Alexandre Racine wrote:
> ...
lrwxrwxrwx 1 root root 36 Jan 25 10:10 /usr/lib/liblapack.so.3 ->
/usr/lib/lapack/atlas/liblapack.so.0.0.0
Starting the program again, I get this:
$ ./smartpca
./smartpca: error while loading shared libraries: liblapack.so.3: cannot
open shared object file: No such file or directory
Are you sure it does exactly that?
I cannot reproduce it. Whether I link /usr/lib/liblapack.so.3 to
/usr/lib/liblapack.so.0 or directly to
/usr/lib/lapack/atlas/liblapack.so.0.0.0 as you did, I get libblas.so.3,
not liblapack.so.3 not found. After linking /usr/lib/libblas.so.3 to
/usr/lib/libblas.so.0 I start smartpca without problem:
> ./smartpca
./smartpca: error while loading shared libraries: liblapack.so.3: cannot
open shared object file: No such file or directory
> sudo ln -s /usr/lib/liblapack.so.0 /usr/lib/liblapack.so.3
> ./smartpca
./smartpca: error while loading shared libraries: libblas.so.3: cannot
open shared object file: No such file or directory
> sudo ln -s /usr/lib/libblas.so.0 /usr/lib/libblas.so.3
> ./smartpca
no parameters
## smartpca version: 7521
You can avoid such ugly symbolic links, if you compile the sources.
With the help of `pkg-config --libs lapack` I adapted Makefile.alt to
the attached Makefile.gcc4 and compiled the sources:
> make -f Makefile.gcc4 all
For now I don't feel like to pay those extra ten to sixty minutes to
write something like a first version of an ebuild, but I thing that it
might be quite straitforward.
With best regards
Honza Macháček
HOMEL=$(PWD)
DEBUG_OPTIONS= -g -pg
BIN=$(HOMEL)/bin
# "make smartpca" to make smartpca program (ditto for other programs)
# "mv smartpca ../bin" or "make install" to place in ../bin directory
# "make clean" to clean up extra files in this directory
# "make clobber" to clobber all files and subdirectories except source files
# so as to enable recompiling from scratch.
NLIB=$(HOMEL)/smartlib/nicklib.a
IDIR=$(HOMEL)/smartinclude
VPATH=.:nicksrc
BLAS = blas
# may need to change to BLAS = blas-3 (depends on blas/lapack installation)
CC=/usr/bin/gcc
FF=/usr/bin/gfortran
CFLAGS= -c -O -I$(IDIR) -Wimplicit
LAPACK_LIBS=-llapack -lblas -lcblas -latlas
eigx.o: eigx.f
$(FF) -c -o eigx.o eigx.f
statsubs.o: nicksrc/statsubs.c
$(CC) $(CFLAGS) -DTWTAB=$(TWTAB) -o statsubs.o nicksrc/statsubs.c
OBJ=strsubs.o sortit.o vsubs.o statsubs.o linsubs.o getpars.o xsearch.o gauss.o
gds.o
TWTAB=\"$(HOMEL)/smarttables/twtable\"
M1=smartpca
M1O=smartpca.o twsubs.o mcio.o admutils.o egsubs.o eigsubs.o eigx.o
M2=convertf
M2O=convertf.o mcio.o admutils.o
M3=twstats
M3O=twstats.o
M4=eigenstrat
M4O=eigenstrat.o
M5=eigenstratQTL
M5O=eigenstratQTL.o
M6=pca
M6O=pca.o eigsubs.o eigx.o
M7=pcatoy
M7O=pcatoy.o eigsubs.o eigx.o
PROGS= smartpca convertf twstats eigenstrat eigenstratQTL pca
all: nicklib $(PROGS)
install: all
cp $(PROGS) $(HOMEL)/bin
uninstall:
rm -f $(BIN)/smartpca
rm -f $(BIN)/convertf
rm -f $(BIN)/twstats
rm -f $(BIN)/eigenstrat
rm -f $(BIN)/eigenstratQTL
rm -f $(BIN)/pca
rm -f $(NLIB)/libnick.a
$(M1): nicklib $(M1O)
gcc -O -I$(IDIR) $(DEBUG_OPTIONS) -L/usr/lib -lm $(LAPACK_LIBS) -o
$(M1) $(M1O) $(NLIB) -Wimplicit
$(M2): nicklib $(M2O)
gcc -O -I$(IDIR) $(DEBUG_OPTIONS) -lm -o $(M2) $(M2O) $(NLIB)
-Wimplicit
$(M3): nicklib $(M3O)
gcc -O -I$(IDIR) $(DEBUG_OPTIONS) -lm -o $(M3) $(M3O) $(NLIB)
-Wimplicit
$(M4): nicklib $(M4O)
gcc -O -I$(IDIR) $(DEBUG_OPTIONS) -lm -o $(M4) $(M4O) $(NLIB)
-Wimplicit
$(M5): nicklib $(M5O)
gcc -O -I$(IDIR) $(DEBUG_OPTIONS) -lm -o $(M5) $(M5O) $(NLIB)
-Wimplicit
$(M6): nicklib $(M6O)
gcc -O -I$(IDIR) $(DEBUG_OPTIONS) -L/usr/lib -lm $(LAPACK_LIBS) -o
$(M6) $(M6O) $(NLIB) -Wimplicit
$(M7): nicklib $(M7O)
gcc -O -I$(IDIR) $(DEBUG_OPTIONS) -L/usr/lib -lm $(LAPACK_LIBS) -o
$(M7) $(M7O) $(NLIB) -Wimplicit
libnick.a: dirs $(OBJ)
ar -r libnick.a $(OBJ)
nicklib: dirs libnick.a
cp libnick.a $(NLIB)
dirs:
mkdir -p $(HOMEL)/smartlib
mkdir -p $(HOMEL)/smarttables
mkdir -p $(HOMEL)/smartinclude
mkdir -p $(BIN)
cp twtable $(HOMEL)/smarttables
cp nicksrc/*.h $(IDIR)
clean:
rm -f *.o
rm -f core
rm -f libnick.a
rm -f $(PROGS)
clobber: clean rmdirs uninstall
rmdirs:
rm -rf $(HOMEL)/smartlib
rm -rf $(HOMEL)/smarttables
rm -rf $(HOMEL)/smartinclude
