From mike from mwgdna.com Thu Sep 13 10:20:23 2007 From: mike from mwgdna.com (Mike Schilling) Date: Thu Sep 13 22:33:36 2007 Subject: [Staden] Fwd: Error during installing Staden-src-1-7-0 package References: Message-ID: <46E95537.3020302@mwgdna.com> Hallo Jean, .. 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 /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 to: 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 /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 /src/mk/linux-x86_64.mk file. Change the line: XBIN = /usr/X11R6/lib in: 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 ... Greetings Mike [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 :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 :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 :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 :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 :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 :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 :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 :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 :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 :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 :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 :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 :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 :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 :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 :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 :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 :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 :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 :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 :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 :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 :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 :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 :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 :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 :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 :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 :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 :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 :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 :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 :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 :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 :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 :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 :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 :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 -- +--------------------------------------------------------------------+ | Mike Schilling Head IT Eurofins MWG | | Eurofins MWG GmbH voice : int+49 8092 8289303 | | Anzinger Strasse 7, fax : int+49 8092 8289561 | | D-85560 Ebersberg, Germany mobile: int+49 172 8270532 | | email : mschilling@mwgdna.com | | Register No.: HRB 165840 web : http://www.mwgdna.com | | Register Court: Munich | | Chief Operating Officer: Bruno Poddevin, Ph.D. | | Ust-IdNr.: DE200191571 | +--------------------------------------------------------------------+