Original report by Kenneth Hoehn (Bitbucket: kbhoehn, GitHub: kbhoehn).
Original message:
Hi Kleinstein-Lab,
could you please open the issue tracker of IgPhyML?
I am having trouble installing it....
[heumos@wave igphyml]$ ./make_phyml_blas_omp
configure.ac:16: installing './compile'
configure.ac:12: installing './config.guess'
configure.ac:12: installing './config.sub'
configure.ac:11: installing './install-sh'
configure.ac:11: installing './missing'
Makefile.am: installing './INSTALL'
src/Makefile.am: installing './depcomp'
src/Makefile.am:38: warning: 'CFLAGS' is a user variable, you should not override it;
src/Makefile.am:38: use 'AM_CFLAGS' instead
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /usr/bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking build system type... x86_64-pc-linux-gnu
checking host system type... x86_64-pc-linux-gnu
0
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables...
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking whether make supports the include directive... yes (GNU style)
checking dependency style of gcc... gcc3
checking for log in -lm... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking float.h usability... yes
checking float.h presence... yes
checking for float.h... yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking for unistd.h... (cached) yes
checking for an ANSI C-conforming const... yes
checking for inline... inline
checking for size_t... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for vprintf... yes
checking for _doprnt... no
checking for floor... yes
checking for pow... yes
checking for rint... yes
checking for sqrt... yes
checking for strchr... yes
checking for strstr... yes
checking whether CC supports -llapack... yes
checking whether CC supports -lblas... yes
checking whether CC supports -lcblas... yes
checking whether CC supports -latlas... no
checking whether CC supports -lsatlas... no
-O3 -fomit-frame-pointer -funroll-loops -fopenmp
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating config.h
config.status: executing depfiles commands
Making clean in src
make[1]: Entering directory '/home/heumos/git/igphyml/src'
test -z "igphyml" || rm -f igphyml
rm -f *.o
make[1]: Leaving directory '/home/heumos/git/igphyml/src'
make[1]: Entering directory '/home/heumos/git/igphyml'
make[1]: Nothing to be done for 'clean-am'.
make[1]: Leaving directory '/home/heumos/git/igphyml'
make all-recursive
make[1]: Entering directory '/home/heumos/git/igphyml'
Making all in src
make[2]: Entering directory '/home/heumos/git/igphyml/src'
gcc -DUNIX -DPHYML -DDEBUG -DBLAS_OMP -I. -I.. -O3 -fomit-frame-pointer -funroll-loops -fopenmp -L/usr/lib64/atlas -L/usr/lib/atlas-base/ -D_GNU_SOURCE -DHTABLE='"/home/heumos/git/igphyml/src/motifs/HTABLE_"' -I/usr/include/atlas/ -MT main.o -MD -MP -MF .deps/main.Tpo -c -o main.o main.c
In file included from spr.h:32,
from main.c:28:
utilities.h:1916:10: fatal error: clapack.h: No such file or directory
#include <clapack.h> //edited by Ken 12/1/2017
^~~~~~~~~~~
compilation terminated.
make[2]: *** [Makefile:695: main.o] Error 1
make[2]: Leaving directory '/home/heumos/git/igphyml/src'
make[1]: *** [Makefile:363: all-recursive] Error 1
make[1]: Leaving directory '/home/heumos/git/igphyml'
make: *** [Makefile:304: all] Error 2
I am trying to install the tool on Archlinux and I have both BLAS and LAPACK installed. Also the CC check above states the both packages are available..... So the building process itself should run through.
Thanks for any help!
Best, Simon
Original report by Kenneth Hoehn (Bitbucket: kbhoehn, GitHub: kbhoehn).
Original message:
Hi Kleinstein-Lab,
could you please open the issue tracker of IgPhyML?
I am having trouble installing it....
I am trying to install the tool on Archlinux and I have both BLAS and LAPACK installed. Also the CC check above states the both packages are available..... So the building process itself should run through.
Thanks for any help!
Best, Simon