glennhickey / progressiveCactus

Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules
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make[3]: *** [th5s.o] Error 1 #58

Closed sklages closed 8 years ago

sklages commented 8 years ago

Hi,

I ran into compiling problem, quite late.

git version 2.4.1 gcc (GCC) 4.9.3 Python 2.7.11 GNU Wget 1.16

make results in an error: [..]

th5s.c:733:9: error: expected expression before ‘/’ token
         // ret = H5Pset_alloc_time(plist_id, alloc_time);
         ^
th5s.c:734:9: error: expected expression before ‘/’ token
         // CHECK(ret, FAIL, "H5Pset_alloc_time");
         ^
In file included from th5s.c:25:0:
th5s.c: At top level:
H5srcdir.h:38:20: warning: ‘H5_get_srcdir_filename’ defined but not used [-Wunused-function]
 static const char *H5_get_srcdir_filename(const char *filename)
                    ^
H5srcdir.h:68:20: warning: ‘H5_get_srcdir’ defined but not used [-Wunused-function]
 static const char *H5_get_srcdir(void)
                    ^
make[3]: *** [th5s.o] Error 1
make[3]: Leaving directory `/scratch/local2/build/progCactus/progressiveCactus/submodules/hdf5/test'
make[2]: *** [all-recursive] Error 1
make[2]: Leaving directory `/scratch/local2/build/progCactus/progressiveCactus/submodules/hdf5'
make[1]: *** [hdf5Rule] Error 2
make[1]: Leaving directory `/scratch/local2/build/progCactus/progressiveCactus/submodules'
make: *** [all] Error 2

Any idea what's going wrong here? How can I fix this?

Let me know if you need any log from progressiveCactus/submodules/hdf5.

best, Sven

sklages commented 8 years ago

oh, i haven't read the error carefully ... // are not working in hdf5.

CFLAGS='-std=gnu9x' didn't fix this issue, but replacing // comments by /* */ did the trick.

glennhickey commented 8 years ago

Yeah, that's annoying. hdf5 puts an option in its makefile (--pedantic or something) that doesn't play well with newer compilers. It's probably time to update the submodule to a newer version.

On Fri, Apr 15, 2016 at 5:41 AM, sklages notifications@github.com wrote:

oh, i haven't read the error carefully ... // are not working in hdf5.

CFLAGS='-std=gnu9x' didn't fix this issue, but replacing // comments by / / did the trick.

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