[package - 93i386-default][science/R-cran-bayesm] Failed for R-cran-bayesm-2.2.5_2 in stage
pkg-fallout at FreeBSD.org
pkg-fallout at FreeBSD.org
Thu May 26 06:15:47 UTC 2016
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 at FreeBSD.org
Last committer: gerald at FreeBSD.org
Ident: $FreeBSD: head/science/R-cran-bayesm/Makefile 367888 2014-09-10 20:50:31Z gerald $
Log URL: http://beefy1.nyi.freebsd.org/data/93i386-default/415869/logs/R-cran-bayesm-2.2.5_2.log
Build URL: http://beefy1.nyi.freebsd.org/build.html?mastername=93i386-default&build=415869
Log:
====>> Building science/R-cran-bayesm
build started at Thu May 26 06:14:48 UTC 2016
port directory: /usr/ports/science/R-cran-bayesm
building for: FreeBSD 93i386-default-job-17 9.3-RELEASE-p42 FreeBSD 9.3-RELEASE-p42 i386
maintained by: wen at FreeBSD.org
Makefile ident: $FreeBSD: head/science/R-cran-bayesm/Makefile 367888 2014-09-10 20:50:31Z gerald $
Poudriere version: 3.1.12
Host OSVERSION: 1100109
Jail OSVERSION: 903000
---Begin Environment---
SHELL=/bin/csh
UNAME_p=i386
UNAME_m=i386
UNAME_v=FreeBSD 9.3-RELEASE-p42
UNAME_r=9.3-RELEASE-p42
BLOCKSIZE=K
MAIL=/var/mail/root
STATUS=1
SAVED_TERM=
MASTERMNT=/usr/local/poudriere/data/.m/93i386-default/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-bayesm-2.2.5_2
OLDPWD=/
PWD=/usr/local/poudriere/data/.m/93i386-default/ref/.p/pool
MASTERNAME=93i386-default
SCRIPTPREFIX=/usr/local/share/poudriere
USER=root
HOME=/root
POUDRIERE_VERSION=3.1.12
SCRIPTPATH=/usr/local/share/poudriere/bulk.sh
LIBEXECPREFIX=/usr/local/libexec/poudriere
LOCALBASE=/usr/local
PACKAGE_BUILDING=yes
OSVERSION=903000
---End Environment---
---Begin OPTIONS List---
---End OPTIONS List---
--CONFIGURE_ARGS--
--End CONFIGURE_ARGS--
--CONFIGURE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/science/R-cran-bayesm/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/R-cran-bayesm/work HOME=/wrkdirs/usr/ports/science/R-cran-bayesm/work TMPDIR="/tmp" SHELL=/bin/sh CONFIG_SHELL=/bin/sh
--End CONFIGURE_ENV--
--MAKE_ENV--
XDG_DATA_HOME=/wrkdirs/usr/ports/science/R-cran-bayesm/work XDG_CONFIG_HOME=/wrkdirs/usr/ports/science/R-cran-bayesm/work HOME=/wrkdirs/usr/ports/science/R-cran-bayesm/work TMPDIR="/tmp" NO_PIE=yes WITHOUT_DEBUG_FILES=yes WITHOUT_KERNEL_SYMBOLS=yes SHELL=/bin/sh NO_LINT=YES PREFIX=/usr/local LOCALBASE=/usr/local LIBDIR="/usr/lib" 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 444" 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/bayesm
OSREL=9.3
PREFIX=%D
LOCALBASE=/usr/local
RESETPREFIX=/usr/local
PORTDOCS=""
PORTEXAMPLES=""
LIB32DIR=lib
DOCSDIR="share/doc/bayesm"
EXAMPLESDIR="share/examples/bayesm"
DATADIR="share/bayesm"
WWWDIR="www/bayesm"
ETCDIR="etc/bayesm"
--End PLIST_SUB--
--SUB_LIST--
PREFIX=/usr/local
LOCALBASE=/usr/local
DATADIR=/usr/local/share/bayesm
DOCSDIR=/usr/local/share/doc/bayesm
EXAMPLESDIR=/usr/local/share/examples/bayesm
WWWDIR=/usr/local/www/bayesm
ETCDIR=/usr/local/etc/bayesm
--End SUB_LIST--
---Begin make.conf---
MACHINE=i386
MACHINE_ARCH=i386
ARCH=${MACHINE_ARCH}
USE_PACKAGE_DEPENDS=yes
BATCH=yes
WRKDIRPREFIX=/wrkdirs
PORTSDIR=/usr/ports
PACKAGES=/packages
DISTDIR=/distfiles
#### /usr/local/etc/poudriere.d/make.conf ####
DISABLE_MAKE_JOBS=poudriere
---End make.conf---
=======================<phase: check-sanity >============================
===> License GPLv2 GPLv3 accepted by the user
===========================================================================
=======================<phase: pkg-depends >============================
===> R-cran-bayesm-2.2.5_2 depends on file: /usr/local/sbin/pkg - not found
===> Installing existing package /packages/All/pkg-1.8.3.txz
[93i386-default-job-17] Installing pkg-1.8.3...
