[Staden] Fwd: Error during installing Staden-src-1-7-0 package

Jean Mao via staden%40net.bio.net (by maoj At helix.nih.gov)
Tue Feb 6 15:43:46 EST 2007


Hi, I have problem compiling the package and here are what I have done. Any
help will be appreciated:

# first compile all the libraries
cd /usr/local/staden/staden-src-1-7-0
export STADENROOT=`pwd`
. staden.profile
cd src
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:

rm /usr/local/staden/staden-src-1-7-0/lib/iwidgets
make -f Makefile.rhirdparty

# at this point everything seems to be fine (but I was just guessing)
# Then I compile the staden package
cd /usr/local/staden/staden-src-1-7-0
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,
                 from sff/linux-x86_64-binaries/../sff.c:26:
include/os.h:131:1: warning: "NEED_VA_COPY" redefined
<command line>:10:1: warning: this is the location of the previous
definition
sff/linux-x86_64-binaries/sff.o
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.outils/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[2]: *** [../lib/linux-x86_64-binaries/libread.so] Error 1
make[2]: Leaving directory `/usr/local/staden/staden-src-1-7-0/src/io_lib'
make[1]: *** [io_lib] Error 2
make[1]: Leaving directory `/usr/local/staden/staden-src-1-7-0/src'
make: *** [all] Error 2

Thank you.
-------------- next part --------------
cd src; make all
make[1]: Entering directory `/usr/local/staden/staden-src-1-7-0/src'
Makefile:75: warning: overriding commands for target `clean'
mk/global.mk:256: warning: ignoring old commands for target `clean'
Makefile:90: warning: overriding commands for target `depend'
mk/global.mk:515: warning: ignoring old commands for target `depend'
Makefile:144: warning: overriding commands for target `distsrc'
mk/global.mk:494: warning: ignoring old commands for target `distsrc'
cd Misc && make  -w all
make[2]: Entering directory `/usr/local/staden/staden-src-1-7-0/src/Misc'
touch linux-x86_64-binaries/.dir
gcc -g -DUSE_NON_CONST  -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -o linux-x86_64-binaries/crash.o -c crash.c
In file included from misc.h:8,
                 from crash.c:1:
os.h:122:1: warning: "NEED_VA_COPY" redefined
<command line>:2:1: warning: this is the location of the previous definition
linux-x86_64-binaries/crash.o
gcc -g -DUSE_NON_CONST  -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -o linux-x86_64-binaries/date.o -c date.c
In file included from misc.h:8,
                 from date.c:1:
os.h:122:1: warning: "NEED_VA_COPY" redefined
<command line>:2:1: warning: this is the location of the previous definition
linux-x86_64-binaries/date.o
gcc -g -DUSE_NON_CONST  -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -o linux-x86_64-binaries/filenames.o -c filenames.c
In file included from misc.h:8,
                 from filenames.c:1:
os.h:122:1: warning: "NEED_VA_COPY" redefined
<command line>:2:1: warning: this is the location of the previous definition
linux-x86_64-binaries/filenames.o
gcc -g -DUSE_NON_CONST  -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -o linux-x86_64-binaries/files.o -c files.c
In file included from misc.h:8,
                 from files.c:1:
os.h:122:1: warning: "NEED_VA_COPY" redefined
<command line>:2:1: warning: this is the location of the previous definition
linux-x86_64-binaries/files.o
gcc -g -DUSE_NON_CONST  -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -o linux-x86_64-binaries/find.o -c find.c
