gsl @1.16_2 +gcc48: configure: error: cannot run C compiled programs

[almage (Roy Miller)]

Hi,

System:  MacMini5,2  (Mid 2011)
OS:  OS X 10.9.1 (13B42)
Xcode:  5.0.2  (5A3005)
Xcode Command Line Tools:  Installed

xcode-select --print-path: /Applications/Xcode.app/Contents/Developer

note: the same results were experienced on an independent computer, a MacBook Pro, upgraded to Mavericks with fresh install of Xcode and Macports.

note 2: on an Early 2009 Mac Pro (MacPro4,1), just upgraded from OS X 10.6.8 to 10.8.5 yesterday, with fresh install of Xcode and Macports, this issue did *not* occur, and I was able to install "gsl +gcc48", along with other ports requiring the gcc48 variant.

I recently updated this Mac mini from OS X 10.8.5 to 10.9.1. I had completely removed Macports, using "sudo port uninstall installed" and "sudo port clean all". Installed new Macports 2.2.1 Base package for Mavericks after the install. A variety of ports were installed, in the order shown here:

Macports Base
  wget  [+ssl]
  lftp
  db46
  python27
  python_select
  ghostscript  [+x11]
  gv  +letter
  ImageMagick  [+x11]
  gcc48

these all installed normally/properly.

the next port to install was "gsl +gcc48", which failed with a configure error.

the relevant parts of the config.log appear to be:

... <snip>
configure:3458: $? = 0
configure:3447: /opt/local/bin/gcc-mp-4.8 -v >&5
Using built-in specs.
COLLECT_GCC=/opt/local/bin/gcc-mp-4.8
COLLECT_LTO_WRAPPER=/opt/local/libexec/gcc/x86_64-apple-darwin13/4.8.2/lto-wrapper
Target: x86_64-apple-darwin13
Configured with: /opt/local/var/macports/build/_opt_mports_dports_lang_gcc48/gcc48/work/gcc-4.8.2/configure --prefix=/opt/local --build=x86_64-apple-darwin13 --enable-languages=c,c++,objc,obj-c++,lto,fortran,java --libdir=/opt/local/lib/gcc48 --includedir=/opt/local/include/gcc48 --infodir=/opt/local/share/info --mandir=/opt/local/share/man --datarootdir=/opt/local/share/gcc-4.8 --with-local-prefix=/opt/local --with-system-zlib --disable-nls --program-suffix=-mp-4.8 --with-gxx-include-dir=/opt/local/include/gcc48/c++/ --with-gmp=/opt/local --with-mpfr=/opt/local --with-mpc=/opt/local --with-cloog=/opt/local --enable-cloog-backend=isl --disable-cloog-version-check --enable-stage1-checking --disable-multilib --enable-lto --enable-libstdcxx-time --with-as=/opt/local/bin/as --with-ld=/opt/local/bin/ld --with-ar=/opt/local/bin/ar --with-bugurl=https://trac.macports.org/newticket --with-pkgversion='MacPorts gcc48 4.8.2_0'
Thread model: posix
gcc version 4.8.2 (MacPorts gcc48 4.8.2_0) 
configure:3458: $? = 0
configure:3447: /opt/local/bin/gcc-mp-4.8 -V >&5
gcc-mp-4.8: error: unrecognized command line option '-V'
gcc-mp-4.8: fatal error: no input files
compilation terminated.
configure:3458: $? = 1
configure:3447: /opt/local/bin/gcc-mp-4.8 -qversion >&5
gcc-mp-4.8: error: unrecognized command line option '-qversion'
gcc-mp-4.8: fatal error: no input files
compilation terminated.
configure:3458: $? = 1
<snip> ...

in particular, the first command to fail was "/opt/local/bin/gcc-mp-4.8 -V >&5", with an unrecognized command line option (-V). I've also seen this configure error as well when attempting to install "hdf5-18 +cxx +gcc48".

attached are the gel config.log and main.log

thanks, Roy

[ryandesign (Ryan Carsten Schmidt)]

The relevant error in the main.log is:

configure: error: cannot run C compiled programs

The config.log says the reason for that is:

conftest.c:12:19: fatal error: stdio.h: No such file or directory

Does /usr/include/stdio.h exist? If not, you probably haven't installed the Xcode command line tools, which are required; run:

xcode-select --install

[ryandesign (Ryan Carsten Schmidt)]

Roy responded by email:

thanks - the Xcode command line tools install is confusing.

I’ve installed Xcode 5.0.2 from the App Store.

On my 10.9.1 system I don’t see Command Line Tools available in the Preference Downloads tab. (gsl install does not work)
On my 10.8.5 system, the Command Line Tools is on the Preference Downloads tab. (gsl install works)

On my 10.9.1 system:

Wed Jan 15 11:44:35 beowulf ~> sudo xcode-select --install
xcode-select: error: no developer tools were found, and no install could be requested (perhaps no UI is present), please install manually from 'developer.apple.com'.
Wed Jan 15 13:13:45 beowulf ~> 

however:

Wed Jan 15 13:21:04 beowulf ~> sudo xcode-select --print-path
/Applications/Xcode.app/Contents/Developer
Wed Jan 15 13:21:20 beowulf ~> 

should I reinstall Xcode from a developer.apple.com download? I can get "Xcode 5.0.2" (11 Nov 2013) and "Command Line Tools (OS Mavericks) for Xcode - Late October" (22 Oct 2013)

Yes, you are correct, the command line tools install was previously in the Download section of the Preferences tab of the Xcode application, but that is no longer the case on Mavericks. Now you need to run xcode-select --install to install them. I do not know why the "install could not be requested" on your system. Perhaps it is because you used "sudo" which is not necessary. Or perhaps you are logging in to the computer over ssh? If so, do it from a Terminal window on the computer itself, not over ssh. You do not need to reinstall Xcode; you only need to install the Xcode command line tools. If running xcode-select --install does not allow you to do so, then download and install "Command Line Tools (OS Mavericks) for Xcode - Late October" from the Apple developer web site.

[almage (Roy Miller)]

thank you!

after installing the Command Line Tools from the dmg file downloaded from developer.apple.com, gel has now successfully been installed.

please feel free to close ticket at your convenience.

[ryandesign (Ryan Carsten Schmidt)]

Great, glad that worked.