sage-6.1.1 build errors out while building conway_polynomials
Saifi Khan
saifi at sina.cn
Mon Mar 3 17:10:43 UTC 2014
Hi:
on attempting to build sage-6.1.1 from the '/usr/ports/math/sage' port, the
build errors out while building a subpackage 'conway_polynomials'.
env
---
FreeBSD x53u 11.0-CURRENT FreeBSD 11.0-CURRENT #0 r262432:
Mon Feb 24 17:50:32 IST 2014
root at x53u:/usr/obj/usr/src/sys/GENERIC amd64
env var
-------
export SPKG_CHECK=yes
export SAGE_KEEP_BUILT_SPKGS=yes
#export SAGE_MATPLOTLIB_GUI=gtk
export SAGE_MATPLOTLIB_GUI=no
export MAKE_JOBS_UNSAFE=yes
SAGE_PARALLEL_SPKG_BUILD="yes"
build log
---------
# make
===> Building for sage-math-6.1.1
gmake[2]: Entering directory `/usr/ports/math/sage/work/sage-6.1.1'
cd build && \
"../build/pipestatus" \
"env SAGE_PARALLEL_SPKG_BUILD='' ./install all 2>&1" \
"tee -a ../logs/install.log"
*** ALL ENVIRONMENT VARIABLES BEFORE BUILD: ***
.MAKE.LEVEL.ENV=MAKELEVEL
ADDR2LINE=/usr/local/bin/addr2line
AR=/usr/local/bin/ar
ARCH=/usr/local/bin/ar
AS=/usr/local/bin/as
AUTOCONF=/usr/local/bin/autoconf-2.69
AUTOCONF_DIR=/usr/local/share/autoconf-2.69
AUTOCONF_VERSION=2.69
AUTOHEADER=/usr/local/bin/autoheader-2.69
AUTOIFNAMES=/usr/local/bin/ifnames-2.69
AUTOM4TE=/usr/local/bin/autom4te-2.69
AUTORECONF=/usr/local/bin/autoreconf-2.69
AUTOSCAN=/usr/local/bin/autoscan-2.69
AUTOUPDATE=/usr/local/bin/autoupdate-2.69
BLOCKSIZE=K
BSD_INSTALL_DATA=install -o root -g wheel -m 444
BSD_INSTALL_LIB=install -s -o root -g wheel -m 444
BSD_INSTALL_MAN=install -o root -g wheel -m 444
BSD_INSTALL_PROGRAM=install -s -o root -g wheel -m 555
BSD_INSTALL_SCRIPT=install -o root -g wheel -m 555
CC=gcc46
CFLAGS=-pipe -Wl,-rpath=/usr/ports/math/sage/work/sage-6.1.1/local/lib
-mfpmath=387 -Wl,-rpath=/usr/local/lib/gcc46
CONFIG_DONE_SAGE=1
CPP=cpp46
CPPFILT=/usr/local/bin/c++filt
CPPFLAGS=
CXX=g++46
CXXFLAGS=-pipe -Wl,-rpath=/usr/ports/math/sage/work/sage-6.1.1/local/lib
-mfpmath=387 -Wl,-rpath=/usr/local/lib/gcc46
-Wl,-rpath=/usr/ports/math/sage/work/sage-6.1.1/local/lib -mfpmath=387
-Wl,-rpath=/usr/local/lib/gcc46
DOT_SAGE=/usr/ports/math/sage/work/sage-6.1.1/tmp/.sage
F77=gfortran46
FCFLAGS=-Wl,-rpath=/usr/local/lib/gcc46
FFLAGS=-pipe -Wl,-rpath=/usr/ports/math/sage/work/sage-6.1.1/local/lib
-mfpmath=387 -Wl,-rpath=/usr/local/lib/gcc46
GDM_LANG=en_US.UTF-8
GPROF=/usr/local/bin/gprof
HOME=/root
LANG=en_US.UTF-8
LD=/usr/local/bin/ld
LDFLAGS=-Wl,-rpath=/usr/ports/math/sage/work/sage-6.1.1/local/lib
-Wl,-rpath=/usr/local/lib/gcc46 -L/usr/local/lib/gcc46