[93i386-default-job-17] Extracting pkg-1.8.3: .......... done
===> R-cran-bayesm-2.2.5_2 depends on file: /usr/local/sbin/pkg - found
===> Returning to build of R-cran-bayesm-2.2.5_2
===========================================================================
=======================<phase: fetch-depends >============================
===========================================================================
=======================<phase: fetch >============================
===> License GPLv2 GPLv3 accepted by the user
===> Fetching all distfiles required by R-cran-bayesm-2.2.5_2 for building
===========================================================================
=======================<phase: checksum >============================
===> License GPLv2 GPLv3 accepted by the user
===> Fetching all distfiles required by R-cran-bayesm-2.2.5_2 for building
=> SHA256 Checksum OK for bayesm_2.2-5.tar.gz.
===========================================================================
=======================<phase: extract-depends>============================
===========================================================================
=======================<phase: extract >============================
===> License GPLv2 GPLv3 accepted by the user
===> Fetching all distfiles required by R-cran-bayesm-2.2.5_2 for building
===> Extracting for R-cran-bayesm-2.2.5_2
=> SHA256 Checksum OK for bayesm_2.2-5.tar.gz.
===========================================================================
=======================<phase: patch-depends >============================
===========================================================================
=======================<phase: patch >============================
===> Patching for R-cran-bayesm-2.2.5_2
===========================================================================
=======================<phase: build-depends >============================
===> R-cran-bayesm-2.2.5_2 depends on file: /usr/local/bin/R - not found
===> Installing existing package /packages/All/R-3.3.0.txz
[93i386-default-job-17] Installing R-3.3.0...
[93i386-default-job-17] `-- Installing indexinfo-0.2.4...
[93i386-default-job-17] `-- Extracting indexinfo-0.2.4: .... done
[93i386-default-job-17] `-- Installing libXt-1.1.5,1...
[93i386-default-job-17] | `-- Installing xproto-7.0.28...
[93i386-default-job-17] | `-- Extracting xproto-7.0.28: .......... done
[93i386-default-job-17] | `-- Installing libSM-1.2.2_3,1...
[93i386-default-job-17] | | `-- Installing libICE-1.0.9_1,1...
[93i386-default-job-17] | | `-- Extracting libICE-1.0.9_1,1: .......... done
[93i386-default-job-17] | `-- Extracting libSM-1.2.2_3,1: .......... done
[93i386-default-job-17] | `-- Installing libX11-1.6.3,1...
[93i386-default-job-17] | | `-- Installing kbproto-1.0.7...
[93i386-default-job-17] | | `-- Extracting kbproto-1.0.7: .......... done
[93i386-default-job-17] | | `-- Installing libXdmcp-1.1.2...
[93i386-default-job-17] | | `-- Extracting libXdmcp-1.1.2: ......... done
[93i386-default-job-17] | | `-- Installing libxcb-1.11.1...
[93i386-default-job-17] | | `-- Installing libxml2-2.9.3...
[93i386-default-job-17] | | | `-- Installing libiconv-1.14_9...
[93i386-default-job-17] | | | `-- Extracting libiconv-1.14_9: .......... done
[93i386-default-job-17] | | `-- Extracting libxml2-2.9.3: .......... done
[93i386-default-job-17] | | `-- Installing libpthread-stubs-0.3_6...
[93i386-default-job-17] | | `-- Extracting libpthread-stubs-0.3_6: ..... done
[93i386-default-job-17] | | `-- Installing libXau-1.0.8_3...
[93i386-default-job-17] | | `-- Extracting libXau-1.0.8_3: .......... done
[93i386-default-job-17] | | `-- Extracting libxcb-1.11.1: .......... done
[93i386-default-job-17] | `-- Extracting libX11-1.6.3,1: .......... done
[93i386-default-job-17] `-- Extracting libXt-1.1.5,1: .......... done
[93i386-default-job-17] `-- Installing pango-1.38.0_1...
[93i386-default-job-17] | `-- Installing encodings-1.0.4_3,1...
[93i386-default-job-17] | | `-- Installing font-util-1.3.1...
