPLESDIR="share/examples/sm"
DATADIR="share/sm"
WWWDIR="www/sm"
ETCDIR="etc/sm"
--End PLIST_SUB--

--SUB_LIST--
PREFIX=/usr/local
LOCALBASE=/usr/local
DATADIR=/usr/local/share/sm
DOCSDIR=/usr/local/share/doc/sm
EXAMPLESDIR=/usr/local/share/examples/sm
WWWDIR=/usr/local/www/sm
ETCDIR=/usr/local/etc/sm
--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=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-p24
#### 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
sbsize                   (bytes, -b)  unlimited
pseudo-terminals                (-p)  unlimited
--End resource limits--
=======================<phase: check-sanity   >============================
===========================================================================
=======================<phase: pkg-depends    >============================
===>   R-cran-sm-2.2.5.4_2 depends on file: /usr/local/sbin/pkg - not found
===>   Installing existing package /packages/All/pkg-1.10.1.txz
[103amd64-quarterly-job-01] Installing pkg-1.10.1...
[103amd64-quarterly-job-01] Extracting pkg-1.10.1: .......... done
===>   R-cran-sm-2.2.5.4_2 depends on file: /usr/local/sbin/pkg - found
===>   Returning to build of R-cran-sm-2.2.5.4_2
===========================================================================
=======================<phase: fetch-depends  >============================
===========================================================================
=======================<phase: fetch          >============================
===> Fetching all distfiles required by R-cran-sm-2.2.5.4_2 for building
===========================================================================
=======================<phase: checksum       >============================
===> Fetching all distfiles required by R-cran-sm-2.2.5.4_2 for building
=> SHA256 Checksum OK for sm_2.2-5.4.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract        >============================
===> Fetching all distfiles required by R-cran-sm-2.2.5.4_2 for building
===>  Extracting for R-cran-sm-2.2.5.4_2
=> SHA256 Checksum OK for sm_2.2-5.4.tar.gz.
===========================================================================
=======================<phase: patch-depends  >============================
===========================================================================
=======================<phase: patch          >============================
===>  Patching for R-cran-sm-2.2.5.4_2
===========================================================================
=======================<phase: build-depends  >============================
===>   R-cran-sm-2.2.5.4_2 depends on file: /usr/local/bin/R - not found
===>   Installing existing package /packages/All/R-3.4.2.txz
[103amd64-quarterly-job-01] Installing R-3.4.2...
[103amd64-quarterly-job-01] `-- Installing cairo-1.14.8_1,2...
[103amd64-quarterly-job-01] |   `-- Installing dri2proto-2.8...
[103amd64-quarterly-job-01] |   `-- Extracting dri2proto-2.8: .... done
[103amd64-quarterly-job-01] |   `-- Installing fontconfig-2.12.1,1...
[103amd64-quarterly-job-01] |   | `-- Installing expat-2.2.1...
[103amd64-quarterly-job-01] |   | `-- Extracting expat-2.2.1: .......... done
[103amd64-quarterly-job-01] |   | `-- Installing freetype2-2.8...
[103amd64-quarterly-job-01] |   | `-- Extracting freetype2-2.8: .......... done
[103amd64-quarterly-job-01] |   `-- 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
[103amd64-quarterly-job-01] |   `-- Installing gettext-runtime-0.19.8.1_1...
[103amd64-quarterly-job-01] |   | `-- Installing indexinfo-0.2.6...
[103amd64-quarterly-job-01] |   | `-- Extracting indexinfo-0.2.6: .... done
[103amd64-quarterly-job-01] |   `-- Extracting gettext-runtime-0.19.8.1_1: .......... done
[103amd64-quarterly-job-01] |   `-- Installing glib-2.50.2_6,1...
[103amd64-quarterly-job-01] |   | `-- Installing libffi-3.2.1_1...
[103amd64-quarterly-job-01] |   | `-- Extracting libffi-3.2.1_1: .......... done
[103amd64-quarterly-job-01] |   | `-- Installing libiconv-1.14_11...
[103amd64-quarterly-job-01] |   | `-- Extracting libiconv-1.14_11: .......... done
[103amd64-quarterly-job-01] |   | `-- Installing pcre-8.40_1...
[103amd64-quarterly-job-01] |   | `-- Extracting pcre-8.40_1: .......... done
[103amd64-quarterly-job-01] |   | `-- Installing perl5-5.24.3...
[103amd64-quarterly-job-01] |   | `-- Extracting perl5-5.24.3: .......... done
[103amd64-quarterly-job-01] |   | `-- Installing python27-2.7.14...
[103amd64-quarterly-job-01] |   |   `-- Installing readline-7.0.3...
[103amd64-quarterly-job-01] |   |   `-- Extracting readline-7.0.3: .......... done
