octave-devel configure failure: to build Octave, you must have the PCRE library and header files installed

[Schamschula (Marius Schamschula)]

While updating octave-devel to version 3.6.4_7 +atlas +gcc48 darwin_10, I found a configuration issue:

:info:configure checking libqhull/libqhull.h usability... no
:info:configure checking libqhull/libqhull.h presence... no
:info:configure checking for libqhull/libqhull.h... no
:info:configure checking qhull/libqhull.h usability... no
:info:configure checking qhull/libqhull.h presence... no
:info:configure checking for qhull/libqhull.h... no
:info:configure checking libqhull.h usability... no
:info:configure checking libqhull.h presence... no
:info:configure checking for libqhull.h... no
:info:configure checking qhull/qhull.h usability... no
:info:configure checking qhull/qhull.h presence... no
:info:configure checking for qhull/qhull.h... no
:info:configure checking qhull.h usability... no
:info:configure checking qhull.h presence... no
:info:configure checking for qhull.h... no
:info:configure configure: WARNING: Qhull library not found -- this will result in loss of functionality of some geometry functions.
:info:configure checking pcre.h usability... no
:info:configure checking pcre.h presence... no
:info:configure checking for pcre.h... no
:info:configure checking pcre/pcre.h usability... no
:info:configure checking pcre/pcre.h presence... no
:info:configure checking for pcre/pcre.h... no
:info:configure checking whether pcre.h defines the macros we need... no
:info:configure configure: error: to build Octave, you must have the PCRE library and header files installed
:info:configure Command failed:  cd "/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org_release_ports_math_octave-devel/octave-devel/work/octave-3.6.4" && ./configure --prefix=/opt/local --disable-dependency-tracking --with-umfpack="-lumfpack -lSuiteSparse" --with-blas="-lcblas -lf77blas -latlas" --disable-docs --without-x --without-opengl --with-cholmod="-lcholmod" 
:info:configure Exit code: 1

Looks like some CPPFLAGS are not being set, as both qhull and pcre headers can't be found.

As I had 3.6.4_6 +atlas +gcc47 darwin_10, working, but I followed the troubleshooting advice and removed it to re-attempt installing the current version. Rebuilding it using the old Portfile...

[ryandesign (Ryan Carsten Schmidt)]

Please attach the main.log file.

[ryandesign (Ryan Carsten Schmidt)]

And let us know your version of Xcode please.

[Schamschula (Marius Schamschula)]

I'm using Xcode 4.2.

[michaelld (Michael Dickens)]

What does "port installed pcre" return?

[michaelld (Michael Dickens)]

Also, what do the following return for you:

gcc -v
cd `port dir qt4-mac`/files/cpath
/usr/bin/gcc -nostdinc -c cpath_test.c
CPATH=. /usr/bin/gcc -nostdinc -c cpath_test.c

[Schamschula (Marius Schamschula)]

marius$ gcc -v Using built-in specs. Target: i686-apple-darwin10 Configured with: /private/var/tmp/llvmgcc42/llvmgcc42-2336.1~3/src/configure --disable-checking --enable-werror --prefix=/Developer/usr/llvm-gcc-4.2 --mandir=/share/man --enable-languages=c,objc,c++,obj-c++ --program-prefix=llvm- --program-transform-name=/^[cg][.-]*$/s/$/-4.2/ --with-slibdir=/usr/lib --build=i686-apple-darwin10 --enable-llvm=/private/var/tmp/llvmgcc42/llvmgcc42-2336.1~3/dst-llvmCore/Developer/usr/local --program-prefix=i686-apple-darwin10- --host=x86_64-apple-darwin10 --target=i686-apple-darwin10 --with-gxx-include-dir=/usr/include/c++/4.2.1 Thread model: posix gcc version 4.2.1 (Based on Apple Inc. build 5658) (LLVM build 2336.1.00)

marius$ /usr/bin/gcc -nostdinc -c cpath_test.c cpath_test.c:1:24: error: no include path in which to search for cpath_test.h

marius$ CPATH=. /usr/bin/gcc -nostdinc -c cpath_test.c /var/folders/+K/+KtVoCAtHtenBwlP19tRrU+++TI/-Tmp-ccY5EIpM.s:unknown:FATAL:can't create output file: cpath_test.o

Note: marius$ sudo CPATH=. /usr/bin/gcc -nostdinc -c cpath_test.c worked as expected.