[93i386-default-job-17] | | `-- Extracting font-util-1.3.1: .......... done
[93i386-default-job-17] | `-- Extracting encodings-1.0.4_3,1: .......... done
[93i386-default-job-17] | `-- Installing fontconfig-2.11.1_2,1...
[93i386-default-job-17] | | `-- Installing expat-2.1.1...
[93i386-default-job-17] | | `-- Extracting expat-2.1.1: .......... done
[93i386-default-job-17] | | `-- Installing freetype2-2.6.3...
[93i386-default-job-17] | | `-- Extracting freetype2-2.6.3: .......... done
[93i386-default-job-17] | `-- Extracting fontconfig-2.11.1_2,1: .......... done
Running fc-cache to build fontconfig cache...
/usr/local/share/fonts: caching, new cache contents: 0 fonts, 2 dirs
/usr/local/share/fonts/encodings: caching, new cache contents: 0 fonts, 1 dirs
/usr/local/share/fonts/encodings/large: caching, new cache contents: 0 fonts, 0 dirs
/usr/local/share/fonts/util: caching, new cache contents: 0 fonts, 0 dirs
/usr/local/lib/X11/fonts: skipping, no such directory
/root/.local/share/fonts: skipping, no such directory
/root/.fonts: skipping, no such directory
Re-scanning /usr/local/share/fonts: caching, new cache contents: 0 fonts, 2 dirs
Re-scanning /usr/local/share/fonts/encodings: caching, new cache contents: 0 fonts, 1 dirs
/var/db/fontconfig: cleaning cache directory
/root/.cache/fontconfig: not cleaning non-existent cache directory
/root/.fontconfig: not cleaning non-existent cache directory
fc-cache: succeeded
[93i386-default-job-17] | `-- Installing libXft-2.3.2_1...
[93i386-default-job-17] | | `-- Installing libXrender-0.9.9...
[93i386-default-job-17] | | `-- Installing renderproto-0.11.1...
[93i386-default-job-17] | | `-- Extracting renderproto-0.11.1: .... done
[93i386-default-job-17] | | `-- Extracting libXrender-0.9.9: .......... done
[93i386-default-job-17] | `-- Extracting libXft-2.3.2_1: ......... done
[93i386-default-job-17] | `-- Installing harfbuzz-1.2.3...
[93i386-default-job-17] | | `-- Installing cairo-1.14.6,2...
[93i386-default-job-17] | | `-- Installing dri2proto-2.8...
[93i386-default-job-17] | | `-- Extracting dri2proto-2.8: .... done
[93i386-default-job-17] | | `-- Installing glproto-1.4.17...
[93i386-default-job-17] | | `-- Extracting glproto-1.4.17: ...... done
[93i386-default-job-17] | | `-- Installing libXext-1.3.3_1,1...
[93i386-default-job-17] | | | `-- Installing xextproto-7.3.0...
[93i386-default-job-17] | | | `-- Extracting xextproto-7.3.0: .......... done
[93i386-default-job-17] | | `-- Extracting libXext-1.3.3_1,1: .......... done
[93i386-default-job-17] | | `-- Installing libEGL-11.1.2...
<snip>
/usr/local/lib/gcc48/include/c++/cmath: At global scope:
/usr/local/lib/gcc48/include/c++/cmath:346:3: error: template with C linkage
template<typename _Tp>
^
/usr/local/lib/gcc48/include/c++/cmath: In function 'long double std::log(long double)':
/usr/local/lib/gcc48/include/c++/cmath:361:22: error: declaration of C function 'long double std::log(long double)' conflicts with
log(long double __x)
^
/usr/local/lib/gcc48/include/c++/cmath:357:3: error: previous declaration 'float std::log(float)' here
log(float __x)
^
/usr/local/lib/gcc48/include/c++/cmath: At global scope:
/usr/local/lib/gcc48/include/c++/cmath:365:3: error: template with C linkage
template<typename _Tp>
^
/usr/local/lib/gcc48/include/c++/cmath: In function 'long double std::log10(long double)':
/usr/local/lib/gcc48/include/c++/cmath:380:24: error: declaration of C function 'long double std::log10(long double)' conflicts with
log10(long double __x)
^
/usr/local/lib/gcc48/include/c++/cmath:376:3: error: previous declaration 'float std::log10(float)' here
log10(float __x)
^
/usr/local/lib/gcc48/include/c++/cmath: At global scope:
/usr/local/lib/gcc48/include/c++/cmath:384:3: error: template with C linkage
template<typename _Tp>
^
/usr/local/lib/gcc48/include/c++/cmath: In function 'long double std::modf(long double, long double*)':
/usr/local/lib/gcc48/include/c++/cmath:399:44: error: declaration of C function 'long double std::modf(long double, long double*)' conflicts with
