gcc44 @4.4.6: malloc.h: No such file or directory

[gjuhasz@…]

I have tried to install shogun toolbox on my Mac, and able to use it with r and octave. Using the description fro the shogun website:

sudo port selfupdate
sudo port install swig -php5 -ruby -perl +python +r +octave
sudo port install shogun +r +octave

The first two went well as far as I see, however the last step stopped with the error:

Error: Target org.macports.build returned: shell command failed (see log for details)
Error: Failed to install gcc44
Log for gcc44 is at: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc44/gcc44/main.log
Error: The following dependencies were not installed: atlas gcc44 gzip texinfo glpk hdf5-18 py26-numpy fftw-3 py26-nose nosetests_select py26-distribute python26 db46 openssl python_select python_select sqlite3 readline swig-octave octave GraphicsMagick freetype jpeg lcms tiff libpng libtool automake autoconf help2man p5.12-locale-gettext perl5.12 gdbm perl5 perl5 perl5 perl5 autoconf libxml2 SuiteSparse arpack curl curl-ca-bundle libidn pkgconfig glib2 libffi fftw-3-single ftgl gawk ghostscript fontconfig jbig2dec lcms2 libpaper xorg-libXext xorg-libX11 xorg-bigreqsproto xorg-inputproto xorg-kbproto xorg-libXau xorg-xproto xorg-libXdmcp xorg-libxcb python27 python27 xorg-libpthread-stubs xorg-xcb-proto xorg-util-macros xorg-xcmiscproto xorg-xextproto xorg-xf86bigfontproto xorg-xtrans xorg-libXt xorg-libsm xorg-libice gnuplot aquaterm gd2 xpm lua pango Xft2 xrender xorg-renderproto cairo libpixman xorg-xcb-util pdflib metis qhull cmake qrupdate swig-python swig-r R icu tcl tk xorg-libXScrnSaver xorg-scrnsaverproto xorg-libXmu
Error: Status 1 encountered during processing.

[ryandesign (Ryan Carsten Schmidt)]

The log says:

:info:build ../../gcc-4.4.6/libiberty/hashtab.c:48:20: error: malloc.h: No such file or directory

However I don't know if I trust this error message since this was not a clean build attempt. Clean and try again and attach the new complete main.log file if it fails again.

sudo port clean gcc44
sudo port install gcc44

[ryandesign (Ryan Carsten Schmidt)]

Replying to gjuhasz@…:

sudo port install swig -php5 -ruby -perl +python +r +octave

While it's unrelated to the gcc44 problem you're experiencing, I wanted to point out that these instructions are out of date; the variants were removed from the swig port in r60006 and a separate port created for each language binding in r60005. This occurred in late 2009. Please advise the people in charge of the shogun documentation that this line should be removed.

[gjuhasz@…]

I have made a clean install as you recommended, and got a similar error message.

{{{Error: Target org.macports.build returned: shell command failed (see log for details) Log for gcc44 is at: /opt/local/var/macports/logs/_opt_local_var_macports_sources_rsync.macports.org_release_tarballs_ports_lang_gcc44/gcc44/main.log Error: Status 1 encountered during processing.}}}

I have atteched the logfile.

Replying to ryandesign@…:

The log says:

:info:build ../../gcc-4.4.6/libiberty/hashtab.c:48:20: error: malloc.h: No such file or directory

However I don't know if I trust this error message since this was not a clean build attempt. Clean and try again and attach the new complete main.log file if it fails again.

sudo port clean gcc44
sudo port install gcc44

[gjuhasz@…]

The new logfile after install.

[basmac]

Getting malloc.h missing trying "gcc46 +gfortran" or just gcc46. gcc46 used to be ok, I just did a self update to 2.0.4 and now gcc46 install fails.

From Jan 19 install, gcc46 installed using 2.0.3

bash-3.2# gcc-mp-4.6 --version gcc-mp-4.6 (GCC) 4.6.2 Copyright (C) 2011 Free Software Foundation, Inc. This is free software; see the source for copying conditions. There is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

bash-3.2# ls -l gcc* lrwxrwxrwx 1 macports admin 25 Feb 23 15:04 gcc -> /opt/local/bin/gcc-mp-4.5 -rwxr-xr-x 1 macports admin 54344 Dec 1 15:59 gcc-apple-4.2 -rwxr-xr-x 3 macports admin 330616 Dec 1 16:43 gcc-mp-4.3 -rwxr-xr-x 3 macports admin 346248 Dec 1 14:54 gcc-mp-4.4 -rwxr-xr-x 3 macports admin 373120 Jan 19 13:51 gcc-mp-4.5 -rwxr-xr-x 3 macports admin 429588 Jan 19 14:16 gcc-mp-4.6

[jmroot (Joshua Root)]

Is this still a problem with 4.4.7?

[jmroot (Joshua Root)]

No response; given that a binary archive for 10.7 exists I'll assume this was fixed.