After feeling confident in confirming the compilation process, I updated my workstation to macOS Catalina 10.15.7 and Xcode Version 12.4 (12D4e)
Following the same procedure as on my personal mac, the process initially failed. I proceeded to rebuild my package install base and tried again without success. I am again arriving at this error:
amber20_src/build/AmberTools/src/leap/src/leap/y.tab.c:1406:16: error: implicit declaration of
function 'yylex' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
yychar = YYLEX;
^
amber20_src/build/AmberTools/src/leap/src/leap/y.tab.c:762:16: note: expanded from macro 'YYLEX'
# define YYLEX yylex ()
^
amber20_src/build/AmberTools/src/leap/src/leap/y.tab.c:1706:7: error: implicit declaration of
function 'yyerror' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
yyerror (YY_("syntax error"));
^
amber20_src/build/AmberTools/src/leap/src/leap/y.tab.c:1852:3: error: implicit declaration of
function 'yyerror' is invalid in C99 [-Werror,-Wimplicit-function-declaration]
yyerror (YY_("memory exhausted"));
^
3 errors generated.
make[2]: *** [AmberTools/src/leap/src/leap/CMakeFiles/leap_leap_obj.dir/y.tab.c.o] Error 1
make[1]: *** [AmberTools/src/leap/src/leap/CMakeFiles/leap_leap_obj.dir/all] Error 2
make: *** [all] Error 2
I remember that this seemed to indicate something with bison/yacc/lex causing some problem, I have removed most packages not directly needed and as far as I can see I am using apple built in versions (bison/yacc/lex/flex) also allowing conda to install all the appropriate dependencies.
I am stumped, rebooting did not solve the issue and as far as I can see I am up to date on everything except my OS and using apple default/built in software except for gfortran where I am at version 9.3.0. Any suggestions on how to proceed or what could cause this is appreciated.
Best regards
// Gustaf
On 14 Jan 2021, at 07:32, Gustaf Olsson <gustaf.olsson.lnu.se<mailto:gustaf.olsson.lnu.se>> wrote:
I rebuilt my entire package system and now I managed to compile serial using clang/clang++ and gfortran-9 from homebrew.
I have not been able to identify the root cause for the problems I was having though it was definitely caused by something related to homebrew.
Best regards
// Gustaf
________________________________
Från: David A Case <david.case.rutgers.edu<mailto:david.case.rutgers.edu>>
Skickat: den 11 januari 2021 14:11:29
Till: AMBER Mailing List
Ämne: Re: [AMBER] Probmlems compiling under macOS
On Sun, Jan 10, 2021, Gustaf Olsson wrote:
> find . -name "parser.y"
> ./AmberTools/src/leap/src/leap/parser.y
>
> ls -la /AmberTools/src/leap/src/leap/parser.y
^^^^^^^^
You left out the "."
....dac
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Received on Mon Feb 08 2021 - 02:30:02 PST