modf(long double __x, long double* __iptr)
^
/usr/local/lib/gcc48/include/c++/cmath:395:3: error: previous declaration 'float std::modf(float, float*)' here
modf(float __x, float* __iptr)
^
/usr/local/lib/gcc48/include/c++/cmath: In function 'long double std::pow(long double, long double)':
/usr/local/lib/gcc48/include/c++/cmath:411:39: error: declaration of C function 'long double std::pow(long double, long double)' conflicts with
pow(long double __x, long double __y)
^
/usr/local/lib/gcc48/include/c++/cmath:407:3: error: previous declaration 'float std::pow(float, float)' here
pow(float __x, float __y)
^
/usr/local/lib/gcc48/include/c++/cmath: In function 'double std::pow(double, int)':
/usr/local/lib/gcc48/include/c++/cmath:418:26: error: declaration of C function 'double std::pow(double, int)' conflicts with
pow(double __x, int __i)
^
/usr/local/lib/gcc48/include/c++/cmath:411:3: error: previous declaration 'long double std::pow(long double, long double)' here
pow(long double __x, long double __y)
^
/usr/local/lib/gcc48/include/c++/cmath:418:26: error: declaration of C function 'double std::pow(double, int)' conflicts with
pow(double __x, int __i)
^
/usr/local/lib/gcc48/include/c++/cmath:407:3: error: previous declaration 'float std::pow(float, float)' here
pow(float __x, float __y)
^
/usr/local/lib/gcc48/include/c++/cmath: In function 'float std::pow(float, int)':
/usr/local/lib/gcc48/include/c++/cmath:422:25: error: declaration of C function 'float std::pow(float, int)' conflicts with
pow(float __x, int __n)
^
/usr/local/lib/gcc48/include/c++/cmath:418:3: error: previous declaration 'double std::pow(double, int)' here
pow(double __x, int __i)
^
/usr/local/lib/gcc48/include/c++/cmath:422:25: error: declaration of C function 'float std::pow(float, int)' conflicts with
pow(float __x, int __n)
^
/usr/local/lib/gcc48/include/c++/cmath:411:3: error: previous declaration 'long double std::pow(long double, long double)' here
pow(long double __x, long double __y)
^
/usr/local/lib/gcc48/include/c++/cmath:422:25: error: declaration of C function 'float std::pow(float, int)' conflicts with
pow(float __x, int __n)
^
/usr/local/lib/gcc48/include/c++/cmath:407:3: error: previous declaration 'float std::pow(float, float)' here
pow(float __x, float __y)
^
/usr/local/lib/gcc48/include/c++/cmath: In function 'long double std::pow(long double, int)':
/usr/local/lib/gcc48/include/c++/cmath:426:31: error: declaration of C function 'long double std::pow(long double, int)' conflicts with
pow(long double __x, int __n)
^
/usr/local/lib/gcc48/include/c++/cmath:422:3: error: previous declaration 'float std::pow(float, int)' here
pow(float __x, int __n)
^
/usr/local/lib/gcc48/include/c++/cmath:426:31: error: declaration of C function 'long double std::pow(long double, int)' conflicts with
pow(long double __x, int __n)
^
/usr/local/lib/gcc48/include/c++/cmath:418:3: error: previous declaration 'double std::pow(double, int)' here
pow(double __x, int __i)
^
/usr/local/lib/gcc48/include/c++/cmath:426:31: error: declaration of C function 'long double std::pow(long double, int)' conflicts with
pow(long double __x, int __n)
^
/usr/local/lib/gcc48/include/c++/cmath:411:3: error: previous declaration 'long double std::pow(long double, long double)' here
pow(long double __x, long double __y)
^
/usr/local/lib/gcc48/include/c++/cmath:426:31: error: declaration of C function 'long double std::pow(long double, int)' conflicts with
pow(long double __x, int __n)
^
/usr/local/lib/gcc48/include/c++/cmath:407:3: error: previous declaration 'float std::pow(float, float)' here
pow(float __x, float __y)
^
/usr/local/lib/gcc48/include/c++/cmath: At global scope:
/usr/local/lib/gcc48/include/c++/cmath:431:3: error: template with C linkage
template<typename _Tp, typename _Up>
^
/usr/local/lib/gcc48/include/c++/cmath: In function 'long double std::sin(long double)':
/usr/local/lib/gcc48/include/c++/cmath:448:22: error: declaration of C function 'long double std::sin(long double)' conflicts with