-Wl,-rpath=/usr/local/lib/gcc46 -L/usr/local/lib/gcc46
LIBDIR=/usr/lib
LOCALBASE=/usr/local
LOGNAME=root
MAIL=/var/mail/root
MAKE=make -j1
MAKEFLAGS=w -- SYSTEMVERSION= OSVERSION=1100004 OSREL=11.0 OPSYS=FreeBSD
CONFIG_DONE_SAGE=1 ARCH=/usr/local/bin/ar .MAKE.LEVEL.ENV=MAKELEVEL
MAKELEVEL=3
MAKEOVERRIDES=${-*-command-variables-*-}
MAKE_JOBS_UNSAFE=yes
MANPREFIX=/usr/local
MFLAGS=-w
MM_CHARSET=UTF-8
NM=/usr/local/bin/nm
NO_LINT=YES
OBJCOPY=/usr/local/bin/objcopy
OBJDUMP=/usr/local/bin/objdump
OPSYS=FreeBSD
OSREL=11.0
OSVERSION=1100004
PAGER=more
PATH=/usr/ports/math/sage/work/sage-6.1.1/src/bin:/usr/ports/math/sage/work/sage-6.1.1/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/usr/games:/usr/local/sbin:/usr/local/bin:/root/bin
PREFIX=/usr/local
PWD=/usr/ports/math/sage/work/sage-6.1.1/build
PYTHONPATH=/usr/ports/math/sage/work/sage-6.1.1/local
RANLIB=/usr/local/bin/ranlib
READELF=/usr/local/bin/readelf
SAGE_ATLAS_LIB=/usr/local/lib
SAGE_EXTCODE=/usr/ports/math/sage/work/sage-6.1.1/local/share/sage/ext
SAGE_FAT_BINARY=yes
SAGE_INSTALL_GCC=no
SAGE_LOCAL=/usr/ports/math/sage/work/sage-6.1.1/local
SAGE_LOGS=/usr/ports/math/sage/work/sage-6.1.1/logs/pkgs
SAGE_PARALLEL_SPKG_BUILD=
SAGE_PORT=yes
SAGE_ROOT=/usr/ports/math/sage/work/sage-6.1.1
SAGE_SPKG_INST=/usr/ports/math/sage/work/sage-6.1.1/local/var/lib/sage/installed
SAGE_SRC=/usr/ports/math/sage/work/sage-6.1.1/src
SAGE_VERSION=6.1.1
SCRIPT=typescript
SHELL=/bin/sh
SHLVL=2
SIZE=/usr/local/bin/size
SPKG_CHECK=yes
STRINGS=/usr/local/bin/strings
SYSTEMVERSION=
TERM=xterm
USER=root
_=/usr/bin/env
***********************************************
make[3]: Entering directory `/usr/ports/math/sage/work/sage-6.1.1/build'
make -j1 base
make[4]: Entering directory `/usr/ports/math/sage/work/sage-6.1.1/build'
make[4]: Nothing to be done for `base'.
make[4]: Leaving directory `/usr/ports/math/sage/work/sage-6.1.1/build'
env SAGE_BUILD_TOOLCHAIN=yes make -j1 toolchain
make[4]: Entering directory `/usr/ports/math/sage/work/sage-6.1.1/build'
make[4]: Nothing to be done for `toolchain'.
make[4]: Leaving directory `/usr/ports/math/sage/work/sage-6.1.1/build'
make -j1 toolchain-deps
make[4]: Entering directory `/usr/ports/math/sage/work/sage-6.1.1/build'
make -j1
/usr/ports/math/sage/work/sage-6.1.1/local/var/lib/sage/installed/zlib-1.2.8.p0
make[5]: Entering directory `/usr/ports/math/sage/work/sage-6.1.1/build'
make[5]:
`/usr/ports/math/sage/work/sage-6.1.1/local/var/lib/sage/installed/zlib-1.2.8.p0'
is up to date.