In file included from misc.h:8,
                 from find.c:15:
os.h:122:1: warning: "NEED_VA_COPY" redefined
<command line>:2:1: warning: this is the location of the previous definition
linux-x86_64-binaries/find.o
gcc -g -DUSE_NON_CONST  -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -o linux-x86_64-binaries/shell.o -c shell.c
In file included from misc.h:8,
                 from shell.c:1:
os.h:122:1: warning: "NEED_VA_COPY" redefined
<command line>:2:1: warning: this is the location of the previous definition
linux-x86_64-binaries/shell.o
gcc -g -DUSE_NON_CONST  -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -o linux-x86_64-binaries/strings.o -c strings.c
In file included from misc.h:8,
                 from strings.c:1:
os.h:122:1: warning: "NEED_VA_COPY" redefined
<command line>:2:1: warning: this is the location of the previous definition
linux-x86_64-binaries/strings.o
gcc -g -DUSE_NON_CONST  -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -o linux-x86_64-binaries/usleep.o -c usleep.c
linux-x86_64-binaries/usleep.o
gcc -g -DUSE_NON_CONST  -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -o linux-x86_64-binaries/error.o -c error.c
linux-x86_64-binaries/error.o
gcc -g -DUSE_NON_CONST  -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -o linux-x86_64-binaries/xerror.o -c xerror.c
In file included from misc.h:8,
                 from xerror.c:16:
os.h:122:1: warning: "NEED_VA_COPY" redefined
<command line>:2:1: warning: this is the location of the previous definition
linux-x86_64-binaries/xerror.o
gcc -g -DUSE_NON_CONST  -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -o linux-x86_64-binaries/xalloc.o -c xalloc.c
linux-x86_64-binaries/xalloc.o
gcc -g -DUSE_NON_CONST  -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -o linux-x86_64-binaries/vlen.o -c vlen.c
linux-x86_64-binaries/vlen.o
gcc -g -DUSE_NON_CONST  -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -o linux-x86_64-binaries/FtoC.o -c FtoC.c
In file included from FtoC.c:1:
os.h:122:1: warning: "NEED_VA_COPY" redefined
<command line>:2:1: warning: this is the location of the previous definition
linux-x86_64-binaries/FtoC.o
gcc -g -DUSE_NON_CONST  -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -o linux-x86_64-binaries/getfile.o -c getfile.c
In file included from misc.h:8,
                 from getfile.c:9:
os.h:122:1: warning: "NEED_VA_COPY" redefined
<command line>:2:1: warning: this is the location of the previous definition
linux-x86_64-binaries/getfile.o
gcc -g -DUSE_NON_CONST  -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -o linux-x86_64-binaries/bitmap.o -c bitmap.c
In file included from bitmap.h:20,
                 from bitmap.c:19:
os.h:122:1: warning: "NEED_VA_COPY" redefined
<command line>:2:1: warning: this is the location of the previous definition
linux-x86_64-binaries/bitmap.o
gcc -g -DUSE_NON_CONST  -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -o linux-x86_64-binaries/array.o -c array.c
linux-x86_64-binaries/array.o
gcc -g -DUSE_NON_CONST  -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -o linux-x86_64-binaries/locks.o -c locks.c
linux-x86_64-binaries/locks.o
gcc -g -DUSE_NON_CONST  -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -o linux-x86_64-binaries/array_arith.o -c array_arith.c
In file included from misc.h:8,
                 from array_arith.c:5:
os.h:122:1: warning: "NEED_VA_COPY" redefined