sin(long double __x)
^
/usr/local/lib/gcc48/include/c++/cmath:444:3: error: previous declaration 'float std::sin(float)' here
sin(float __x)
^
/usr/local/lib/gcc48/include/c++/cmath: At global scope:
/usr/local/lib/gcc48/include/c++/cmath:452:3: error: template with C linkage
template<typename _Tp>
^
/usr/local/lib/gcc48/include/c++/cmath: In function 'long double std::sinh(long double)':
/usr/local/lib/gcc48/include/c++/cmath:467:23: error: declaration of C function 'long double std::sinh(long double)' conflicts with
sinh(long double __x)
^
/usr/local/lib/gcc48/include/c++/cmath:463:3: error: previous declaration 'float std::sinh(float)' here
sinh(float __x)
^
/usr/local/lib/gcc48/include/c++/cmath: At global scope:
/usr/local/lib/gcc48/include/c++/cmath:471:3: error: template with C linkage
template<typename _Tp>
^
/usr/local/lib/gcc48/include/c++/cmath: In function 'long double std::sqrt(long double)':
/usr/local/lib/gcc48/include/c++/cmath:486:23: error: declaration of C function 'long double std::sqrt(long double)' conflicts with
sqrt(long double __x)
^
/usr/local/lib/gcc48/include/c++/cmath:482:3: error: previous declaration 'float std::sqrt(float)' here
sqrt(float __x)
^
/usr/local/lib/gcc48/include/c++/cmath: At global scope:
/usr/local/lib/gcc48/include/c++/cmath:490:3: error: template with C linkage
template<typename _Tp>
^
/usr/local/lib/gcc48/include/c++/cmath: In function 'long double std::tan(long double)':
/usr/local/lib/gcc48/include/c++/cmath:505:22: error: declaration of C function 'long double std::tan(long double)' conflicts with
tan(long double __x)
^
/usr/local/lib/gcc48/include/c++/cmath:501:3: error: previous declaration 'float std::tan(float)' here
tan(float __x)
^
/usr/local/lib/gcc48/include/c++/cmath: At global scope:
/usr/local/lib/gcc48/include/c++/cmath:509:3: error: template with C linkage
template<typename _Tp>
^
/usr/local/lib/gcc48/include/c++/cmath: In function 'long double std::tanh(long double)':
/usr/local/lib/gcc48/include/c++/cmath:524:23: error: declaration of C function 'long double std::tanh(long double)' conflicts with
tanh(long double __x)
^
/usr/local/lib/gcc48/include/c++/cmath:520:3: error: previous declaration 'float std::tanh(float)' here
tanh(float __x)
^
/usr/local/lib/gcc48/include/c++/cmath: At global scope:
/usr/local/lib/gcc48/include/c++/cmath:528:3: error: template with C linkage
template<typename _Tp>
^
/usr/local/lib/gcc48/include/c++/cmath:805:3: error: template with C linkage
template<typename _Tp>
^
/usr/local/lib/gcc48/include/c++/cmath:815:3: error: template with C linkage
template<typename _Tp>
^
/usr/local/lib/gcc48/include/c++/cmath:824:3: error: template with C linkage
template<typename _Tp>
^
/usr/local/lib/gcc48/include/c++/cmath:833:3: error: template with C linkage
template<typename _Tp>
^
/usr/local/lib/gcc48/include/c++/cmath:842:3: error: template with C linkage
template<typename _Tp>
^
/usr/local/lib/gcc48/include/c++/cmath:851:3: error: template with C linkage
template<typename _Tp>
^
/usr/local/lib/gcc48/include/c++/cmath:860:3: error: template with C linkage
template<typename _Tp>
^
/usr/local/lib/gcc48/include/c++/cmath:869:3: error: template with C linkage
template<typename _Tp>
^
/usr/local/lib/gcc48/include/c++/cmath:878:3: error: template with C linkage
template<typename _Tp>
^
/usr/local/lib/gcc48/include/c++/cmath:887:3: error: template with C linkage
template<typename _Tp>
^
/usr/local/lib/gcc48/include/c++/cmath:896:3: error: template with C linkage
template<typename _Tp>
^
/usr/local/lib/gcc48/include/c++/cmath:905:3: error: template with C linkage
template<typename _Tp>
^
*** [bayesmcpp.o] Error code 1
Stop in /wrkdirs/usr/ports/science/R-cran-bayesm/work/bayesm/src.
ERROR: compilation failed for package 'bayesm'
* removing '/wrkdirs/usr/ports/science/R-cran-bayesm/work/stage/usr/local/lib/R/library/bayesm'
*** [do-install] Error code 1
Stop in /usr/ports/science/R-cran-bayesm.
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