Hi, I have problem compile the package and here are what I have done:
# first compile all the libraries
make -f Makefile.thirdparty
# the program ran for a while then an error appear saying /usr/local/staden/staden-src-1-7-0/lib/iwidgets can't be removed because it's a directory. So I manually delete the directory and rerun make:
make -f Makefile.rhirdparty
# at this point everything seems to be fine (but I was just guessing)
# Then I compile the staden package
make 2>&1 | tee make.out
# then the program ran for a while and show the errors below (far below):
In file included from include/Read.h:43,
include/os.h:131:1: warning: "NEED_VA_COPY" redefined
<command line>:10:1: warning: this is the location of the previous definition
cc -L../lib/linux-x86_64-binaries -shared -o ../lib/linux-x86_64-binaries/libread.so read/linux-x86_64-binarie
s/Read.o read/linux-x86_64-binaries/translate.o read/linux-x86_64-binaries/scf_extras.o utils/linux-x86_64-binar
ies/find.o utils/linux-x86_64-binaries/mach-io.o utils/linux-x86_64-binaries/traceType.o utils/linux-x86_64-bina
ries/read_alloc.o utils/linux-x86_64-binaries/compress.o utils/linux-x86_64-binaries/open_trace_file.o utils/lin
ux-x86_64-binaries/hash_table.o utils/linux-x86_64-binaries/mFILE.o utils/linux-x86_64-binaries/vlen.o scf/linux
-x86_64-binaries/read_scf.o scf/linux-x86_64-binaries/write_scf.o scf/linux-x86_64-binaries/misc_scf.o exp_file/
linux-x86_64-binaries/expFileIO.o plain/linux-x86_64-binaries/seqIOPlain.o abi/linux-x86_64-binaries/fpoint.o ab
i/linux-x86_64-binaries/seqIOABI.o alf/linux-x86_64-binaries/seqIOALF.o ctf/linux-x86_64-binaries/ctfCompress.o
ctf/linux-x86_64-binaries/seqIOCTF.o ztr/linux-x86_64-binaries/compression.o ztr/linux-x86_64-binaries/ztr_trans
late.o ztr/linux-x86_64-binaries/ztr.o sff/linux-x86_64-binaries/sff.o -lz -lmisc -L/usr/lib64 -lcurl -L/usr
/kerberos/lib -L/usr/kerberos/lib64 -lssl -lcrypto -lgssapi_krb5 -lkrb5 -lcom_err -lk5crypto -lresolv -ldl -lz -
lgssapi_krb5 -lkrb5 -lk5crypto -lcom_err -lresolv -L/usr/kerberos/lib -L/usr/kerberos/lib64 -lidn -lssl -lcrypto
-lssl -lcrypto -lgssapi_krb5 -lkrb5 -lcom_err -lk5crypto -lresolv -ldl -lz -lz
/usr/bin/ld: ../lib/linux-x86_64-binaries/libz.a(crc32.o): relocation R_X86_64_32 against `a local symbol' can n
ot be used when making a shared object; recompile with -fPIC
../lib/linux-x86_64-binaries/libz.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
make: *** [../lib/linux-x86_64-binaries/libread.so] Error 1
make: Leaving directory `/usr/local/staden/staden-src-1-7-0/src/io_lib'
make: *** [io_lib] Error 2
make: Leaving directory `/usr/local/staden/staden-src-1-7-0/src'
make: *** [all] Error 2
# I am going to send you an email with an attachment of 'make.out' file in addition to the above same text. Is the email address 'firstname.lastname@example.org' working?? Do you mind sending your reply to email@example.com also? THank you very much!
I got the exact same problem on my x86_64 system. Did you solve yours?
... I solved the problem you had using the following procedure:
The problem is indeed the compiled libz.a . To recompile that piece using the -fPIC compiler option solves the problem. How to do this:
1. go into the directory <wherever_you_inst_it>/src/zlib (zlib should be a symlink to zlib-1.2.2)
2. do a "make clean"
3. edit Makefile and change the following line
CFLAGS=-O3 -DUSE_MMAP -fPIC
4. run "make" - it should compile the zlib.a file
5. cp the zlib.a file to ../lib/linux-x86_64-binaries/libz.a
6. cd to <wherever_you_inst_it>/src and do a "make -f Makefile.thirdparty" again
... I encounter in another problem after that:
the wrong(32bit) libX was uses in linking stuff in tk_utils. To prevent that problem you will have to edit the <wherever_you_inst_it>/src/mk/linux-x86_64.mk file.
Change the line:
XBIN = /usr/X11R6/lib
XBIN = /usr/X11R6/lib64 (or wherever X11 is installed)
This was on my RHEL Linux - but should be the same on Fedora for instance ...
Doing again a "make -f Makefile.thirdparty" should now compile the rest of the Staden package ...
... hope this will help you a bit ... I posted it also to the bio.net list ...
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