Closed edzeta closed 1 year ago
This looks like a portability problem (times()
and struct tms
are not defined on your system) that may be limited to makehmmerdb
, because our configure script checks for these automatically and the rest of the code should be using our configure-time HAVE_TIMES
flag. So a workaround might be to comment out makehmmerdb
in src/Makefile, and I bet the rest of the code should compile.
Meanwhile we'll fix this in a future release. Let me know if the workaround works in the meantime. Thanks for reporting it!
If you don't have a particular reason to be using Cygwin, you might try Windows Subsystem for Linux instead as an alternate approach. I've found that to work well.
-Nick
On Wed, Oct 12, 2022 at 4:50 PM edzeta @.***> wrote:
Hi,
I am trying to install hmmer-3.3.2 using cygwim on windows. Unfortunately, there is a problem whenever I use made. I get the following error message:
$ make SUBDIR easel SUBDIR miniapps SUBDIR libdivsufsort SUBDIR src SUBDIR impl_sse CC makehmmerdb.o makehmmerdb.c: In function ‘main’: makehmmerdb.c:378:14: error: storage size of ‘ts1’ isn’t known 378 | struct tms ts1, ts2; | ^~~ makehmmerdb.c:378:19: error: storage size of ‘ts2’ isn’t known 378 | struct tms ts1, ts2; | ^~~ makehmmerdb.c:473:8: warning: implicit declaration of function ‘times’; did you mean ‘time’? [-Wimplicit-function-declaration] 473 | t1 = times(&ts1); | ^~~~~ | time make[1]: [Makefile:278: makehmmerdb.o] Error 1 make: [Makefile:92: all] Error 2
Does anybody know what could be the issue here?
Thanks in advance!
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This looks like a portability problem (
times()
andstruct tms
are not defined on your system) that may be limited tomakehmmerdb
, because our configure script checks for these automatically and the rest of the code should be using our configure-timeHAVE_TIMES
flag. So a workaround might be to comment outmakehmmerdb
in src/Makefile, and I bet the rest of the code should compile.Meanwhile we'll fix this in a future release. Let me know if the workaround works in the meantime. Thanks for reporting it!
Thanks it solved the problem! The code compile without any problem, including the Tutorial.
Hi,
I am trying to install hmmer-3.3.2 using cygwim on windows. Unfortunately, there is a problem whenever I use
made
. I get the following error message:$ make SUBDIR easel SUBDIR miniapps SUBDIR libdivsufsort SUBDIR src SUBDIR impl_sse CC makehmmerdb.o makehmmerdb.c: In function ‘main’: makehmmerdb.c:378:14: error: storage size of ‘ts1’ isn’t known 378 | struct tms ts1, ts2; | ^~~ makehmmerdb.c:378:19: error: storage size of ‘ts2’ isn’t known 378 | struct tms ts1, ts2; | ^~~ makehmmerdb.c:473:8: warning: implicit declaration of function ‘times’; did you mean ‘time’? [-Wimplicit-function-declaration] 473 | t1 = times(&ts1); | ^~~~~ | time make[1]: *** [Makefile:278: makehmmerdb.o] Error 1 make: *** [Makefile:92: all] Error 2
Does anybody know what could be the issue here?
Thanks in advance!