<command line>:2:1: warning: this is the location of the previous definition
linux-x86_64-binaries/array_arith.o
gcc -g -DUSE_NON_CONST  -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -o linux-x86_64-binaries/parse_db.o -c parse_db.c
In file included from misc.h:8,
                 from parse_db.c:25:
os.h:122:1: warning: "NEED_VA_COPY" redefined
<command line>:2:1: warning: this is the location of the previous definition
linux-x86_64-binaries/parse_db.o
gcc -g -DUSE_NON_CONST  -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -o linux-x86_64-binaries/dstring.o -c dstring.c
linux-x86_64-binaries/dstring.o
cc -L../lib/linux-x86_64-binaries  -shared -o ../lib/linux-x86_64-binaries/libmisc.so  linux-x86_64-binaries/crash.o linux-x86_64-binaries/date.o linux-x86_64-binaries/filenames.o linux-x86_64-binaries/files.o linux-x86_64-binaries/find.o linux-x86_64-binaries/shell.o linux-x86_64-binaries/strings.o linux-x86_64-binaries/usleep.o linux-x86_64-binaries/error.o linux-x86_64-binaries/xerror.o linux-x86_64-binaries/xalloc.o linux-x86_64-binaries/vlen.o linux-x86_64-binaries/FtoC.o linux-x86_64-binaries/getfile.o linux-x86_64-binaries/bitmap.o linux-x86_64-binaries/array.o linux-x86_64-binaries/locks.o linux-x86_64-binaries/array_arith.o linux-x86_64-binaries/parse_db.o linux-x86_64-binaries/dstring.o     -lm 
make[2]: Leaving directory `/usr/local/staden/staden-src-1-7-0/src/Misc'
cd io_lib && make  -w all
make[2]: Entering directory `/usr/local/staden/staden-src-1-7-0/src/io_lib'
Makefile:172: warning: overriding commands for target `distsrc'
../mk/global.mk:494: warning: ignoring old commands for target `distsrc'
Makefile:202: warning: overriding commands for target `depend'
../mk/global.mk:515: warning: ignoring old commands for target `depend'
cd include; \
for i in abi alf ctf exp_file plain read scf sff utils ztr;	\
do \
    ln -s ../$i/*.h .;\
done
touch include/.links
touch read/linux-x86_64-binaries/.dir
touch utils/linux-x86_64-binaries/.dir
touch abi/linux-x86_64-binaries/.dir
touch alf/linux-x86_64-binaries/.dir
touch ctf/linux-x86_64-binaries/.dir
touch exp_file/linux-x86_64-binaries/.dir
touch plain/linux-x86_64-binaries/.dir
touch progs/linux-x86_64-binaries/.dir
touch scf/linux-x86_64-binaries/.dir
touch ztr/linux-x86_64-binaries/.dir
touch sff/linux-x86_64-binaries/.dir
make[2]: [read/linux-x86_64-binaries/Read.o] Error 1 (ignored)
gcc -g -DUSE_NON_CONST -DIOLIB_SCF -DIOLIB_EXP -DIOLIB_PLN -DIOLIB_ABI -DIOLIB_ALF -DIOLIB_CTF -DIOLIB_ZTR -DIOLIB_SFF -Iinclude -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -I../zlib -DHAVE_LIBCURL -o read/linux-x86_64-binaries/Read.o -c read/linux-x86_64-binaries/../Read.c
In file included from read/linux-x86_64-binaries/../Read.h:43,
                 from read/linux-x86_64-binaries/../Read.c:40:
include/os.h:131:1: warning: "NEED_VA_COPY" redefined
<command line>:10:1: warning: this is the location of the previous definition
read/linux-x86_64-binaries/Read.o
make[2]: [read/linux-x86_64-binaries/translate.o] Error 1 (ignored)
gcc -g -DUSE_NON_CONST -DIOLIB_SCF -DIOLIB_EXP -DIOLIB_PLN -DIOLIB_ABI -DIOLIB_ALF -DIOLIB_CTF -DIOLIB_ZTR -DIOLIB_SFF -Iinclude -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -I../zlib -DHAVE_LIBCURL -o read/linux-x86_64-binaries/translate.o -c read/linux-x86_64-binaries/../translate.c
In file included from include/misc.h:8,
                 from read/linux-x86_64-binaries/../translate.c:28:
