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mockle

Member

Registered: 2009-02-22

Posts: 5

advice on building clustalw-mpi

Hi,

When I try to install clustalw-mpi (http://aur.archlinux.org/packages.php?ID=25187) using yaourt I get a segmentation fault during compilation. However, when I compile the source from a terminal using identical commands to those in the PKGBUILD (simply "make") the software compiles without problems.

I was wondering if anybody could suggest why this should be the case?

Here is the output from yaourt:

==> Building and installing package
==> Making package: clustalw-mpi 0.13-1 x86_64 (Mon Apr 27 06:41:33 PDT 2009)
==> Checking Runtime Dependencies...
==> Checking Buildtime Dependencies...
==> Retrieving Sources...
  -> Found clustalw-mpi-0.13.tar.gz in build dir
==> Validating source files with md5sums...
    clustalw-mpi-0.13.tar.gz ... Passed
==> Extracting Sources...
  -> bsdtar -x -f clustalw-mpi-0.13.tar.gz
==> Removing existing pkg/ directory...
==> Entering fakeroot environment...
==> Starting build()...
mpicc  -c -O3 clustalw-mpi.c
make: *** [clustalw-mpi.o] Segmentation fault
==> ERROR: Build Failed.
    Aborting...
Error: Makepkg was unable to build clustalw-mpi package.

and here's the output from typing "make" into a console using the identical source downloaded by yaourt:

[mick@pangolin clustalw-mpi-0.13]$ make
mpicc  -c -O3 clustalw-mpi.c
mpicc  -c -O3 interface.c
mpicc  -c -O3 sequence.c
mpicc  -c -O3 showpair.c
mpicc  -c -O3 malign.c
mpicc  -c -O3 malign_mpi_progressive.c
malign_mpi_progressive.c: In function 'key_compare':
malign_mpi_progressive.c:843: warning: cast to pointer from integer of different size
malign_mpi_progressive.c:844: warning: cast to pointer from integer of different size
mpicc  -c -O3 malign_mpi_pdiff.c
mpicc  -c -O3 util.c
mpicc  -DSERIAL_NJTREE -c -O3 trees.c
mpicc  -c -O3 gcgcheck.c
mpicc  -c -O3 prfalign_mpi_pdiff.c
mpicc  -c -O3 prfalign_mpi_progressive.c
mpicc  -DDYNAMIC_SCHEDULING_PAIRALIGN  -c -O3 pairalign_new.c
mpicc  -c -O3 calcgapcoeff.c
mpicc  -c -O3 calcprf1.c
mpicc  -c -O3 calcprf2.c
mpicc  -c -O3 calctree.c
mpicc  -c -O3 readmat.c
mpicc  -c -O3 alnscore.c
mpicc  -c -O3 random.c
mpicc  -DDYNAMIC_SCHEDULING_PAIRALIGN  -c -O3 parallel_compare.c
mpicc  -c -O3 prfalign.c
mpicc  -c -O3 stupid.c
mpicc  -o clustalw-mpi clustalw-mpi.o interface.o sequence.o showpair.o malign.o malign_mpi_progressive.o malign_mpi_pdiff.o util.o trees.o gcgcheck.o prfalign_mpi_pdiff.o prfalign_mpi_progressive.o pairalign_new.o calcgapcoeff.o calcprf1.o calcprf2.o calctree.o readmat.o alnscore.o random.o parallel_compare.o prfalign.o stupid.o -lm