[Schamschula (Marius Schamschula)]

marius$ port installed pcre The following ports are currently installed:

pcre @7.9_0 pcre @8.10_0 pcre @8.12_0 pcre @8.12_1 pcre @8.33_0 (active)

[michaelld (Michael Dickens)]

Thanks. The issue has something to do with permissions of your computer's filesystem. Can you run Disk Utility.app and have it repair disk permissions, then try

CPATH=. /usr/bin/gcc -v -nostdinc -c cpath_test.c

to see if it now works? If not, post the results here, surrounded by three { }; that's how I get the special box just above reading "CPATH ...".

[Schamschula (Marius Schamschula)]

Replying to michaelld@…:

Thanks. The issue has something to do with permissions of your computer's filesystem. Can you run Disk Utility.app and have it repair disk permissions, then try

CPATH=. /usr/bin/gcc -v -nostdinc -c cpath_test.c

to see if it now works? If not, post the results here, surrounded by three { }; that's how I get the special box just above reading "CPATH ...".

I ran Repair Permissions on the boot HD.

However,

CPATH=. /usr/bin/gcc -v -nostdinc -c cpath_test.c

still fails.

Note when I do a ls -l on the enclosing directory for cpath I get

drwxr-xr-x  6 root  admin    204 Aug 26 12:52 cpath

Thus, no surprise why the .o file can't be written.

[michaelld (Michael Dickens)]

OK; try this:

cd ~/Desktop
cp -rp `port dir qt4-mac`/files/cpath cpath_test
cd cpath_test
CPATH=. /usr/bin/gcc -v -nostdinc -c cpath_test.c

and see if that works. Permissions should be OK for this test, at least in your local directory; I think the permission issue is with /var/.....

[Schamschula (Marius Schamschula)]

Replying to michaelld@…:

OK; try this:

cd ~/Desktop
cp -rp `port dir qt4-mac`/files/cpath cpath_test
cd cpath_test
CPATH=. /usr/bin/gcc -v -nostdinc -c cpath_test.c

and see if that works. Permissions should be OK for this test, at least in your local directory; I think the permission issue is with /var/.....

Works just fine.

I'm assuming you meant /opt/local/var. Listing the enclosing directory:

marius$ ls -l
total 8
drwxr-xr-x     5 root  wheel    170 Aug 21 11:18 Library
drwxr-xr-x    13 root  admin    442 Aug 22 14:21 apache2
drwxr-xr-x  2299 root  admin  78166 Aug 26 10:59 bin
drwxr-xr-x    14 root  admin    476 Aug 21 13:56 dx
drwxr-xr-x    43 root  admin   1462 Aug 26 10:08 etc
drwxr-xr-x   594 root  admin  20196 Aug 26 10:59 include
drwxr-xr-x  1884 root  admin  64056 Aug 26 10:59 lib
drwxr-xr-x    48 root  admin   1632 Aug 26 09:56 libexec
lrwxr-xr-x     1 root  admin      9 Mar 27  2012 man -> share/man
drwxr-xr-x    70 root  admin   2380 Aug 22 16:54 sbin
drwxr-xr-x   168 root  admin   5712 Aug 26 10:26 share
drwxr-xr-x     3 root  admin    102 Aug 22 16:46 src
drwxr-xr-x    13 root  admin    442 Aug 22 16:28 var
drwxr-xr-x     2 root  admin     68 Jan  6  2010 www

[michaelld (Michael Dickens)]

Hmm .. interesting; CPATH is working, so I would expect octave's configure script to pick up the headers and such for pcre and qhull. I was not referring to /opt/local/var, but thanks. Can you attach the file "port dir octave-devel/work/octave-3.6.4/config.log"?