include/os.h:131:1: warning: "NEED_VA_COPY" redefined
<command line>:10:1: warning: this is the location of the previous definition
read/linux-x86_64-binaries/translate.o
make[2]: [read/linux-x86_64-binaries/scf_extras.o] Error 1 (ignored)
gcc -g -DUSE_NON_CONST -DIOLIB_SCF -DIOLIB_EXP -DIOLIB_PLN -DIOLIB_ABI -DIOLIB_ALF -DIOLIB_CTF -DIOLIB_ZTR -DIOLIB_SFF -Iinclude -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -I../zlib -DHAVE_LIBCURL -o read/linux-x86_64-binaries/scf_extras.o -c read/linux-x86_64-binaries/../scf_extras.c
In file included from include/misc.h:8,
                 from read/linux-x86_64-binaries/../scf_extras.c:28:
include/os.h:131:1: warning: "NEED_VA_COPY" redefined
<command line>:10:1: warning: this is the location of the previous definition
read/linux-x86_64-binaries/scf_extras.o
make[2]: [utils/linux-x86_64-binaries/find.o] Error 1 (ignored)
gcc -g -DUSE_NON_CONST -DIOLIB_SCF -DIOLIB_EXP -DIOLIB_PLN -DIOLIB_ABI -DIOLIB_ALF -DIOLIB_CTF -DIOLIB_ZTR -DIOLIB_SFF -Iinclude -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -I../zlib -DHAVE_LIBCURL -o utils/linux-x86_64-binaries/find.o -c utils/linux-x86_64-binaries/../find.c
In file included from utils/linux-x86_64-binaries/../misc.h:8,
                 from utils/linux-x86_64-binaries/../find.c:15:
utils/linux-x86_64-binaries/../os.h:131:1: warning: "NEED_VA_COPY" redefined
<command line>:10:1: warning: this is the location of the previous definition
utils/linux-x86_64-binaries/find.o
make[2]: [utils/linux-x86_64-binaries/mach-io.o] Error 1 (ignored)
gcc -g -DUSE_NON_CONST -DIOLIB_SCF -DIOLIB_EXP -DIOLIB_PLN -DIOLIB_ABI -DIOLIB_ALF -DIOLIB_CTF -DIOLIB_ZTR -DIOLIB_SFF -Iinclude -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -I../zlib -DHAVE_LIBCURL -o utils/linux-x86_64-binaries/mach-io.o -c utils/linux-x86_64-binaries/../mach-io.c
In file included from utils/linux-x86_64-binaries/../mach-io.h:41,
                 from utils/linux-x86_64-binaries/../mach-io.c:44:
utils/linux-x86_64-binaries/../os.h:131:1: warning: "NEED_VA_COPY" redefined
<command line>:10:1: warning: this is the location of the previous definition
utils/linux-x86_64-binaries/mach-io.o
make[2]: [utils/linux-x86_64-binaries/traceType.o] Error 1 (ignored)
gcc -g -DUSE_NON_CONST -DIOLIB_SCF -DIOLIB_EXP -DIOLIB_PLN -DIOLIB_ABI -DIOLIB_ALF -DIOLIB_CTF -DIOLIB_ZTR -DIOLIB_SFF -Iinclude -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -I../zlib -DHAVE_LIBCURL -o utils/linux-x86_64-binaries/traceType.o -c utils/linux-x86_64-binaries/../traceType.c
In file included from include/Read.h:43,
                 from utils/linux-x86_64-binaries/../traceType.h:34,
                 from utils/linux-x86_64-binaries/../traceType.c:34:
include/os.h:131:1: warning: "NEED_VA_COPY" redefined
<command line>:10:1: warning: this is the location of the previous definition
utils/linux-x86_64-binaries/traceType.o
make[2]: [utils/linux-x86_64-binaries/read_alloc.o] Error 1 (ignored)
gcc -g -DUSE_NON_CONST -DIOLIB_SCF -DIOLIB_EXP -DIOLIB_PLN -DIOLIB_ABI -DIOLIB_ALF -DIOLIB_CTF -DIOLIB_ZTR -DIOLIB_SFF -Iinclude -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -I../zlib -DHAVE_LIBCURL -o utils/linux-x86_64-binaries/read_alloc.o -c utils/linux-x86_64-binaries/../read_alloc.c
In file included from utils/linux-x86_64-binaries/../misc.h:8,
                 from utils/linux-x86_64-binaries/../read_alloc.c:39:
utils/linux-x86_64-binaries/../os.h:131:1: warning: "NEED_VA_COPY" redefined
<command line>:10:1: warning: this is the location of the previous definition
utils/linux-x86_64-binaries/read_alloc.o
make[2]: [utils/linux-x86_64-binaries/compress.o] Error 1 (ignored)
gcc -g -DUSE_NON_CONST -DIOLIB_SCF -DIOLIB_EXP -DIOLIB_PLN -DIOLIB_ABI -DIOLIB_ALF -DIOLIB_CTF -DIOLIB_ZTR -DIOLIB_SFF -Iinclude -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -I../zlib -DHAVE_LIBCURL -o utils/linux-x86_64-binaries/compress.o -c utils/linux-x86_64-binaries/../compress.c
In file included from utils/linux-x86_64-binaries/../compress.c:36:
utils/linux-x86_64-binaries/../os.h:131:1: warning: "NEED_VA_COPY" redefined
<command line>:10:1: warning: this is the location of the previous definition
utils/linux-x86_64-binaries/compress.o
make[2]: [utils/linux-x86_64-binaries/open_trace_file.o] Error 1 (ignored)
gcc -g -DUSE_NON_CONST -DIOLIB_SCF -DIOLIB_EXP -DIOLIB_PLN -DIOLIB_ABI -DIOLIB_ALF -DIOLIB_CTF -DIOLIB_ZTR -DIOLIB_SFF -Iinclude -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -I../zlib -DHAVE_LIBCURL -o utils/linux-x86_64-binaries/open_trace_file.o -c utils/linux-x86_64-binaries/../open_trace_file.c
In file included from utils/linux-x86_64-binaries/../open_trace_file.c:18:
utils/linux-x86_64-binaries/../os.h:131:1: warning: "NEED_VA_COPY" redefined
<command line>:10:1: warning: this is the location of the previous definition
utils/linux-x86_64-binaries/open_trace_file.o
make[2]: [utils/linux-x86_64-binaries/hash_table.o] Error 1 (ignored)
gcc -g -DUSE_NON_CONST -DIOLIB_SCF -DIOLIB_EXP -DIOLIB_PLN -DIOLIB_ABI -DIOLIB_ALF -DIOLIB_CTF -DIOLIB_ZTR -DIOLIB_SFF -Iinclude -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -I../zlib -DHAVE_LIBCURL -o utils/linux-x86_64-binaries/hash_table.o -c utils/linux-x86_64-binaries/../hash_table.c
In file included from utils/linux-x86_64-binaries/../hash_table.c:4:
utils/linux-x86_64-binaries/../os.h:131:1: warning: "NEED_VA_COPY" redefined
<command line>:10:1: warning: this is the location of the previous definition
utils/linux-x86_64-binaries/hash_table.o
make[2]: [utils/linux-x86_64-binaries/mFILE.o] Error 1 (ignored)
gcc -g -DUSE_NON_CONST -DIOLIB_SCF -DIOLIB_EXP -DIOLIB_PLN -DIOLIB_ABI -DIOLIB_ALF -DIOLIB_CTF -DIOLIB_ZTR -DIOLIB_SFF -Iinclude -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -I../zlib -DHAVE_LIBCURL -o utils/linux-x86_64-binaries/mFILE.o -c utils/linux-x86_64-binaries/../mFILE.c
In file included from utils/linux-x86_64-binaries/../mFILE.c:11:
utils/linux-x86_64-binaries/../os.h:131:1: warning: "NEED_VA_COPY" redefined
<command line>:10:1: warning: this is the location of the previous definition
utils/linux-x86_64-binaries/mFILE.o
make[2]: [utils/linux-x86_64-binaries/vlen.o] Error 1 (ignored)
gcc -g -DUSE_NON_CONST -DIOLIB_SCF -DIOLIB_EXP -DIOLIB_PLN -DIOLIB_ABI -DIOLIB_ALF -DIOLIB_CTF -DIOLIB_ZTR -DIOLIB_SFF -Iinclude -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -I../zlib -DHAVE_LIBCURL -o utils/linux-x86_64-binaries/vlen.o -c utils/linux-x86_64-binaries/../vlen.c
utils/linux-x86_64-binaries/vlen.o
make[2]: [scf/linux-x86_64-binaries/read_scf.o] Error 1 (ignored)
gcc -g -DUSE_NON_CONST -DIOLIB_SCF -DIOLIB_EXP -DIOLIB_PLN -DIOLIB_ABI -DIOLIB_ALF -DIOLIB_CTF -DIOLIB_ZTR -DIOLIB_SFF -Iinclude -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -I../zlib -DHAVE_LIBCURL -o scf/linux-x86_64-binaries/read_scf.o -c scf/linux-x86_64-binaries/../read_scf.c
