[Dock-fans] DOCK 6 installation -reg

John J. Irwin jji at cgl.ucsf.edu
Thu May 10 08:54:26 PDT 2007


Hi -

Are you really using RedHat 4.2?
I suggest you upgrade to a more recent version. We use Fedora Core 4, 5
or 6.

Good luck!

John


Abdul Hameed, MohamedDiwanMo wrote:
>
> Hello all,
>
>  
>
> I am trying to install DOCK 6 on Linux (redhat 4.2).
>
>  
>
> Initially I had problems with flex and yacc. But after installing flex
> and bison, I am able to complete the installation of dock.
>
>  
>
> During the installation process I am getting the warning message
> (given below), particularly about an incompatible pointer type.
>
> Can we ignore this warning?
>
> Is there any particular reason to get this warning message? If someone
> can suggest why we get this, it will be very helpful.
>
>  
>
> / ar: creating nab.a /
>
> / In file included from
> /usr/lib/gcc/i386-redhat-linux/3.4.4/../../../../include/c++/3.4.4/backward/strstream:51,
> /
>
> /                  from sphere_selector.cpp:7: /
>
> /
> /usr/lib/gcc/i386-redhat-linux/3.4.4/../../../../include/c++/3.4.4/backward/backward_warning.h:32:2:
> warning: #warning This file includes at least one deprecated or
> antiquated header. Please consider using one of the 32 headers found
> in section 17.4.1.2 of the C++ standard. Examples include substituting
> the <X> header for the <X.h> header for C++ includes, or <iostream>
> instead of the deprecated header <iostream.h>. To disable this warning
> use -Wno-deprecated. /
>
> / residue.c: In function `ResidueConnect': /
>
> / residue.c:336: warning: passing arg 1 of `AtomBondTo' from
> incompatible pointer type /
>
> / residue.c:336: warning: passing arg 2 of `AtomBondTo' from
> incompatible pointer type /
>
> / residue.c: In function `ResidueMutate': /
>
> / residue.c:464: warning: passing arg 1 of `BuildFixInternals' from
> incompatible pointer type /
>
> / unitio.c: In function `zUnitIOSaveAmberParmFormat': /
>
> / unitio.c:4047: warning: passing arg 1 of `SortByInteger' from
> incompatible pointer type /
>
> / unitio.c:4047: warning: passing arg 4 of `SortByInteger' from
> incompatible pointer type /
>
> / unitio.c: In function `zUnitIOSaveAmberParmFormat_old': /
>
> / unitio.c:6055: warning: passing arg 1 of `SortByInteger' from
> incompatible pointer type /
>
> / unitio.c:6055: warning: passing arg 4 of `SortByInteger' from
> incompatible pointer type /
>
> / graphUtil.c: In function `GraphUtilFindAllSmallestRingsAndRingGroups': /
>
> / graphUtil.c:675: warning: passing arg 1 of `SortByInteger' from
> incompatible pointer type /
>
> / graphUtil.c:675: warning: passing arg 4 of `SortByInteger' from
> incompatible pointer type /
>
> / amber.c: In function `uAmberReadUnitFromPrep': /
>
> / amber.c:986: warning: passing arg 1 of `SortByInteger' from
> incompatible pointer type /
>
> / amber.c:986: warning: passing arg 4 of `SortByInteger' from
> incompatible pointer type /
>
> / build.c: In function `bBuildFlipChiralityFor': /
>
> / build.c:1901: warning: passing arg 1 of `SortByInteger' from
> incompatible pointer type /
>
> / build.c:1901: warning: passing arg 4 of `SortByInteger' from
> incompatible pointer type /
>
> / build.c:1907: warning: passing arg 1 of
> `GraphUtilFindAllSmallestRings' from incompatible pointer type /
>
> / build.c: In function `BuildInternalsForSimpleRings': /
>
> / build.c:2185: warning: passing arg 1 of
> `GraphUtilFindAllSmallestRingsAndRingGroups' from incompatible pointer
> type /
>
> / model.c: In function `zModelOrderAtoms': /
>
> / model.c:497: warning: passing arg 1 of `Sift' from incompatible
> pointer type /
>
> / pdbFile.c: In function `zPdbBuildCoordinatesForContainer': /
>
> / pdbFile.c:1088: warning: passing arg 1 of `BuildFixInternals' from
> incompatible pointer type /
>
> / pdbFile.c: In function `zPdbAddAtom': /
>
> / pdbFile.c:1207: warning: passing arg 1 of
> `BuildInternalsForContainer' from incompatible pointer type /
>
> / pdbFile.c: In function `writeTER': /
>
> / pdbFile.c:1761: warning: initialization from incompatible pointer type /
>
> / tools.c: In function `iToolDistanceSearch': /
>
> / tools.c:1643: warning: passing arg 1 of `SortByDouble' from
> incompatible pointer type /
>
> / tools.c:1643: warning: passing arg 4 of `SortByDouble' from
> incompatible pointer type /
>
> / tools.c: In function `ToolOrientPrincipleAxisAlongCoordinateAxis': /
>
> / tools.c:1714: warning: passing arg 2 of `MathOpDiagonalize' from
> incompatible pointer type /
>
> / conflicts: 6 shift/reduce /
>
> / commands.c: In function `oCmd_impose': /
>
> / commands.c:3835: warning: passing arg 1 of
> `bBuildChangeInternalBond' from incompatible pointer type /
>
> / commands.c:3859: warning: passing arg 1 of
> `bBuildChangeInternalAngle' from incompatible pointer type /
>
> / commands.c:3885: warning: passing arg 1 of
> `bBuildChangeInternalTorsion' from incompatible pointer type /
>
> /   /
>
> Thank you,
>
> Mohamed Diwan
>
> Graduate student
>
> University of Kentucky
>
>  
>
> ------------------------------------------------------------------------
>
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>   


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