[Schamschula (Marius Schamschula)]

Replying to michaelld@…:

Hmm .. interesting; CPATH is working, so I would expect octave's configure script to pick up the headers and such for pcre and qhull. I was not referring to /opt/local/var, but thanks. Can you attach the file "port dir octave-devel/work/octave-3.6.4/config.log"?

I get

marius$ port dir octave-devel/work/octave-3.6.4/config.logError: Port octave-devel/work/octave-3.6.4/config.log not found

[michaelld (Michael Dickens)]

Sorry, bad wiki formatting. I meant: "`port dir octave-devel`/work/octave-3.6.4/config.log" if you copy the text from the wiki.

[Schamschula (Marius Schamschula)]

Replying to mschamschula@…:

Replying to michaelld@…:

Hmm .. interesting; CPATH is working, so I would expect octave's configure script to pick up the headers and such for pcre and qhull. I was not referring to /opt/local/var, but thanks. Can you attach the file "port dir octave-devel/work/octave-3.6.4/config.log"?

I get

marius$ port dir octave-devel/work/octave-3.6.4/config.logError: Port octave-devel/work/octave-3.6.4/config.log not found

Never mind. I found it manually.

[michaelld (Michael Dickens)]

OK; next up:

cd ~/Desktop
cp -rp `port dir qt4-mac`/files/cpath cpath_test_2
cd cpath_test_2
CPATH=. /usr/bin/clang -v -nostdinc -c cpath_test.c

and see if that works.

[Schamschula (Marius Schamschula)]

Replying to michaelld@…:

OK; next up:

cd ~/Desktop
cp -rp `port dir qt4-mac`/files/cpath cpath_test_2
cd cpath_test_2
CPATH=. /usr/bin/clang -v -nostdinc -c cpath_test.c

and see if that works.

Nope:

marius$ CPATH=. /usr/bin/clang -v -nostdinc -c cpath_test.c
Apple clang version 3.0 (tags/Apple/clang-211.10.1) (based on LLVM 3.0svn)
Target: x86_64-apple-darwin10.8.0
Thread model: posix
 "/usr/bin/clang" -cc1 -triple x86_64-apple-macosx10.6.8 -emit-obj -mrelax-all -disable-free -disable-llvm-verifier -main-file-name cpath_test.c -pic-level 1 -mdisable-fp-elim -relaxed-aliasing -masm-verbose -munwind-tables -target-cpu core2 -target-linker-version 127.2 -v -coverage-file cpath_test.o -nostdinc -resource-dir /usr/bin/../lib/clang/3.0 -ferror-limit 19 -fmessage-length 80 -stack-protector 1 -fblocks -fdiagnostics-show-option -fcolor-diagnostics -o cpath_test.o -x c cpath_test.c
clang -cc1 version 3.0 based upon llvm 3.0svn hosted on x86_64-apple-darwin10.8.0
#include "..." search starts here:
End of search list.
cpath_test.c:1:10: fatal error: 'cpath_test.h' file not found
#include <cpath_test.h>
         ^
1 error generated.

[michaelld (Michael Dickens)]

Excellent! I'll create a compiler blacklist for this port, since it relies on CPATH functionality which is clearly not present in the version of CLANG in Xcode 4.2. Back shortly.

[michaelld (Michael Dickens)]

Fixed in r110134. You'll want to do

sudo port selfupdate

before trying again.

[Schamschula (Marius Schamschula)]

Replying to michaelld@…:

Fixed in r110134. You'll want to do

sudo port selfupdate

before trying again.

Works for me.

Thanks!

[michaelld (Michael Dickens)]

Great! Thanks for the feedback.