make[5]: Leaving directory `/usr/ports/math/sage/work/sage-6.1.1/build'
make -j1
/usr/ports/math/sage/work/sage-6.1.1/local/var/lib/sage/installed/mpir-2.6.0.p4
make[5]: Entering directory `/usr/ports/math/sage/work/sage-6.1.1/build'
make[5]:
`/usr/ports/math/sage/work/sage-6.1.1/local/var/lib/sage/installed/mpir-2.6.0.p4'
is up to date.
make[5]: Leaving directory `/usr/ports/math/sage/work/sage-6.1.1/build'
make -j1
/usr/ports/math/sage/work/sage-6.1.1/local/var/lib/sage/installed/mpfr-3.1.2.p0
make[5]: Entering directory `/usr/ports/math/sage/work/sage-6.1.1/build'
make[5]:
`/usr/ports/math/sage/work/sage-6.1.1/local/var/lib/sage/installed/mpfr-3.1.2.p0'
is up to date.
make[5]: Leaving directory `/usr/ports/math/sage/work/sage-6.1.1/build'
make -j1
/usr/ports/math/sage/work/sage-6.1.1/local/var/lib/sage/installed/mpc-1.0.p0
make[5]: Entering directory `/usr/ports/math/sage/work/sage-6.1.1/build'
make[5]:
`/usr/ports/math/sage/work/sage-6.1.1/local/var/lib/sage/installed/mpc-1.0.p0'
is up to date.
make[5]: Leaving directory `/usr/ports/math/sage/work/sage-6.1.1/build'
make -j1
/usr/ports/math/sage/work/sage-6.1.1/local/var/lib/sage/installed/ppl-1.1pre9.p0
make[5]: Entering directory `/usr/ports/math/sage/work/sage-6.1.1/build'
make[5]:
`/usr/ports/math/sage/work/sage-6.1.1/local/var/lib/sage/installed/ppl-1.1pre9.p0'
is up to date.
make[5]: Leaving directory `/usr/ports/math/sage/work/sage-6.1.1/build'
make[4]: Leaving directory `/usr/ports/math/sage/work/sage-6.1.1/build'
make -j1 all-sage
make[4]: Entering directory `/usr/ports/math/sage/work/sage-6.1.1/build'
/usr/ports/math/sage/work/sage-6.1.1/build/pipestatus "sage-spkg
${SAGE_SPKG_OPTS} conway_polynomials-0.4.p0 2>&1" "tee -a
/usr/ports/math/sage/work/sage-6.1.1/logs/pkgs/conway_polynomials-0.4.p0.log"
Found local metadata for conway_polynomials-0.4.p0
Found local sources at
/usr/ports/math/sage/work/sage-6.1.1/upstream/conway_polynomials-0.4.tar.bz2
Checksum: 25b7abe5c935d20c3ebcde943308652c412d14dc vs
25b7abe5c935d20c3ebcde943308652c412d14dc
conway_polynomials-0.4.p0
====================================================
Setting up build directory for conway_polynomials-0.4.p0
Finished set up
****************************************************
C compiler: gcc
C compiler version:
Using built-in specs.
COLLECT_GCC=/usr/local/bin/gcc46
COLLECT_LTO_WRAPPER=/usr/local/libexec/gcc46/gcc/x86_64-portbld-freebsd11.0/4.6.4/lto-wrapper
Target: x86_64-portbld-freebsd11.0
Configured with: ./../gcc-4.6.4/configure --disable-bootstrap --disable-nls
--libdir=/usr/local/lib/gcc46 --libexecdir=/usr/local/libexec/gcc46
--program-suffix=46 --with-as=/usr/local/bin/as --with-gmp=/usr/local
--with-gxx-include-dir=/usr/local/lib/gcc46/include/c++/
--with-ld=/usr/local/bin/ld --with-pkgversion='FreeBSD Ports Collection'
--with-system-zlib --with-ecj-jar=/usr/local/share/java/ecj-4.5.jar
--enable-languages=c,c++,objc,fortran,java --prefix=/usr/local
--mandir=/usr/local/man --infodir=/usr/local/info/gcc46
--build=x86_64-portbld-freebsd11.0
Thread model: posix
gcc version 4.6.4 (FreeBSD Ports Collection)
****************************************************
------------------------------------------------------------------------
Attaching gdb to process id 2051.