[103amd64-quarterly-job-01] |   | `-- Extracting python27-2.7.14: .......... done
[103amd64-quarterly-job-01] |   `-- Extracting glib-2.50.2_6,1: .......... done
No schema files found: doing nothing.
<snip>
[103amd64-quarterly-job-01] |   | `-- Extracting dejavu-2.37: .......... done
[103amd64-quarterly-job-01] |   | `-- Installing font-bh-ttf-1.0.3_3...
[103amd64-quarterly-job-01] |   | `-- Extracting font-bh-ttf-1.0.3_3: .......... done
[103amd64-quarterly-job-01] |   | `-- Installing font-misc-ethiopic-1.0.3_3...
[103amd64-quarterly-job-01] |   | `-- Extracting font-misc-ethiopic-1.0.3_3: ... done
[103amd64-quarterly-job-01] |   | `-- Installing font-misc-meltho-1.0.3_3...
[103amd64-quarterly-job-01] |   | `-- Extracting font-misc-meltho-1.0.3_3: .......... done
[103amd64-quarterly-job-01] `-- Extracting pango-1.40.6: .......... done
[103amd64-quarterly-job-01] `-- Installing tcl86-8.6.7...
[103amd64-quarterly-job-01] `-- Extracting tcl86-8.6.7: .......... done
[103amd64-quarterly-job-01] `-- Installing tk86-8.6.7...
[103amd64-quarterly-job-01] `-- Extracting tk86-8.6.7: .......... done
[103amd64-quarterly-job-01] 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-3.32.1:
********************************* 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-sm-2.2.5.4_2 depends on file: /usr/local/bin/R - found
===>   Returning to build of R-cran-sm-2.2.5.4_2
===>   R-cran-sm-2.2.5.4_2 depends on executable: gfortran6 - not found
===>   Installing existing package /packages/All/gcc6-6.4.0_2.txz
[103amd64-quarterly-job-01] Installing gcc6-6.4.0_2...
[103amd64-quarterly-job-01] `-- Installing binutils-2.28,1...
[103amd64-quarterly-job-01] `-- Extracting binutils-2.28,1: .......... done
[103amd64-quarterly-job-01] `-- Installing gcc-ecj-4.5...
[103amd64-quarterly-job-01] `-- Extracting gcc-ecj-4.5: . done
[103amd64-quarterly-job-01] `-- Installing mpc-1.0.3...
[103amd64-quarterly-job-01] |   `-- Installing mpfr-3.1.6...
[103amd64-quarterly-job-01] |   `-- Extracting mpfr-3.1.6: .......... done
[103amd64-quarterly-job-01] `-- Extracting mpc-1.0.3: ...... done
[103amd64-quarterly-job-01] 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-sm-2.2.5.4_2 depends on executable: gfortran6 - found
===>   Returning to build of R-cran-sm-2.2.5.4_2
===>   R-cran-sm-2.2.5.4_2 depends on file: /usr/local/bin/as - found
===========================================================================
=======================<phase: lib-depends    >============================
===========================================================================
=======================<phase: configure      >============================
===>  Configuring for R-cran-sm-2.2.5.4_2
===========================================================================
=======================<phase: build          >============================
===========================================================================
=======================<phase: run-depends    >============================
===>   R-cran-sm-2.2.5.4_2 depends on file: /usr/local/bin/R - found
===>   R-cran-sm-2.2.5.4_2 depends on executable: gfortran6 - found
===========================================================================
=======================<phase: stage          >============================
===>  Staging for R-cran-sm-2.2.5.4_2
===>   Generating temporary packing list
* installing *source* package 'sm' ...
** package 'sm' successfully unpacked and MD5 sums checked
** libs
gmake[1]: Entering directory '/wrkdirs/usr/ports/math/R-cran-sm/work/sm/src'
cc -I/usr/local/lib/R/include -DNDEBUG   -DLIBICONV_PLUG -I/usr/local/include -isystem /usr/local/include   -fpic  -O2 -pipe  -DLIBICONV_PLUG -fstack-protector -isystem /usr/local/include -fno-strict-aliasing  -c fgamma.c -o fgamma.o
flang   -g  -c  variogram.f90 -o variogram.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 -shared -L/usr/local/lib/R/lib -L/usr/local/flang/lib -lflang -lexecinfo -L/usr/local/lib -fstack-protector -o sm.so fgamma.o variogram.o -L/usr/local/lib/R/lib -lR
/usr/bin/ld: variogram.o: relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC
variogram.o: could not read symbols: Bad value
clang-4.0: error: linker command failed with exit code 1 (use -v to see invocation)
gmake[1]: *** [/usr/local/lib/R/share/make/shlib.mk:6: sm.so] Error 1
gmake[1]: Leaving directory '/wrkdirs/usr/ports/math/R-cran-sm/work/sm/src'
ERROR: compilation failed for package 'sm'
* removing '/wrkdirs/usr/ports/math/R-cran-sm/work/stage/usr/local/lib/R/library/sm'
*** Error code 1

Stop.
make: stopped in /usr/ports/math/R-cran-sm



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