> > arb_replace: error while loading shared libraries: libARBDB.so: cannot open
> > shared object file: No such file or directory
> Ahh, thanks for this hint. This kind of bugs occure if you don't compile
> packages
> in a clean chroot. I had installed a former version of arb on the box I
> builded
> the package. Thus the library was found which is not the case if you compile
> the
> package on a clean box.
> I'll foreward this problem upstream.
This can be also fixed with following in debian/rules.
--- debian/rules~ 2005-08-31 07:18:37.000000000 +0000
+++ debian/rules 2005-09-08 08:05:21.000000000 +0000
@@ -28,11 +28,13 @@
export ARBHOME=`pwd` ; \
export LC_ALL=C ; \
export PATH=$${ARBHOME}/bin:$${PATH} ; \
+ export LD_LIBRARY_PATH=$${ARBHOME}/lib:$${LD_LIBRARY_PATH}; \
$(MAKE) all
# export GCC=gcc-2.95 ; \ ####
export ARBHOME=`pwd` ; \
export LC_ALL=C ; \
export PATH=$${ARBHOME}/bin:$${PATH} ; \
+ export LD_LIBRARY_PATH=$${ARBHOME}/lib:$${LD_LIBRARY_PATH}; \
$(MAKE) arbxtras
touch build-stamp
The missing -fpic/-fPIC can be fixed by:
--- WINDOW/Makefile~ 2005-09-08 08:37:53.000000000 +0000
+++ WINDOW/Makefile 2005-09-08 08:37:53.000000000 +0000
@@ -21,7 +21,7 @@
$(CCPLIB) $(cflags) -c $< $(CPPINCLUDES)
.c.o:
- $(ACC) $(cflags) -c $< $(CPPINCLUDES)
+ $(CCLIB) $(cflags) -c $< $(CPPINCLUDES)
DEPENDS = $(OBJECTS:.o=.depend)
depends: $(DEPENDS)
But arb depends on xview which is not 64 bit clean and is unavailable
on all 64 bit archs, including amd64.
Even with patches above and xview patch from
http://debian-ppc64.alioth.debian.org/gcc4/patches/xview_3.2p1.4-19.0.0.1.gcc4.patch
arb cannot be built on amd64 - "error: cast from 'void*' to 'int' loses
precision".
This can be "fixed" by changing cast (int) to (long),
(as in attached patch) but according to warnings in build log,
the arb is definitely not 64 bit clean.
Therefore, I suggest to apply only patch for debian/rules and
WINDOW/Makefile and restrict architectures similarly as xview.
Andreas J., I am just curious, are these patches also sufficient for ppc64 ?
Regards
Petr
diff -ur /home/sid32/tmp/26/arb-0.0.20050526/ALIV3/a3_helix.cxx
arb-0.0.20050526/ALIV3/a3_helix.cxx
--- /home/sid32/tmp/26/arb-0.0.20050526/ALIV3/a3_helix.cxx 2005-01-05
13:08:24.000000000 +0100
+++ arb-0.0.20050526/ALIV3/a3_helix.cxx 2005-09-08 11:59:20.000000000 +0200
@@ -65,12 +65,12 @@
matrix.Set(back - left,pos - left,(vp)1)) error = 3;
{
if (last < 0) last =
mark.Add((vp)pos);
- else if ((back - (int)mark[last]) > 1) last =
mark.Add((vp)pos);
+ else if ((back - (long)mark[last]) > 1) last =
mark.Add((vp)pos);
}
}
else if (increment < 0)
{
- int back = (int)mark[last],
+ int back = (long)mark[last],
backend = left,
tmp = back;
@@ -78,7 +78,7 @@
back = tmp - 1;
- if (last > 0) backend = (int)mark[last - 1] + 1;
+ if (last > 0) backend = (long)mark[last - 1] + 1;
while (back >= backend)
{
@@ -101,7 +101,7 @@
if (last >= 0) mark.Del(last--);
if (last < 0) last =
mark.Add((vp)pos);
- else if ((back - (int)mark[last]) > 1) last =
mark.Add((vp)pos);
+ else if ((back - (long)mark[last]) > 1) last =
mark.Add((vp)pos);
break;
}
@@ -112,7 +112,7 @@
{
if (last >= 0) mark.Del(last--);
- if (last > 0) backend = (int)mark[last - 1] + 1;
+ if (last > 0) backend = (long)mark[last - 1] + 1;
else backend = left;
}
diff -ur /home/sid32/tmp/26/arb-0.0.20050526/ALIV3/a3_matrix.cxx
arb-0.0.20050526/ALIV3/a3_matrix.cxx
--- /home/sid32/tmp/26/arb-0.0.20050526/ALIV3/a3_matrix.cxx 2005-01-05
13:08:24.000000000 +0100
+++ arb-0.0.20050526/ALIV3/a3_matrix.cxx 2005-09-08 11:44:40.000000000
+0200
@@ -141,7 +141,7 @@
int p = l + x;
if (edump) edump(matrix[p]);
- else cout << " " << (int)matrix[p];
+ else cout << " " << (long)matrix[p];
x++;
}
diff -ur /home/sid32/tmp/26/arb-0.0.20050526/AWT/AWT_tree_cb.cxx
arb-0.0.20050526/AWT/AWT_tree_cb.cxx
--- /home/sid32/tmp/26/arb-0.0.20050526/AWT/AWT_tree_cb.cxx 2004-10-22
18:45:14.000000000 +0200
+++ arb-0.0.20050526/AWT/AWT_tree_cb.cxx 2005-09-08 11:29:43.000000000
+0200
@@ -119,7 +119,7 @@
}
static int nt_sequence_is_partial(GBDATA *gb_species, void *cd_partial) {
- int wanted = (int)cd_partial;
+ int wanted = (long)cd_partial;
awt_assert(wanted == 0 || wanted == 1);
int partial = GBT_is_partial(gb_species, 1-wanted, 0);
--- arb-0.0.20050526/TRS/trs_server.cxx~ 2005-09-08 10:16:52.000000000
+0000
+++ arb-0.0.20050526/TRS/trs_server.cxx 2005-09-08 10:16:52.000000000 +0000
@@ -76,7 +76,7 @@
char *eq = strchr(out,'=');
if (!eq) continue;
*(eq) = 0;
- TRS_write_hash(hash,out,(int)(eq+1));
+ TRS_write_hash(hash,out,(long)(eq+1));
}
return hash;
}
