Build of sagemath_3.0.5dfsg-2ubuntu1 using prevu fails on Kubuntu Intrepid

3 views
Skip to first unread message

R (Chandra) Chandrasekhar

unread,
Mar 10, 2009, 9:42:49 PM3/10/09
to debia...@googlegroups.com, sage-...@googlegroups.com
Dear Folks,

I am on an AMD64 PC running Kubuntu Intrepid 8.04 and KDE4.2. The Linux
kernel is 2.6.27-11-generic.

I downloaded the source package sagemath_3.0.5dfsg-2ubuntu1 from the
jaunty archives and tried compiling it, after having installed other
necessary packages and built them without incident using prevu.

The build progressed well until I got these messages:

===
building 'sage.matrix.matrix_mod2_dense' extension
gcc -fno-strict-aliasing -DNDEBUG -g -fwrapv -O2 -Wall
-Wstrict-prototypes -g -O2 -g -Wall -O2 -fPIC
-I/var/cache/prevu/src/6184/source/local//include
-I/var/cache/prevu/src/6184/source/local//include/csage
-I/var/cache/prevu/src/6184/source/devel//sage/sage/ext -I/usr/include
-I/usr/include/numpy -I/usr/include/FLINT -I/usr/include/givaro
-I/usr/include/gsl -I/usr/include/fplll -I/usr/include/eclib
-I/usr/include/gmp++ -I/usr/include/linbox -I/usr/include/NTL
-I/usr/include/pari -I/usr/include/qd -I/usr/include/singular
-I/usr/include/singular/singular -I/usr/include/symmetrica
-I/usr/include/polybori -I/usr/include/cudd
-I/usr/include/polybori/groebner -I/usr/include/zn_poly
-I/usr/include/python2.5 -c sage/matrix/matrix_mod2_dense.c -o
build/temp.linux-x86_64-2.5/sage/matrix/matrix_mod2_dense.o -w -w
sage/matrix/matrix_mod2_dense.c: In function
'__pyx_pf_4sage_6matrix_17matrix_mod2_dense_17Matrix_mod2_dense___init__':
sage/matrix/matrix_mod2_dense.c:1834: error: 'BIT' undeclared (first use
in this function)
sage/matrix/matrix_mod2_dense.c:1834: error: (Each undeclared identifier
is reported only once
sage/matrix/matrix_mod2_dense.c:1834: error: for each function it
appears in.)
sage/matrix/matrix_mod2_dense.c:1834: error: expected ';' before '__pyx_9'
sage/matrix/matrix_mod2_dense.c:2041: error: '__pyx_9' undeclared (first
use in this function)
sage/matrix/matrix_mod2_dense.c: In function
'__pyx_f_4sage_6matrix_17matrix_mod2_dense_17Matrix_mod2_dense_set_unsafe':
sage/matrix/matrix_mod2_dense.c:2159: error: 'BIT' undeclared (first use
in this function)
sage/matrix/matrix_mod2_dense.c:2159: error: expected ';' before '__pyx_3'
sage/matrix/matrix_mod2_dense.c:2173: error: '__pyx_3' undeclared (first
use in this function)
sage/matrix/matrix_mod2_dense.c: In function
'__pyx_f_4sage_6matrix_17matrix_mod2_dense_17Matrix_mod2_dense_get_unsafe':
sage/matrix/matrix_mod2_dense.c:2198: error: 'BIT' undeclared (first use
in this function)
sage/matrix/matrix_mod2_dense.c:2198: error: expected ';' before '__pyx_1'
sage/matrix/matrix_mod2_dense.c:2207: error: '__pyx_1' undeclared (first
use in this function)
sage/matrix/matrix_mod2_dense.c: In function
'__pyx_pf_4sage_6matrix_17matrix_mod2_dense_17Matrix_mod2_dense__list':
sage/matrix/matrix_mod2_dense.c:3718: error: 'BIT' undeclared (first use
in this function)
sage/matrix/matrix_mod2_dense.c:3718: error: expected ';' before '__pyx_4'
sage/matrix/matrix_mod2_dense.c:3760: error: '__pyx_4' undeclared (first
use in this function)
sage/matrix/matrix_mod2_dense.c: In function
'__pyx_pf_4sage_6matrix_17matrix_mod2_dense_17Matrix_mod2_dense__pivots':
sage/matrix/matrix_mod2_dense.c:4312: error: 'BIT' undeclared (first use
in this function)
sage/matrix/matrix_mod2_dense.c:4312: error: expected ';' before '__pyx_4'
sage/matrix/matrix_mod2_dense.c:4399: error: '__pyx_4' undeclared (first
use in this function)
sage/matrix/matrix_mod2_dense.c: In function
'__pyx_pf_4sage_6matrix_17matrix_mod2_dense_17Matrix_mod2_dense_randomize':
sage/matrix/matrix_mod2_dense.c:4665: error: 'packedmatrix' has no
member named 'ncols'
sage/matrix/matrix_mod2_dense.c: In function
'__pyx_pf_4sage_6matrix_17matrix_mod2_dense_17Matrix_mod2_dense_submatrix':
sage/matrix/matrix_mod2_dense.c:5887: error: 'packedmatrix' has no
member named 'ncols'
sage/matrix/matrix_mod2_dense.c:5900: error: 'packedmatrix' has no
member named 'ncols'
sage/matrix/matrix_mod2_dense.c:5923: error: 'packedmatrix' has no
member named 'nrows'
sage/matrix/matrix_mod2_dense.c:5936: error: 'packedmatrix' has no
member named 'nrows'
error: command 'gcc' failed with exit status 1
sage: There was an error installing modified sage library code.

