Atlas 3.9.47 build failure

[boydb@…]

Atlas is failing to upgrade on my OS 10.6.8 tower:

$ sudo port clean atlas
--->  Cleaning atlas
$ sudo port upgrade atlas
--->  Computing dependencies for atlas
--->  Fetching archive for atlas
--->  Attempting to fetch atlas-3.9.47_0+gcc44.darwin_10.x86_64.tgz from http://packages.macports.org/atlas
--->  Fetching atlas
--->  Verifying checksum(s) for atlas
--->  Extracting atlas
--->  Applying patches to atlas
--->  Configuring atlas
--->  Building atlas
Error: Target org.macports.build returned: shell command failed (see log for details)
Log for atlas is at: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_atlas/atlas/main.log
Error: Unable to upgrade port: 1
To report a bug, see <http://guide.macports.org/#project.tickets>

[macporter90210@…]

Perhaps some issues with Macports not installing gcc's binutils, as discussed at ​http://sourceforge.net/tracker/?func=detail&aid=3455327&group_id=23725&atid=379483 are pertinent to this?

[Veence (Vincent)]

This problem has occurred before. It seems sometimes Xcode does not install the right headers at the right place. In this case, you lack /usr/include/stdint.h.

What do you get if you type ls -l /usr/include/std* in a terminal window? You should get this:

-> ls -l /usr/include/std*
-r--r--r--  1 root  wheel   1752  1 aoû 04:19 /usr/include/stdbool.h
-r--r--r--  1 root  wheel   5124  1 aoû 04:19 /usr/include/stddef.h
-r--r--r--  1 root  wheel   6383  1 aoû 04:19 /usr/include/stdint.h
-r--r--r--  1 root  wheel  18275  1 aoû 04:19 /usr/include/stdio.h
-r--r--r--  1 root  wheel  12455  1 aoû 04:19 /usr/include/stdlib.h
-> 

[boydb@…]

$ ls -l /usr/include/std*
-r--r--r--  1 root  wheel   234B Apr  7  2010 /usr/include/stdarg.h
-r--r--r--  1 root  wheel   1.7K Apr  7  2010 /usr/include/stdbool.h
-r--r--r--  1 root  wheel   5.0K Apr  7  2010 /usr/include/stddef.h
lrwxr-xr-x  1 root  wheel    27B Aug 21 21:03 /usr/include/stdint.h -> gcc/darwin/default/stdint.h
-r--r--r--  1 root  wheel    16K Apr  7  2010 /usr/include/stdio.h
-r--r--r--  1 root  wheel    11K Apr  7  2010 /usr/include/stdlib.h

[boydb@…]

Oh and that linked file does appear to exist:

$ ls -l /usr/include/gcc/darwin/default/std*
-rw-r--r--  1 root  wheel   6.3K Feb 11  2011 /usr/include/gcc/darwin/default/stdint.h

[boydb@…]

Ah geez, wrong computer. The computer that has the issue does not have the stdint.h file in that location:

$ ls -l /usr/include/std*
-r--r--r--  1 root  wheel    234 Apr  7  2010 /usr/include/stdarg.h
-r--r--r--  1 root  wheel   1764 Apr  7  2010 /usr/include/stdbool.h
-r--r--r--  1 root  wheel   5124 Apr  7  2010 /usr/include/stddef.h
-r--r--r--  1 root  wheel  16756 Apr  7  2010 /usr/include/stdio.h
-r--r--r--  1 root  wheel  11765 Apr  7  2010 /usr/include/stdlib.h

And a brief search of the filesystem didn't reveal it anywhere. What's the process for obtaining that file?

[boydb@…]

Answered my own question (wow, need more sleep...), as my other computer obviously had the solution already. The stdint.h file is there, just buried in the gcc folder:

ln -s /usr/include/gcc/darwin/default/stdint.h /usr/include/stdint.h

This puts stdint where atlas is expecting it and it compiles just fine.

[Veence (Vincent)]

Great! I close the bug then. Have fun.