In file included from scf/linux-x86_64-binaries/../scf.h:32,
                 from scf/linux-x86_64-binaries/../read_scf.c:39:
include/os.h:131:1: warning: "NEED_VA_COPY" redefined
<command line>:10:1: warning: this is the location of the previous definition
scf/linux-x86_64-binaries/read_scf.o
make[2]: [scf/linux-x86_64-binaries/write_scf.o] Error 1 (ignored)
gcc -g -DUSE_NON_CONST -DIOLIB_SCF -DIOLIB_EXP -DIOLIB_PLN -DIOLIB_ABI -DIOLIB_ALF -DIOLIB_CTF -DIOLIB_ZTR -DIOLIB_SFF -Iinclude -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -I../zlib -DHAVE_LIBCURL -o scf/linux-x86_64-binaries/write_scf.o -c scf/linux-x86_64-binaries/../write_scf.c
In file included from scf/linux-x86_64-binaries/../scf.h:32,
                 from scf/linux-x86_64-binaries/../write_scf.c:56:
include/os.h:131:1: warning: "NEED_VA_COPY" redefined
<command line>:10:1: warning: this is the location of the previous definition
scf/linux-x86_64-binaries/write_scf.o
make[2]: [scf/linux-x86_64-binaries/misc_scf.o] Error 1 (ignored)
gcc -g -DUSE_NON_CONST -DIOLIB_SCF -DIOLIB_EXP -DIOLIB_PLN -DIOLIB_ABI -DIOLIB_ALF -DIOLIB_CTF -DIOLIB_ZTR -DIOLIB_SFF -Iinclude -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -I../zlib -DHAVE_LIBCURL -o scf/linux-x86_64-binaries/misc_scf.o -c scf/linux-x86_64-binaries/../misc_scf.c
In file included from scf/linux-x86_64-binaries/../scf.h:32,
                 from scf/linux-x86_64-binaries/../misc_scf.c:29:
include/os.h:131:1: warning: "NEED_VA_COPY" redefined
<command line>:10:1: warning: this is the location of the previous definition
scf/linux-x86_64-binaries/misc_scf.o
make[2]: [exp_file/linux-x86_64-binaries/expFileIO.o] Error 1 (ignored)
gcc -g -DUSE_NON_CONST -DIOLIB_SCF -DIOLIB_EXP -DIOLIB_PLN -DIOLIB_ABI -DIOLIB_ALF -DIOLIB_CTF -DIOLIB_ZTR -DIOLIB_SFF -Iinclude -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -I../zlib -DHAVE_LIBCURL -o exp_file/linux-x86_64-binaries/expFileIO.o -c exp_file/linux-x86_64-binaries/../expFileIO.c
In file included from exp_file/linux-x86_64-binaries/../expFileIO.h:33,
                 from exp_file/linux-x86_64-binaries/../expFileIO.c:71:
include/os.h:131:1: warning: "NEED_VA_COPY" redefined
<command line>:10:1: warning: this is the location of the previous definition
exp_file/linux-x86_64-binaries/expFileIO.o
make[2]: [plain/linux-x86_64-binaries/seqIOPlain.o] Error 1 (ignored)
gcc -g -DUSE_NON_CONST -DIOLIB_SCF -DIOLIB_EXP -DIOLIB_PLN -DIOLIB_ABI -DIOLIB_ALF -DIOLIB_CTF -DIOLIB_ZTR -DIOLIB_SFF -Iinclude -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -I../zlib -DHAVE_LIBCURL -o plain/linux-x86_64-binaries/seqIOPlain.o -c plain/linux-x86_64-binaries/../seqIOPlain.c
In file included from include/misc.h:8,
                 from plain/linux-x86_64-binaries/../seqIOPlain.c:55:
include/os.h:131:1: warning: "NEED_VA_COPY" redefined
<command line>:10:1: warning: this is the location of the previous definition
plain/linux-x86_64-binaries/seqIOPlain.o
make[2]: [abi/linux-x86_64-binaries/fpoint.o] Error 1 (ignored)
gcc -g -DUSE_NON_CONST -DIOLIB_SCF -DIOLIB_EXP -DIOLIB_PLN -DIOLIB_ABI -DIOLIB_ALF -DIOLIB_CTF -DIOLIB_ZTR -DIOLIB_SFF -Iinclude -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -I../zlib -DHAVE_LIBCURL -o abi/linux-x86_64-binaries/fpoint.o -c abi/linux-x86_64-binaries/../fpoint.c
abi/linux-x86_64-binaries/fpoint.o
make[2]: [abi/linux-x86_64-binaries/seqIOABI.o] Error 1 (ignored)
