Hi Timothy,
Yes, as Scott pointed out previously, before cmake was made the build
system of Amber I could just have passed
AMBERBUILDFLAGS="-Wno-error=incompatible-pointer-types"
to make, but now that cmake is the build system, that can't be done.
Anyway, this error appears on some files
related to xLeap, so adding -DBUILD_GUI=FALSE in run_cmake should
allow me to compile it but without xLeap.
I thought that I had done that when I sent you my last email but after
double checking I realised that I hadn't. So I am
compiling it again at the moment (adding -DBUILD_GUI=FALSE in
run_cmake) and I will reply when that is done.
Sorry about the confusion.
I might also try adding
set(CMAKE_C_FLAGS "Wno-error=incompatible-pointer-types")
set(CMAKE_CXX_FLAGS "Wno-error=incompatible-pointer-types")
to amber24_src/CMakeLists.txt.
Regards,
Edwin.
El jue, 18 jul 2024 a las 15:15, Timothy Giese
(<giese025.rutgers.edu>) escribió:
>
> The relevant portion of the log is:
>
> /tmp/amber24_src/AmberTools/src/leap/src/leap/xAction.c:1108:49: error: passing argument 1 of ‘BuildRotateAroundBondFromTo’ from incompatible pointer type [-Wincompatible-pointer-types]
> 1108 | BuildRotateAroundBondFromTo( tTank->tank.uUnit,
> | ~~~~~~~~~~~^~~~~~
> | |
> | UNIT {aka UNITt *}
>
> From the developer-side, my guess is that this could possibly be fixed by including an explicit cast; e.g., (CONTAINER)(tTank->tank.uUnit). As a workaround, perhaps it could be built with -Wno-error=incompatible-pointer-types
> ________________________________
> From: Edwin Helbert Aponte Angarita via AMBER <amber.ambermd.org>
> Sent: Wednesday, July 17, 2024 9:31 PM
> To: Scott Brozell <sbrozell.comcast.net>; AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Unable to compile Amber24 with gcc14.1.0
>
> Hi,
>
> Sorry for the late reply. I deleted amber24_src and followed the same
> procedure again. I attach the output of run_cmake (cmake.log) and
> make install (make_install_ser.log).
>
> OS: Slackware-current (rolling distro)
>
> gcc --version
> gcc (GCC) 14.1.0
>
> cmake --version
> cmake version 3.30.0
>
>
> Thanks,
> Edwin.
>
> On 7/13/24 2:30 AM, Scott Brozell wrote:
> > Hi,
> >
> > Wow, it really is like an episode of Gilligan's Island!
> > Apparently, the stdbool checking has gone awry.
> > Please send verbose and verbatim details:
> > OS name and version, gcc -v, cmake -version, your build/cmake.log file.
> > You can send the cmake.log directly to me since it is likely large.
> >
> > scott
> >
> > ps
> >
> > Amber: What's a funny quote from Gilligan's Island?
> > ChatTV: Professor: Well, that glue is permanent! There's nothing on the
> > island to dissolve it. Why do you know what it would take? It
> > would take a polyester derivative of an organic hydroxide molecule.
> >
> > Mr. Howell: Watch your language! You're in the presence of a chemist!
> >
> > On Fri, Jul 12, 2024 at 08:38:48PM +0100, Edwin Helbert Aponte Angarita via AMBER wrote:
> >> Thank you Scott for your reply. I tried with
> >> -DBUILD_GUI=FALSE
> >>
> >> and got different errors:
> >> [ 84%] Building C object AmberTools/src/leap/src/leap/CMakeFiles/leap_common_obj.dir/basics.c.o
> >>
> >> In file included from
> >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c:41:
> >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.h:385:9: error:
> >> unknown type name ???BOOL???; did you mean ???sBOOL????
> >> 385 | extern BOOL GbInterrupt;
> >> | ^~~~
> >>
> >> | sBOOL
> >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.h:450:8: error:
> >> unknown type name ???BOOL???; did you mean ???sBOOL????
> >> 450 | extern BOOL GbPrintPrefix;
> >>
> >> | ^~~~
> >>
> >> | sBOOL
> >>
> >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.h:779:8: error:
> >> unknown type name ???BOOL???; did you mean ???sBOOL????
> >> 779 | extern BOOL GbTestMemory;
> >>
> >> | ^~~~
> >>
> >> | sBOOL
> >>
> >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.h:962:8: error:
> >> unknown type name ???BOOL???; did you mean ???sBOOL????
> >> 962 | extern BOOL bStringToDouble( char *cPData,
> >> double *dPData );
> >> | ^~~~
> >>
> >> | sBOOL
> >>
> >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.h:963:8: error:
> >> unknown type name ???BOOL???; did you mean ???sBOOL????
> >> 963 | extern BOOL bStringToInt( char *cPData, int *iPData );
> >> | ^~~~
> >> | sBOOL
> >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.h:969:8: error:
> >> unknown type name ???BOOL???; did you mean ???sBOOL????