GNU gdb 6.1.1 [FreeBSD]
Copyright 2004 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and you are
welcome to change it and/or distribute copies of it under certain conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB. Type "show warranty" for details.
This GDB was configured as "amd64-marcel-freebsd".
(gdb) Hangup detected on fd 0
error detected on stdin
Your system GDB is an old version that does not work with pipes
Install the gdb spkg (sage -f gdb) for enhanced tracebacks.
------------------------------------------------------------------------
Unhandled SIGSEGV: A segmentation fault occurred in Sage.
This probably occurred because a *compiled* component of Sage has a bug
in it and is not properly wrapped with sig_on(), sig_off().
Sage will now terminate.
------------------------------------------------------------------------
/usr/ports/math/sage/work/sage-6.1.1/src/bin/sage-spkg: line 697: 2051
Segmentation fault (core dumped) ./spkg-install
real 0m4.720s
user 0m1.450s
sys 0m3.096s
************************************************************************
Error installing package conway_polynomials-0.4.p0
************************************************************************
Please email sage-devel (http://groups.google.com/group/sage-devel)
explaining the problem and including the relevant part of the log file
/usr/ports/math/sage/work/sage-6.1.1/logs/pkgs/conway_polynomials-0.4.p0.log
Describe your computer, operating system, etc.
If you want to try to fix the problem yourself, *don't* just cd to
/usr/ports/math/sage/work/sage-6.1.1/local/var/tmp/sage/build/conway_polynomials-0.4.p0
and type 'make' or whatever is appropriate.
Instead, the following commands setup all environment variables
correctly and load a subshell for you to debug the error:
(cd
'/usr/ports/math/sage/work/sage-6.1.1/local/var/tmp/sage/build/conway_polynomials-0.4.p0'
&& '/usr/ports/math/sage/work/sage-6.1.1/sage' --sh)
When you are done debugging, you can type "exit" to leave the subshell.
************************************************************************
make[4]: ***
[/usr/ports/math/sage/work/sage-6.1.1/local/var/lib/sage/installed/conway_polynomials-0.4.p0]
Error 1
make[4]: Leaving directory `/usr/ports/math/sage/work/sage-6.1.1/build'
make[3]: *** [all] Error 2
make[3]: Leaving directory `/usr/ports/math/sage/work/sage-6.1.1/build'
real 0m7.937s
user 0m2.667s
sys 0m5.249s
***************************************************************
Error building Sage.
The following package(s) may have failed to build:
package: conway_polynomials-0.4.p0
log file:
/usr/ports/math/sage/work/sage-6.1.1/logs/pkgs/conway_polynomials-0.4.p0.log
build directory:
/usr/ports/math/sage/work/sage-6.1.1/local/var/tmp/sage/build/conway_polynomials-0.4.p0
The build directory may contain configuration files and other potentially
helpful information. WARNING: if you now run 'make' again, the build
directory will, by default, be deleted. Set the environment variable
SAGE_KEEP_BUILT_SPKGS to 'yes' to prevent this.
gmake[2]: *** [build] Error 1
gmake[2]: Leaving directory `/usr/ports/math/sage/work/sage-6.1.1'
*** Error code 1
Stop.
make[1]: stopped in /usr/ports/math/sage
*** Error code 1
Stop.
make: stopped in /usr/ports/math/sage
# exit
----
Has anybody encountered this situation ? Is there a workaround for
this ?
Thanks in advance.
thanks
Saifi.
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