gcc -g -DUSE_NON_CONST -DIOLIB_SCF -DIOLIB_EXP -DIOLIB_PLN -DIOLIB_ABI -DIOLIB_ALF -DIOLIB_CTF -DIOLIB_ZTR -DIOLIB_SFF -Iinclude -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -I../zlib -DHAVE_LIBCURL -o abi/linux-x86_64-binaries/seqIOABI.o -c abi/linux-x86_64-binaries/../seqIOABI.c
In file included from abi/linux-x86_64-binaries/../seqIOABI.h:19,
                 from abi/linux-x86_64-binaries/../seqIOABI.c:87:
include/os.h:131:1: warning: "NEED_VA_COPY" redefined
<command line>:10:1: warning: this is the location of the previous definition
abi/linux-x86_64-binaries/seqIOABI.o
make[2]: [alf/linux-x86_64-binaries/seqIOALF.o] Error 1 (ignored)
gcc -g -DUSE_NON_CONST -DIOLIB_SCF -DIOLIB_EXP -DIOLIB_PLN -DIOLIB_ABI -DIOLIB_ALF -DIOLIB_CTF -DIOLIB_ZTR -DIOLIB_SFF -Iinclude -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -I../zlib -DHAVE_LIBCURL -o alf/linux-x86_64-binaries/seqIOALF.o -c alf/linux-x86_64-binaries/../seqIOALF.c
In file included from include/Read.h:43,
                 from alf/linux-x86_64-binaries/../seqIOALF.c:82:
include/os.h:131:1: warning: "NEED_VA_COPY" redefined
<command line>:10:1: warning: this is the location of the previous definition
alf/linux-x86_64-binaries/seqIOALF.o
make[2]: [ctf/linux-x86_64-binaries/ctfCompress.o] Error 1 (ignored)
gcc -g -DUSE_NON_CONST -DIOLIB_SCF -DIOLIB_EXP -DIOLIB_PLN -DIOLIB_ABI -DIOLIB_ALF -DIOLIB_CTF -DIOLIB_ZTR -DIOLIB_SFF -Iinclude -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -I../zlib -DHAVE_LIBCURL -o ctf/linux-x86_64-binaries/ctfCompress.o -c ctf/linux-x86_64-binaries/../ctfCompress.c
In file included from include/Read.h:43,
                 from ctf/linux-x86_64-binaries/../seqIOCTF.h:4,
                 from ctf/linux-x86_64-binaries/../ctfCompress.c:8:
include/os.h:131:1: warning: "NEED_VA_COPY" redefined
<command line>:10:1: warning: this is the location of the previous definition
ctf/linux-x86_64-binaries/ctfCompress.o
make[2]: [ctf/linux-x86_64-binaries/seqIOCTF.o] Error 1 (ignored)
gcc -g -DUSE_NON_CONST -DIOLIB_SCF -DIOLIB_EXP -DIOLIB_PLN -DIOLIB_ABI -DIOLIB_ALF -DIOLIB_CTF -DIOLIB_ZTR -DIOLIB_SFF -Iinclude -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -I../zlib -DHAVE_LIBCURL -o ctf/linux-x86_64-binaries/seqIOCTF.o -c ctf/linux-x86_64-binaries/../seqIOCTF.c
In file included from include/Read.h:43,
                 from ctf/linux-x86_64-binaries/../seqIOCTF.c:20:
include/os.h:131:1: warning: "NEED_VA_COPY" redefined
<command line>:10:1: warning: this is the location of the previous definition
ctf/linux-x86_64-binaries/seqIOCTF.o
make[2]: [ztr/linux-x86_64-binaries/compression.o] Error 1 (ignored)
gcc -g -DUSE_NON_CONST -DIOLIB_SCF -DIOLIB_EXP -DIOLIB_PLN -DIOLIB_ABI -DIOLIB_ALF -DIOLIB_CTF -DIOLIB_ZTR -DIOLIB_SFF -Iinclude -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -I../zlib -DHAVE_LIBCURL -o ztr/linux-x86_64-binaries/compression.o -c ztr/linux-x86_64-binaries/../compression.c
In file included from include/Read.h:43,
                 from ztr/linux-x86_64-binaries/../ztr.h:4,
                 from ztr/linux-x86_64-binaries/../compression.c:13:
include/os.h:131:1: warning: "NEED_VA_COPY" redefined
<command line>:10:1: warning: this is the location of the previous definition
ztr/linux-x86_64-binaries/compression.o
make[2]: [ztr/linux-x86_64-binaries/ztr_translate.o] Error 1 (ignored)