ERROR installing SAGE

real 15m0.155s
user 14m0.613s
sys 0m36.502s
sage: An error occurred while installing sage-3.0.5.debian
Please email sage-devel http://groups.google.com/group/sage-devel
explaining the problem and send the relevant part of
of /var/cache/prevu/src/6184/source/install.log. Describe your
computer, operating system, etc.
If you want to try to fix the problem, yourself *don't* just cd to
/var/cache/prevu/src/6184/source/spkg/build/sage-3.0.5.debian and type
'make'.
Instead type "/var/cache/prevu/src/6184/source/sage -sh"
in order to set all environment variables correctly, then cd to
/var/cache/prevu/src/6184/source/spkg/build/sage-3.0.5.debian
(When you are done debugging, you can type "exit" to leave the
subshell.)
make[2]: *** [installed/sage-3.0.5.debian] Error 1
make[2]: Leaving directory `/var/cache/prevu/src/6184/source/spkg'
Command exited with non-zero status 2
1143.37user 64.68system 20:44.06elapsed 97%CPU (0avgtext+0avgdata
0maxresident)k
32896inputs+1746272outputs (33major+9583683minor)pagefaults 0swaps
make[1]: Leaving directory `/var/cache/prevu/src/6184/source'
touch debian/stamp-makefile-build
DEB_MAKE_CHECK_TARGET unset, not running checks
fakeroot debian/rules binary
test -x debian/rules
dh_testroot
dh_clean -k
dh_installdirs -A
mkdir -p "."
DEB_MAKE_CHECK_TARGET unset, not running checks
DEB_MAKE_INSTALL_TARGET unset, skipping default makefile.mk
common-install target
dh_installdirs -psagemath
dh_installdocs -psagemath
dh_installexamples -psagemath
dh_installman -psagemath
dh_installinfo -psagemath
dh_installmenu -psagemath
dh_installcron -psagemath
dh_installinit -psagemath
dh_installdebconf -psagemath
dh_installemacsen -psagemath
dh_installcatalogs -psagemath
dh_installpam -psagemath
dh_installlogrotate -psagemath
dh_installlogcheck -psagemath
dh_installchangelogs -psagemath
dh_installudev -psagemath
dh_lintian -psagemath
dh_install -psagemath
dh_link -psagemath /usr/bin/gfortran
/usr/lib/sagemath/local/bin/sage_fortran.bin
dh_installmime -psagemath
rm -rf cython-tmp
ln -sf /usr/lib/libsingular.so local/lib/
mkdir -p debian/sagemath/usr/lib/sagemath/
mv usr/lib/python2.5 debian/sagemath/usr/lib/
mv: cannot stat `usr/lib/python2.5': No such file or directory
make: *** [binary-post-install/sagemath] Error 1
dpkg-buildpackage: failure: fakeroot debian/rules binary gave error exit
status 2
Copying back the cached apt archive contents
-> new cache content libboost-python1.35-dev_1.35.0-8ubuntu1_amd64.deb
added
-> new cache content libmpfi0_1.3.4~rc4~cvs20080519-1_amd64.deb added
-> new cache content r-base-dev_2.7.1-2_all.deb added
-> new cache content python-matplotlib_0.98.3-4ubuntu1_amd64.deb added
-> new cache content libmpfi-dev_1.3.4~rc4~cvs20080519-1_amd64.deb added
-> new cache content zip_2.32-1_amd64.deb added
-> new cache content libpari-dev_2.3.3-2_amd64.deb added
-> new cache content unzip_5.52-11ubuntu1_amd64.deb added
-> new cache content python-tk_2.5.2-1ubuntu1_amd64.deb added
-> new cache content r-base-core_2.7.1-2_amd64.deb added
-> new cache content
libboost-serialization1.35-dev_1.35.0-8ubuntu1_amd64.deb added
-> new cache content libm4ri0_0.0.20071224-1_amd64.deb added
-> new cache content blt_2.4z-4ubuntu3_amd64.deb added
-> new cache content libboost-python1.35.0_1.35.0-8ubuntu1_amd64.deb added
