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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Received on Sun Oct 24 2021 - 13:30:02 PDT
