[Dock-fans] Error during installation

[Scott Brozell]

Hi,

On Mon, 27 Aug 2007, wrote:

> I have few questions about the errors occurred
> during the installation of dock6. Here are the messages. Are there normal or
> is there anything I can fix? Thanks a lot and I really really appreciate it.
>
> Sincerely,
> Byoung-Chul
>
> (1) sff.c:1614: warning: incompatible implicit declaration of built-in
> function 'strdup'

This is unusual, but probably is not a problem.
Is your Mac powerbook OS X 10.4.10 a 32 or 64 bit machine ?
What is the version of gcc ?

The other types of warnings are normal.
For a little explanation see
http://blur.compbio.ucsf.edu/pipermail/dock-fans/2007-May/001029.html

Scott

> (2) In file included from /usr/include/c++/4.0.0/backward/strstream:51,
>                  from sphere_selector.cpp:7:
> /usr/include/c++/4.0.0/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.
>
> (3) pdb_sprntf.c:279: warning: incompatible implicit declaration of built-in
> function 'strlen'

> (4) residue.c:336: warning: passing argument 1 of 'AtomBondTo' from
> incompatible pointer type
> residue.c:336: warning: passing argument 2 of 'AtomBondTo' from incompatible
> pointer type
> residue.c:464: warning: passing argument 1 of 'BuildFixInternals' from
> incompatible pointer typ
>
> (5) unitio.c: In function 'zUnitIOSaveAmberParmFormat':
> unitio.c:4047: warning: passing argument 1 of 'SortByInteger' from
> incompatible pointer type
> unitio.c:4047: warning: passing argument 4 of 'SortByInteger' from
> incompatible pointer type
> unitio.c: In function 'zUnitIOSaveAmberParmFormat_old':
> unitio.c:6055: warning: passing argument 1 of 'SortByInteger' from
> incompatible pointer type
> unitio.c:6055: warning: passing argument 4 of 'SortByInteger' from
> incompatible pointer type
> gcc -c -O2 -DSYSV graphUtil.c
> graphUtil.c: In function 'GraphUtilFindAllSmallestRingsAndRingGroups':
> graphUtil.c:675: warning: passing argument 1 of 'SortByInteger' from
> incompatible pointer type
> graphUtil.c:675: warning: passing argument 4 of 'SortByInteger' from
> incompatible pointer type
> gcc -c -O2 -DSYSV select.c
> gcc -c -O2 -DSYSV amber.c
> amber.c: In function 'uAmberReadUnitFromPrep':
> amber.c:986: warning: passing argument 1 of 'SortByInteger' from
> incompatible pointer type
> amber.c:986: warning: passing argument 4 of 'SortByInteger' from
> incompatible pointer type
> gcc -c -O2 -DSYSV build.c
> build.c: In function 'bBuildFlipChiralityFor':
> build.c:1901: warning: passing argument 1 of 'SortByInteger' from
> incompatible pointer type
> build.c:1901: warning: passing argument 4 of 'SortByInteger' from
> incompatible pointer type
> build.c:1907: warning: passing argument 1 of 'GraphUtilFindAllSmallestRings'
> from incompatible pointer type
> build.c: In function 'BuildInternalsForSimpleRings':
> build.c:2185: warning: passing argument 1 of
> 'GraphUtilFindAllSmallestRingsAndRingGroups' from incompatible pointer type
>
> (6) model.c: In function 'zModelOrderAtoms':
> model.c:497: warning: passing argument 1 of 'Sift' from incompatible pointer
> type
> gcc -c -O2 -DSYSV parmLib.c
> gcc -c -O2 -DSYSV pdbFile.c
> pdbFile.c: In function 'zPdbBuildCoordinatesForContainer':
> pdbFile.c:1088: warning: passing argument 1 of 'BuildFixInternals' from
> incompatible pointer type
> pdbFile.c: In function 'zPdbAddAtom':
> pdbFile.c:1207: warning: passing argument 1 of 'BuildInternalsForContainer'
> from incompatible pointer type
> pdbFile.c: In function 'writeTER':
> pdbFile.c:1761: warning: initialization from incompatible pointer type
> gcc -c -O2 -DSYSV tools.c
> tools.c: In function 'iToolDistanceSearch':
> tools.c:1643: warning: passing argument 1 of 'SortByDouble' from
> incompatible pointer type
> tools.c:1643: warning: passing argument 4 of 'SortByDouble' from
> incompatible pointer type
> tools.c: In function 'ToolOrientPrincipleAxisAlongCoordinateAxis':
> tools.c:1714: warning: passing argument 2 of 'MathOpDiagonalize' from
> incompatible pointer type
>
> (7) yacc: 6 shift/reduce conflicts.
> (The warning 'conflicts: 6 shift/reduce' is normal)
>
> (8) commands.c: In function 'oCmd_impose':
> commands.c:3835: warning: passing argument 1 of 'bBuildChangeInternalBond'
> from incompatible pointer type
> commands.c:3859: warning: passing argument 1 of 'bBuildChangeInternalAngle'
> from incompatible pointer type
> commands.c:3885: warning: passing argument 1 of
> 'bBuildChangeInternalTorsion' from incompatible pointer type
>
>
> On 8/15/07 3:39 PM, "John J. Irwin" wrote:
>
> > Hi - if it is correctly installed, then log out and log back in and type
> > which g77 and it should tell you where it is. If it can't find it, then
> > there is a problem. You can look in /usr/bin/g77 . If you find it there,
> > then you need to add /usr/bin to your path. you can also do   find /
> > -name 'g77'  to find where g77 lives, and then add that directory to
> > your path.
> >
> > good luck.
> >
> >
> > Byoung-Chul Lee wrote:
> >> Dear John,
> >>
> >> I just got the g77 3.4 binary files for Mac. I think I installed the g77.
> >> But still I got the same message that g77 is not found. Can you please let
> >> me know how to make the g77 work for DOCK installation? Thanks a lot.
> >>
> >> Sincerely,
> >>
> >> Byoung-Chul
> >>
> >>
> >> On 8/15/07 10:07 AM, "John J. Irwin" wrote:
> >>
> >>
> >>> Hi Byoung-Chul
> >>>
> >>> You need to install g77.
> >>>
> >>> Good luck.
> >>>
> >>> John
> >>>
> >>>
> >>> Byoung-Chul Lee wrote:
> >>>
> >>>> Dear whom it may concern,
> >>>>
> >>>> I am currently installing the Dock6 in my Mac powerbook OS X 10.4.10.
> >>>> During
> >>>> installation, I got the following error message at the end.
> >>>>
> >>>> make[2]: g77: Command not found
> >>>> make[2]: *** [showbox.o] Error 127
> >>>> make[1]: *** [utils] Error 2
> >>>> make: *** [install] Error 2
> >>>>
> >>>> Is this a serious error? Can you please let me know how I can fix the
> >>>> problem? Thanks!!!