Dear David,
Thank you for your help.
The response of ./update_amber --show-applied-patches of from the request
is
AmberTools 21 Applied Patches:
------------------------------
update.1, update.2, update.3, update.4, update.5, update.6, update.7,
update.8, update.9, update.10,
update.11
Best Regards,
Victor
>
>
> -------- Пересылаемое сообщение --------
> От кого: David A Case <david.case.rutgers.edu>
> Кому: AMBER Mailing List <amber.ambermd.org>
> Дата: Воскресенье, 24 октября 2021, 23:11 +03:00
> Тема: Re: [AMBER] Fwd: Ambertools21 installation problems
>
> On Sat, Oct 23, 2021, Victor Nazarychev wrote:
> >
> >I tried to install AmberTools21 using Option 1 in the instruction manual
> >from the website https://ambermd.org/GetAmber.php#ambertools .
> >
> >I use Ubuntu 21.10, cmake 3.22.0-rcc, gcc-9.4.0 ,
>
> Can you do this:
>
> cd to your amber_20_src folder
> ./update_amber --show-applied-patches
>
> [Dan and others: this might be(?) a problem with update.11 with ubuntu
> 21.10/gcc9. I doubt that any developer yet has this release. I wonder
> if the declarations at lines 46, 117 and 133 are really needed? When I
> get home, I can try things out on ubunutu 21.04, which might have system
> libraries the same as ubunutu 21.10.]
>
> [Another aside: even older versions of ubuntu declare write() to be
> ssize_t,
> not int, in /usr/include/unist.h. So the fact that this becomes an error
> rather than a warning might be compiler-dependent? But surely, things like
> malloc(), read() and write() should no longer be declared as int in our
> codes, but the declarations should rather be always taken for <unistd.h>.]
>
> ....dac
>
> >#################################################################
> >
> > [ 94%] Building C object
> >AmberTools/src/leap/src/leap/CMakeFiles/leap_common_obj.dir/getline.c.o
> >
>
> >/home/victor/src/amber20_src/AmberTools/src/leap/src/leap/getline.c:117:17:
> >error: conflicting types for ‘write’
> >
> >117 | extern int write();
> >
> >| ^~~~~
> >
> >In file included from /usr/include/x86_64-linux-gnu/bits/sigstksz.h:24,
> >
> >from /usr/include/signal.h:328,
> >
> >from
> /home/victor/src/amber20_src/AmberTools/src/leap/src/leap/getline.c:36:
> >
> >/usr/include/unistd.h:378:16: note: previous declaration of ‘write’ was
> here
> >
> >378 | extern ssize_t write (int __fd, const void *__buf, size_t __n) __wur
> >
> >| ^~~~~
> >
>
> >/home/victor/src/amber20_src/AmberTools/src/leap/src/leap/getline.c:133:17:
> >error: conflicting types for ‘read’
> >
> >133 | extern int read();
> >
> >| ^~~~
> >
> >In file included from /usr/include/unistd.h:1200,
> >
> >from /usr/include/x86_64-linux-gnu/bits/sigstksz.h:24,
> >
> >from /usr/include/signal.h:328,
> >
> >from
> /home/victor/src/amber20_src/AmberTools/src/leap/src/leap/getline.c:36:
> >
> >/usr/include/x86_64-linux-gnu/bits/unistd.h:36:1: note: previous
> definition
> >of ‘read’ was here
> >
> >36 | read (int __fd, void *__buf, size_t __nbytes)
> >
> >| ^~~~
> >
> >/home/victor/src/amber20_src/AmberTools/src/leap/src/leap/getline.c: In
> >function ‘hist_save’:
> >
>
> >/home/victor/src/amber20_src/AmberTools/src/leap/src/leap/getline.c:920:25:
> >warning: ‘malloc’ argument 1 type is ‘int’ where ‘long unsigned int’ is
> >expected in a call to built-in function declared without prototype
> >[-Wbuiltin-declaration-mismatch]
> >
> >920 | if ((s = malloc(len)) != 0) {
> >
> >| ^~~
> >
> >/home/victor/src/amber20_src/AmberTools/src/leap/src/leap/getline.c:46:17:
> >note: built-in ‘malloc’ declared here
> >
> >46 | extern void *malloc();
> >
> >| ^~~~~~
> >
>
> >/home/victor/src/amber20_src/AmberTools/src/leap/src/leap/getline.c:925:28:
> >warning: ‘malloc’ argument 1 type is ‘int’ where ‘long unsigned int’ is
> >expected in a call to built-in function declared without prototype
> >[-Wbuiltin-declaration-mismatch]
> >
> >925 | if ((s = malloc(len+1)) != 0) {
> >
> >| ~~~^~
> >
> >/home/victor/src/amber20_src/AmberTools/src/leap/src/leap/getline.c:46:17:
> >note: built-in ‘malloc’ declared here
> >
> >46 | extern void *malloc();
> >
> >| ^~~~~~
> >
> >make[2]: ***
>
> >[AmberTools/src/leap/src/leap/CMakeFiles/leap_common_obj.dir/build.make:132:
> >AmberTools/src/leap/src/leap/CMakeFiles/leap_common_obj.dir/getline.c.o]
> >Ошибка 1
> >
> >make[1]: *** [CMakeFiles/Makefile2:6295:
> >AmberTools/src/leap/src/leap/CMakeFiles/leap_common_obj.dir/all] Ошибка 2
> >
> >make: *** [Makefile:156: all] Ошибка 2
> >_______________________________________________
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> >http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Oct 25 2021 - 02:00:03 PDT