gcc -g -DUSE_NON_CONST -DIOLIB_SCF -DIOLIB_EXP -DIOLIB_PLN -DIOLIB_ABI -DIOLIB_ALF -DIOLIB_CTF -DIOLIB_ZTR -DIOLIB_SFF -Iinclude -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -I../zlib -DHAVE_LIBCURL -o ztr/linux-x86_64-binaries/ztr_translate.o -c ztr/linux-x86_64-binaries/../ztr_translate.c
In file included from include/Read.h:43,
                 from ztr/linux-x86_64-binaries/../ztr.h:4,
                 from ztr/linux-x86_64-binaries/../ztr_translate.c:4:
include/os.h:131:1: warning: "NEED_VA_COPY" redefined
<command line>:10:1: warning: this is the location of the previous definition
ztr/linux-x86_64-binaries/../ztr_translate.c:128: warning: 'ztr_encode_samples_A' defined but not used
ztr/linux-x86_64-binaries/../ztr_translate.c:134: warning: 'ztr_encode_samples_C' defined but not used
ztr/linux-x86_64-binaries/../ztr_translate.c:140: warning: 'ztr_encode_samples_G' defined but not used
ztr/linux-x86_64-binaries/../ztr_translate.c:146: warning: 'ztr_encode_samples_T' defined but not used
ztr/linux-x86_64-binaries/../ztr_translate.c:293: warning: 'ztr_encode_confidence_1' defined but not used
ztr/linux-x86_64-binaries/ztr_translate.o
make[2]: [ztr/linux-x86_64-binaries/ztr.o] Error 1 (ignored)
gcc -g -DUSE_NON_CONST -DIOLIB_SCF -DIOLIB_EXP -DIOLIB_PLN -DIOLIB_ABI -DIOLIB_ALF -DIOLIB_CTF -DIOLIB_ZTR -DIOLIB_SFF -Iinclude -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -I../zlib -DHAVE_LIBCURL -o ztr/linux-x86_64-binaries/ztr.o -c ztr/linux-x86_64-binaries/../ztr.c
In file included from include/Read.h:43,
                 from ztr/linux-x86_64-binaries/../ztr.h:4,
                 from ztr/linux-x86_64-binaries/../ztr.c:7:
include/os.h:131:1: warning: "NEED_VA_COPY" redefined
<command line>:10:1: warning: this is the location of the previous definition
ztr/linux-x86_64-binaries/ztr.o
make[2]: [sff/linux-x86_64-binaries/sff.o] Error 1 (ignored)
gcc -g -DUSE_NON_CONST -DIOLIB_SCF -DIOLIB_EXP -DIOLIB_PLN -DIOLIB_ABI -DIOLIB_ALF -DIOLIB_CTF -DIOLIB_ZTR -DIOLIB_SFF -Iinclude -I. -I../Misc  -Wimplicit -Wreturn-type -Wunused -Wswitch -Wcomment -Wformat -Wstrict-prototypes -DNEED_VA_COPY=1 -D_FILE_OFFSET_BITS=64 -fPIC  -I../zlib -DHAVE_LIBCURL -o sff/linux-x86_64-binaries/sff.o -c sff/linux-x86_64-binaries/../sff.c
In file included from include/Read.h:43,
                 from sff/linux-x86_64-binaries/../sff.c:26:
include/os.h:131:1: warning: "NEED_VA_COPY" redefined
<command line>:10:1: warning: this is the location of the previous definition
sff/linux-x86_64-binaries/sff.o
cc -L../lib/linux-x86_64-binaries  -shared -o ../lib/linux-x86_64-binaries/libread.so  read/linux-x86_64-binaries/Read.o read/linux-x86_64-binaries/translate.o read/linux-x86_64-binaries/scf_extras.o utils/linux-x86_64-binaries/find.o utils/linux-x86_64-binaries/mach-io.o utils/linux-x86_64-binaries/traceType.o utils/linux-x86_64-binaries/read_alloc.o utils/linux-x86_64-binaries/compress.o utils/linux-x86_64-binaries/open_trace_file.o utils/linux-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 abi/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_translate.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 not 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[2]: *** [../lib/linux-x86_64-binaries/libread.so] Error 1
make[2]: Leaving directory `/usr/local/staden/staden-src-1-7-0/src/io_lib'
make[1]: *** [io_lib] Error 2
make[1]: Leaving directory `/usr/local/staden/staden-src-1-7-0/src'
make: *** [all] Error 2


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