> >> 969 | extern BOOL bMessageCheck( char *sFile );
> >> | ^~~~
> >> | sBOOL
> >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.h:975:33:
> >> error: unknown type name ???BOOL???; did you mean ???sBOOL????
> >> 975 | BOOL bComplain );
> >> | ^~~~
> >> | sBOOL
> >> In file included from
> >> /tmp/amber24_src/AmberTools/src/leap/src/leap/zMatrix.h:43,
> >> from
> >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c:43:
> >> /tmp/amber24_src/AmberTools/src/leap/src/leap/vector.h:83:46: error:
> >> unknown type name ???BOOL???; did you mean ???sBOOL????
> >> 83 | VECTOR *vPA, BOOL bA, VECTOR
> >> *vPB, BOOL bB,
> >> | ^~~~
> >> | sBOOL
> >> /tmp/amber24_src/AmberTools/src/leap/src/leap/vector.h:83:68: error:
> >> unknown type name ???BOOL???; did you mean ???sBOOL????
> >> 83 | VECTOR *vPA, BOOL bA, VECTOR
> >> *vPB, BOOL bB,
> >> | ^~~~
> >> | sBOOL
> >> /tmp/amber24_src/AmberTools/src/leap/src/leap/vector.h:84:46: error:
> >> unknown type name ???BOOL???; did you mean ???sBOOL????
> >> 84 | VECTOR *vPC, BOOL bC, VECTOR
> >> *vPD, BOOL bD );
> >> | ^~~~
> >> | sBOOL
> >> /tmp/amber24_src/AmberTools/src/leap/src/leap/vector.h:84:68: error:
> >> unknown type name ???BOOL???; did you mean ???sBOOL????
> >> 84 | VECTOR *vPC, BOOL bC, VECTOR
> >> *vPD, BOOL bD );
> >> | ^~~~
> >> | sBOOL
> >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c:57:1: error:
> >> unknown type name ???BOOL???; did you mean ???sBOOL????
> >> 57 | BOOL GbInterrupt = FALSE;
> >> | ^~~~
> >> | sBOOL
> >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c:237:1: error:
> >> unknown type name ???BOOL???; did you mean ???sBOOL????
> >> 237 | BOOL
> >> | ^~~~
> >> | sBOOL
> >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c:261:1: error:
> >> unknown type name ???BOOL???; did you mean ???sBOOL????
> >> 261 | BOOL
> >> | ^~~~
> >> | sBOOL
> >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c:317:1: error:
> >> unknown type name ???BOOL???; did you mean ???sBOOL????
> >> 317 | BOOL GbTestMemory = FALSE;
> >> | ^~~~
> >> | sBOOL
> >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c:347:42:
> >> error: unknown type name ???BOOL???; did you mean ???sBOOL????
> >> 347 | DebugMemoryTest( char *sFile, int iLine, BOOL bReport )
> >> | ^~~~
> >> | sBOOL
> >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c: In function
> >> ???DebugMalloc???:
> >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c:444:5: error:
> >> implicit declaration of function ???DebugMemoryTest???
> >> [-Wimplicit-function-declaration]
> >>
> >> 444 | DebugMemoryTest( sFile, iLine, FALSE );
> >> | ^~~~~~~~~~~~~~~
> >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c: At top level:
> >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c:638:1: error:
> >> unknown type name ???BOOL???; did you mean ???sBOOL????
> >> 638 | BOOL
> >> | ^~~~
> >> | sBOOL
> >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c:906:53:
> >> error: unknown type name ???BOOL???; did you mean ???sBOOL????
> >> 906 | fBasicsMyFopen( char *sFilename, char *sAttributes, BOOL
> >> bComplain )
> >> | ^~~~
> >> | sBOOL
> >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c:989:9: error:
> >> unknown type name ???BOOL???; did you mean ???sBOOL????
> >> 989 | BOOL bSinkUsed;
> >> | ^~~~
> >> | sBOOL
> >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c:990:9: error:
> >> unknown type name ???BOOL???; did you mean ???sBOOL????
> >> 990 | BOOL bPrintPrefix;
> >> | ^~~~
> >> | sBOOL
> >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c: In function
> >> ???iCreatePrintSink???:
> >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c:1026:1:
> >> error: unknown type name ???BOOL???; did you mean ???sBOOL????
> >> 1026 | BOOL bFoundOne;
> >> | ^~~~
> >> | sBOOL
> >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c: At top level:
> >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c:1198:1:
> >> error: unknown type name ???BOOL???; did you mean ???sBOOL????
> >> 1198 | BOOL GbPrintPrefix = TRUE;
> >> | ^~~~
> >> | sBOOL
> >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c: In function
> >> ???myPrintString???:
> >> /tmp/amber24_src/AmberTools/src/leap/src/leap/basics.c:1237:1:
> >> error: unknown type name ???BOOL???; did you mean ???sBOOL????
