I'm trying to compile some software for OSX, that was developed on
linux (tarball available at http://microarray.org/data/download/
g2c-1.0.tar.gz), and ran into a number of problems, some of which I
solved (or appeared to solve), but I'm now stuck. Any help would be
greatly appreciated. The problems I encountered thus far were:
1. The first problem is when it tries to compile dust.c:
ccsr-2255b-g5 1002 % make all
compiling g2c.c
compiling g2clib.c
compiling gopt.c
compiling blast.c
compiling complementation.c
compiling complexity.c
compiling dust.c
dust.c:2:20: error: malloc.h: No such file or directory
make: *** [dust.o ] Error 1
This is easy to get around - just remove the line:
#include <malloc.h>
from dust.c, as I think the malloc functions are provided from
stdlib.h on OSX.
2. There was a problem with the -lexpat rule:
ccsr-2255b-g5 1004 % make all
compiling dust.c
compiling energy.c
compiling energy_data.c
compiling fasta.c
compiling lzw.c
compiling nucleotide.c
compiling util.c
compiling self.c
compiling SmithWaterman.c
compiling wublast.c
checking adt.a
ar rv ../adt.a FragmentSequence.o FragmentSequenceGroup.o GenomeTag.o
IndexValue.o Integer.o MatchingSequence.o MatchingSequenceLine.o
PositionEvidence.o
ar: creating archive ../adt.a
a - FragmentSequence.o
a - FragmentSequenceGroup.o
a - GenomeTag.o
a - IndexValue.o
a - Integer.o
a - MatchingSequence.o
a - MatchingSequenceLine.o
a - PositionEvidence.o
ranlib ../adt.a
checking util.a
ar rv ../util.a sht.o list.o Hashtable.o
ar: creating archive ../util.a
a - sht.o
a - list.o
a - Hashtable.o
ranlib ../util.a
making g2c
compiling readWuBlast.c
making readwu
make: *** No rule to make target `-lexpat', needed by `libg2c.so'.
Stop.
To get around this, I simply copied libexpat.a to my working directory.
3. -shared problem
ccsr-2255b-g5 1016 % cp /usr/local/lib/libexpat.a ./
ccsr-2255b-g5 1017 % make clean
.
.
.
ccsr-2255b-g5 1020 % make all
.
.
.
making g2c
compiling readWuBlast.c
making readwu
making libg2c.so
powerpc-apple-darwin8-gcc-4.0.1: unrecognized option '-shared'
/usr/bin/ld: Undefined symbols:
_main
collect2: ld returned 1 exit status
make: *** [libg2c.so] Error 1
Looking into Apple's docs, I found -dynamic is the replacement for -
shared on OSX (see http://developer.apple.com/technotes/tn2002/
tn2071.html#Section5), but still no success when I replace the option:
making libg2c.so
/usr/bin/ld: Undefined symbols:
_main
collect2: ld returned 1 exit status
make: *** [libg2c.so] Error 1
I then tried -dynamiclib instead (I have no idea if I should do
this), which got me past the last error, but now this resulted in a
different error:
.
.
.
making g2c
compiling readWuBlast.c
making readwu
making libg2c.so
ld: common symbols not allowed with MH_DYLIB output format with the -
multi_module option
energy_data.o definition of common _WC_Matrix (size 2500)
energy_data.o definition of common _bulge (size 124)
energy_data.o definition of common _loop (size 124)
lzw.o definition of common _append_character (size 4)
lzw.o definition of common _code_value (size 4)
lzw.o definition of common _decode_stack (size 4000)
lzw.o definition of common _prefix_code (size 4)
wublast.o definition of common _token (size 1024)
/usr/bin/libtool: internal link edit command failed
make: *** [libg2c.so] Error 1
and now I'm well and truly stuck.
I'm on 10.4.6 on PowerPC, with the latest version of XCode. gcc --
version says:
ccsr-2255b-g5 1066 % gcc --version
powerpc-apple-darwin8-gcc-4.0.1 (GCC) 4.0.1 (Apple Computer, Inc.
build 5247)
Copyright (C) 2005 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There
is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE.
Many thanks for any help,
Cheers,
Gavin
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