atlas @3.9.47 build failure (can't find stdint.h)

[matt_langston@…]

Build failure on Mac OS X 10.6.8 because /opt/local/bin/gcc-mp-4.4 can't find stdint.h. Full build log attached. Relevent section of build log included below.

:info:build make[7]: Entering directory `/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_atlas/atlas/work/atlas-3.9.47/build/src/blas/gemm/KERNEL'
:info:build /opt/local/bin/gcc-mp-4.4 -DL2SIZE=4194304 -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_atlas/atlas/work/atlas-3.9.47/build/include -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_atlas/atlas/work/atlas-3.9.47/build/..//include -I/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_atlas/atlas/work/atlas-3.9.47/build/..//include/contrib -DAdd_ -DF77_INTEGER=int -DStringSunStyle -DATL_OS_OSX -DATL_ARCH_Core2 -DATL_CPUMHZ=2800 -DATL_SSE3 -DATL_SSE2 -DATL_SSE1 -DATL_USE64BITS -DATL_GAS_x8664 -DPentiumCPS=2800 -DATL_FULL_LAPACK -DATL_NCPU=2 -DATL_UCLEANM -DATL_UCLEANN -DATL_UCLEANK -fomit-frame-pointer -mfpmath=sse -msse3 -O2 -fPIC -m64 -c ATL_sNBmm_b0.c
:info:build ATL_sNBmm_b0.c:54:20: error: stdint.h: No such file or directory

[Veence (Vincent)]

Can you try again with the +gcc45 option and tell me if this error shows up again? Thanks

[jmroot (Joshua Root)]

Please remember to cc the maintainer.

[jmroot (Joshua Root)]

Just to check, you do have /usr/include/stdint.h right?

[matt_langston@…]

Replying to vince@…:

Can you try again with the +gcc45 option and tell me if this error shows up again? Thanks

I tried "sudo port install atlas +gcc45", but there was a build failure when installing gcc45 (i.e. I never even got to compiling atlas).

[matt_langston@…]

Replying to jmr@…:

Just to check, you do have /usr/include/stdint.h right?

There is no /usr/include/stdint.h, but there is /opt/local/include/gcc44/c++/tr1/stdint.h:

$ find /opt/ -type f -name "stdint.h"
/opt//local/include/gcc44/c++/tr1/stdint.h

[Veence (Vincent)]

Then Joshua was right. Something is broken in your installation. You should get this:

-> ls /usr/include/std*
/usr/include/stdbool.h	/usr/include/stdint.h	/usr/include/stdlib.h
/usr/include/stddef.h	/usr/include/stdio.h

[matt_langston@…]

I have stdint.h installed and it works fine for me. This simple test produces no errors:

$ cat test.c
#include <stdint.h>

int main(int atgc, char** argv) {
  return 0;
}
$ gcc test.c

I don't think stdint.h should be installed in /usr/local because it is an implementation detail of the compiler one is using (i.e. it is part of the C99 standard library).

I have multiple version of stdint.h installed on my system for various MacOSX and iOS SDKs that I use.

$ mdfind -name stdint.h | wc -l
     146

[Veence (Vincent)]

What about:

gcc-mp-4.4 test.c

?

[matt_langston@…]

I get the same error as atlas:

$ gcc-mp-4.4 test.c
test.c:1:20: error: stdint.h: No such file or directory

$ gcc-mp-4.4 -std=c99 test.c
test.c:1:20: error: stdint.h: No such file or directory

It looks like the gcc44 port is to blame? The system provided gcc (i.e. /usr/bin/gcc) works fine:

$ /usr/bin/gcc test.c
$ echo $?
0

[Veence (Vincent)]

Something is definitely rotten in your kingdom :) I cannot help you for gcc44, no more than I can explain why you lack stdint.h in /usr/include. Furthermore, I do not understand why you cannot compile gcc45, that seems to build flawlessly elsewhere. Try to ask directly on the Macports user list? Since this seems not directly linked to Atlas as such, I close the bug, but don’t forget to ask.

[skymoo (Adam Mercer)]

If /usr/include/stdint.h is missing then I imagine that Xcode isn't installed correctly.

[carmi.grushko@…]

After installing Xcode, MacOsX 10.6 has its stdint.h in /Developer/usr/include/gcc/darwin/4.2/ You can either copy it to /usr/include/ (ugly) or somehow point MacPorts to this directory. I copied it; it successfully build, though I don't know if it's working.

Anyway - I believe this issue should be further investigated, because it happens for more than one user...