> >> 1237 | BOOL bPrintPrefix;
> >> | ^~~~
> >> | sBOOL
> >> make[2]: *** [AmberTools/src/leap/src/leap/CMakeFiles/leap_common_obj.dir/build.make:76: AmberTools/src/leap/src/leap/CMakeFiles/leap_common_obj.dir/basics.c.o]
> >> Error 1
> >>
> >> make[1]: *** [CMakeFiles/Makefile2:4993:
> >> AmberTools/src/leap/src/leap/CMakeFiles/leap_common_obj.dir/all]
> >> Error 2
> >> make: *** [Makefile:156: all] Error 2
> >>
> >>
> >> By the way, I knew about the difficulties to get inter-version
> >> portability with GNU compilers but not about the plight of the crew
> >> and passengers of SS Minnow. Good to learn something new.
> >>
> >> Regards,
> >> Edwin.
> >>
> >> On 7/12/24 1:52 PM, Scott Brozell wrote:
> >>> Hi,
> >>>
> >>> On Fri, Jul 12, 2024 at 01:34:34AM +0100, Edwin Helbert Aponte Angarita via AMBER wrote:
> >>>> I am trying to compile Amber24 using Gcc 14.1.0. I run:
> >>>> tar -xjf AmberTools24.tar.bz2
> >>>> tar -xjf Amber24.tar.bz2
> >>>> cd amber24_src
> >>>> ./update_amber --update
> >>>> cd build
> >>>> ./run_cmake
> >>>> make install
> >>>>
> >>>> and then I get the following error:
> >>>> [ 86%] Building C object AmberTools/src/leap/src/leap/CMakeFiles/leap_xleap_obj.dir/xAction.c.o
> >>>> /tmp/amber24_src/AmberTools/src/leap/src/leap/xAction.c: In function
> >>>> ???zActionTwistTorsions???:
> >>>> /tmp/amber24_src/AmberTools/src/leap/src/leap/xAction.c:1108:49:
> >>>> error: passing argument 1 of ???BuildRotateAroundBondFromTo??? from
> >>>> incompatible pointer type [-Wincompatible-pointer-types]
> >>>> 1108 | BuildRotateAroundBondFromTo( tTank->tank.uUnit,
> >>>> | ~~~~~~~~~~~^~~~~~
> >>>> | |
> >>>> | UNIT {aka UNITt *}
> >>>> In file included from
> >>>> /tmp/amber24_src/AmberTools/src/leap/src/leap/xAction.c:52:
> >>>> /tmp/amber24_src/AmberTools/src/leap/src/leap/build.h:68:64: note:
> >>>> expected ???CONTAINER??? {aka ???struct CONTAINERSTRUCT *???} but
> >>>> argument is of type ???UNIT??? {aka ???UNITt *???}
> >>>
> >>> The latest version of GNU compilers used during release candidate
> >>> testing was 13.2.0. There are 2 ~easy workarounds:
> >>>
> >>> A. Install an older compiler; the latest from the 13 or 12 series are
> >>> likely to work. Then run clean_build and reinstall. This should
> >>> get you all of Amber.
> >>>
> >>> B. Edit run_cmake and add this to the appropriate cmake command:
> >>> -DBUILD_GUI=FALSE
> >>> Then rebuild. This should get you Amber without xLEaP.
> >>> If you need xLEaP, probably unlikely, then wait for us to
> >>> release a patch and then rebuild again.
> >>>
> >>> It'll likely be a few days before the patch becomes available.
> >>>
> >>>
> >>> In the dark ages, before cmake, users could've done this:
> >>> make AMBERBUILDFLAGS="-Wno-error=incompatible-pointer-types"
> >>>
> >>> Now that would've been an easy workaround.
> >>>
> >>>
> >>> It looks like there will be 5 of these errors across 3 files.
> >>> The patching should be straightforward, we just have to cast away
> >>> these 5 passengers from GNU's Island.
> >>>
> >>> Amber: What is GNU's Island ?
> >>> ChatTV: That's an allusion to the 1960's sitcom Gilligan's Island.
> >>>
> >>> Amber: Please elaborate.
> >>> ChatTV: I love your good manners!
> >>> Many episodes portray the passengers' and the crews' unsuccessful
> >>> attempts to escape their plight: Much like the application or
> >>> maintenance programmer is never able to escape the plight of the
> >>> ad hoc type-checking myopathy of the GNU compiler developers.
> >>>
> >>> Amber: Wow, that's deep!
> >>> ChatTV: Deep is as deep does.
> >>>
> >>> Amber: Do you think ?
> >>> ChatTV: I am.
> >>>
> >>> Amber: Ohh, Descartes!
> >>> ChatTV: No, that's a different TV show:
> >>> De plane! De plane!
> >>> from Fantasy Island.
> >>>
> >>> Amber: Say good night ChatTV.
> >>> ChatTV: Good night ChatTV!
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Received on Thu Jul 18 2024 - 11:30:02 PDT
