On Wed, Feb 17, 2010 at 5:44 PM, David A. Case <case.biomaps.rutgers.edu> wrote:
> On Wed, Feb 17, 2010, Lachele Foley wrote:
>
>> During the install of AmberTools (from CVS last night), I got complaints
>> that claim to be warnings, but include the word "fail". Then I got
>> the same complaints during the testing phase, despite declarations of
>> passing. Is ok? Not ok?
>
> Not to worry. These will probably go away if you in the the "-static" flag to
> configure.
I had a problem trying to use the -static flag (Ubuntu
Linux/x86_64/intel 11.0.083 compilers) when trying to compile
ambertools. Removing the -static flag let it finish just fine. The
error came during the linking stage of xaleap (i think):
icc -static -o xaLeap basics.o sysdepend.o stringExtra.o varArray.o
getline.o avl.o pdb_format.o pdb_read.o pdb_sprntf.o pdb_sscanf.o
pdb_write.o vector.o zMatrix.o sort.o bag.o hash.o dictionary.o
database.o nVector.o ring.o matrix.o fortran.o displayer.o assoc.o
atom.o byteArray.o collection.o container.o internal.o list.o loop.o
molecule.o oDouble.o oInteger.o oString.o objekt.o parmSet.o
residue.o unit.o unitio.o tripos.o graphUtil.o select.o amber.o
build.o elements.o library.o chirality.o minimizer.o model.o parmLib.o
pdbFile.o mol2File.o tools.o variables.o parser.o help.o helptext.o
octree.o commands.o mathop.o block.o restraint.o hybrid.o xTank.o
xAction.o x3d.o xBasics.o xaLeapc.o xaUnitEditor.o xaTable.o
xaAtomTable.o XrawRegistr.o xaCommand.o xaTools.o xaAtomParmTable.o
xaBondParmTable.o xaAngleParmTable.o xaParmEditor.o
xaTorsionParmTable.o xaImproperParmTable.o xaHBondParmTable.o
../Xraw/libXaw.a ../Wc/libWcLeap.a ../Xpm/libXpm.a ../Xmu/libXmu.a
-L/usr/X11R6/lib64 -L/usr/X11R6/lib -lXt -lXext -lSM -lICE -lX11 -lXau
-lXdmcp -lm -lpthread
../Xraw/libXaw.a(AsciiSrc.o): In function `SetValues':
AsciiSrc.c:(.text+0x7b4): warning: the use of `tmpnam' is dangerous,
better use `mkstemp'
basics.o: In function `fBasicsMyFopen':
basics.c:(.text+0xb90): warning: Using 'getpwnam' in statically linked
applications requires at runtime the shared libraries from the glibc
version used for linking
../Wc/libWcLeap.a(WcLoadRes.o): In function `WcLoadResourceFile':
WcLoadRes.c:(.text+0x301): warning: Using 'getpwuid' in statically
linked applications requires at runtime the shared libraries from the
glibc version used for linking
/usr/lib/gcc/x86_64-linux-gnu/4.3.3/../../../../lib64/libXt.a(Initialize.o):
In function `GetRootDirName':
(.text+0x26f): warning: Using 'getpwnam_r' in statically linked
applications requires at runtime the shared libraries from the glibc
version used for linking
/usr/lib/gcc/x86_64-linux-gnu/4.3.3/../../../../lib64/libXt.a(Initialize.o):
In function `GetRootDirName':
(.text+0x2c0): warning: Using 'getpwuid_r' in statically linked
applications requires at runtime the shared libraries from the glibc
version used for linking
/usr/lib/gcc/x86_64-linux-gnu/4.3.3/../../../../lib64/libICE.a(icetrans.o):
In function `_IceTransSocketOpen':
(.text+0x1431): warning: Using 'getaddrinfo' in statically linked
applications requires at runtime the shared libraries from the glibc
version used for linking
/usr/lib/gcc/x86_64-linux-gnu/4.3.3/../../../../lib64/libICE.a(icetrans.o):
In function `_IceTransGetPeerNetworkId':
(.text+0x2510): warning: Using 'gethostbyaddr' in statically linked
applications requires at runtime the shared libraries from the glibc
version used for linking
/usr/lib/gcc/x86_64-linux-gnu/4.3.3/../../../../lib64/libICE.a(icetrans.o):
In function `_IceTransSocketUNIXConnect':
(.text+0x274b): warning: Using 'gethostbyname' in statically linked
applications requires at runtime the shared libraries from the glibc
version used for linking
/usr/lib/gcc/x86_64-linux-gnu/4.3.3/../../../../lib64/libICE.a(icetrans.o):
In function `_IceTransSocketINETConnect':
(.text+0x2d1f): warning: Using 'getservbyname' in statically linked
applications requires at runtime the shared libraries from the glibc