-> new cache content libecm0_6.2-1_amd64.deb added
-> new cache content python-numpy_1%3a1.1.1-1_amd64.deb added
-> new cache content libsymmetrica-dev_2.0-1_amd64.deb added
-> new cache content python-glade2_2.13.0-0ubuntu8_amd64.deb added
-> new cache content python-matplotlib-data_0.98.3-4ubuntu1_all.deb added
-> new cache content
libboost-serialization1.35.0_1.35.0-8ubuntu1_amd64.deb added
-> new cache content cython_0.9.6.14-1_all.deb added
-> new cache content python-gobject_2.15.3-0ubuntu5_amd64.deb added
-> new cache content libpari2-gmp_2.3.3-2_amd64.deb added
-> new cache content libpaper-utils_1.1.23+nmu1_amd64.deb added
-> new cache content python-gtk2_2.13.0-0ubuntu8_amd64.deb added
-> new cache content libglade2-0_1%3a2.6.3-0ubuntu1_amd64.deb added
-> new cache content libsymmetrica-2.0_2.0-1_amd64.deb added
-> new cache content tk8.4_8.4.19-1_amd64.deb added
-> new cache content python-tz_2008b-3ubuntu1_all.deb added
-> new cache content tcl8.4_8.4.19-2_amd64.deb added
-> new cache content libicu38_3.8.1-2_amd64.deb added
-> new cache content python-numeric_24.2-9_amd64.deb added
-> new cache content python-pyparsing_1.5.0-1_all.deb added
-> new cache content libecm-dev_6.2-1_amd64.deb added
-> new cache content libboost1.35-dev_1.35.0-8ubuntu1_amd64.deb added
-> new cache content python-cairo_1.4.12-1_amd64.deb added
-> new cache content libm4ri-dev_0.0.20071224-1_amd64.deb added
-> new cache content gccxml_0.9.0+cvs20080525-1_amd64.deb added
-> new cache content libffi5_3.0.5-4_amd64.deb added
-> new cache content python-dateutil_1.4-1ubuntu2_all.deb added
-> new cache content python-excelerator_0.6.3a-3_all.deb added
-> new cache content rsync_3.0.3-2ubuntu1_amd64.deb added
-> new cache content gfortran_4%3a4.3.1-1ubuntu2_amd64.deb added
-> new cache content time_1.7-22_amd64.deb added
-> new cache content gfortran-4.3_4.3.2-1ubuntu12_amd64.deb added
-> unmounting /var/cache/prevu/src/6184 filesystem
-> unmounting /var/cache/prevu/intrepid-debs filesystem
-> unmounting dev/pts filesystem
-> unmounting proc filesystem
-> cleaning the build env
-> removing directory /var/cache/prevu/builds/6261 and its
subdirectories
========================
Prevu Error: Build failed.
Prevu encountered an error performing your build. The actual
error message may be further up in the scrollback before pbuilder
exited. Please look for a failed dependency or compile error in
the full output.
===

Can someone please take a look and tell me what more I should do to
build the package successfully from source?

Thanks.

Chandra

Tim Abbott

unread,
Mar 10, 2009, 10:14:06 PM3/10/09
to debia...@googlegroups.com, sage-...@googlegroups.com
I'm guessing your issue is too old m4ri. Try upgrading to libm4ri-dev
from jaunty.

-Tim Abbott

R (Chandra) Chandrasekhar

unread,
Mar 11, 2009, 9:38:27 AM3/11/09
to debia...@googlegroups.com, sage-...@googlegroups.com
Tim Abbott wrote:

> I'm guessing your issue is too old m4ri. Try upgrading to libm4ri-dev from jaunty.

Thank you. Installing libm4ri-dev from jaunty allowed sagemath to be
built. After that, I needed to I needed to compile from source the
following packages:
lcalc
gfan
gap-guava
libcdd-test

I could then install sagemath and use it.

Thanks.

Chandra

Reply all
Reply to author
Forward
0 new messages