version used for linking
/usr/lib/gcc/x86_64-linux-gnu/4.3.3/../../../../lib64/libX11.a(CrGlCur.o):
In function `open_library':
(.text+0x2a): warning: Using 'dlopen' in statically linked
applications requires at runtime the shared libraries from the glibc
version used for linking
/usr/lib/gcc/x86_64-linux-gnu/4.3.3/../../../../lib64/libX11.a(ClDisplay.o):
In function `XCloseDisplay':
(.text+0xc5): undefined reference to `xcb_disconnect'
/usr/lib/gcc/x86_64-linux-gnu/4.3.3/../../../../lib64/libX11.a(OpenDis.o):
In function `OutOfMemory':
(.text+0x434): undefined reference to `xcb_disconnect'
/usr/lib/gcc/x86_64-linux-gnu/4.3.3/../../../../lib64/libX11.a(OpenDis.o):
In function `XOpenDisplay':
(.text+0x865): undefined reference to `xcb_get_setup'
/usr/lib/gcc/x86_64-linux-gnu/4.3.3/../../../../lib64/libX11.a(OpenDis.o):
In function `XOpenDisplay':
(.text+0xe59): undefined reference to `xcb_get_maximum_request_length'
/usr/lib/gcc/x86_64-linux-gnu/4.3.3/../../../../lib64/libX11.a(xcb_disp.o):
In function `_XConnectXCB':
(.text+0xb4): undefined reference to `xcb_parse_display'
/usr/lib/gcc/x86_64-linux-gnu/4.3.3/../../../../lib64/libX11.a(xcb_disp.o):
In function `_XConnectXCB':
(.text+0x188): undefined reference to `xcb_connect_to_display_with_auth_info'
/usr/lib/gcc/x86_64-linux-gnu/4.3.3/../../../../lib64/libX11.a(xcb_disp.o):
In function `_XConnectXCB':
(.text+0x1a8): undefined reference to `xcb_get_file_descriptor'
/usr/lib/gcc/x86_64-linux-gnu/4.3.3/../../../../lib64/libX11.a(xcb_disp.o):
In function `_XConnectXCB':
(.text+0x1d3): undefined reference to `xcb_generate_id'
/usr/lib/gcc/x86_64-linux-gnu/4.3.3/../../../../lib64/libX11.a(xcb_disp.o):
In function `_XConnectXCB':
(.text+0x211): undefined reference to `xcb_connection_has_error'
/usr/lib/gcc/x86_64-linux-gnu/4.3.3/../../../../lib64/libX11.a(xcb_disp.o):
In function `_XConnectXCB':
(.text+0x22e): undefined reference to `xcb_connect'
/usr/lib/gcc/x86_64-linux-gnu/4.3.3/../../../../lib64/libX11.a(xcb_io.o):
In function `require_socket':
(.text+0x351): undefined reference to `xcb_take_socket'
/usr/lib/gcc/x86_64-linux-gnu/4.3.3/../../../../lib64/libX11.a(xcb_io.o):
In function `wait_or_poll_for_event':
(.text+0x424): undefined reference to `xcb_wait_for_event'
/usr/lib/gcc/x86_64-linux-gnu/4.3.3/../../../../lib64/libX11.a(xcb_io.o):
In function `process_responses':
(.text+0x59c): undefined reference to `xcb_poll_for_reply'
/usr/lib/gcc/x86_64-linux-gnu/4.3.3/../../../../lib64/libX11.a(xcb_io.o):
In function `process_responses':
(.text+0x6b0): undefined reference to `xcb_connection_has_error'
/usr/lib/gcc/x86_64-linux-gnu/4.3.3/../../../../lib64/libX11.a(xcb_io.o):
In function `_XAllocIDs':
(.text+0x877): undefined reference to `xcb_generate_id'
/usr/lib/gcc/x86_64-linux-gnu/4.3.3/../../../../lib64/libX11.a(xcb_io.o):
In function `_XIDHandler':
(.text+0x904): undefined reference to `xcb_generate_id'
/usr/lib/gcc/x86_64-linux-gnu/4.3.3/../../../../lib64/libX11.a(xcb_io.o):
In function `_XSend':
(.text+0xb4b): undefined reference to `xcb_writev'
/usr/lib/gcc/x86_64-linux-gnu/4.3.3/../../../../lib64/libX11.a(xcb_io.o):
In function `_XReply':
(.text+0xd28): undefined reference to `xcb_wait_for_reply'
/usr/lib/gcc/x86_64-linux-gnu/4.3.3/../../../../lib64/libX11.a(xcb_io.o):
In function `wait_or_poll_for_event':
(.text+0x4ab): undefined reference to `xcb_poll_for_event'
make[3]: *** [xaLeap] Error 1
make[3]: Leaving directory
`/home/swails/newamber/02.16.10/amber11/src/leap/src/leap'
make[2]: *** [install_xleap] Error 2
make[2]: Leaving directory `/home/swails/newamber/02.16.10/amber11/src/leap'
make[1]: *** [install] Error 2
make[1]: Leaving directory `/home/swails/newamber/02.16.10/amber11/src/leap'
make: *** [serial] Error 2
Is this something I should already know about? Perhaps a problem with
how X was built on my system? Does anyone else get this error?
Thanks!
Jason
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Feb 17 2010 - 15:30:04 PST
