Bug: io_lib from svn won't bootstrap on OS X

John Nash
2013-01-17
2013-04-18
  • John Nash

    John Nash - 2013-01-17

    Every few months, I check what the Staden team have done with the package, and if there significant bug fixes, I update the version on both my production Linux servers (mainly used for running tg_index) and the Mac minis on which the post-docs and students run gap5 to proof-read (bacterial) genomes.

    The process has been working for about two years, and I rarely have difficulties installing the Staden package on either the Macs or the Linux servers - and if I do, I usually file bug reports, and often associated fixes here. Here is one:

    Problem:  When installing io_lib from svn on Mac, the process dies after running './bootstrap'.

    I'm using newish Mac minis running OS X Lion or Mountain Lion. *Most* of them have the latest MacPorts and updates installed, i.e. 'sudo port selfupdate' and 'sudo port upgrade outdated' were run. This happened on 5 out of 6 systems - the one where the crash didn't happen was one where I was too lazy to update MacPorts, so it's a MacPorts issue which has broken io_lib's ./bootstrap.

    Note: On the Mac, after updating MacPorts, in my hands, one *must* run 'sudo port activate tcl @8.5.12' and 'sudo port activate tk @8.5.12' or else gap5 will crash and burn using newer MacPorts versions of tcl and tk.

    [u]Reproducing the bootstrap failure. Steps[/u]:
    $ mkdir test1
    $ cd test1
    $ svn co https://staden.svn.sourceforge.net/svnroot/staden/io_lib/trunk io_lib.trunk
    $ cd io_lib.trunk
    $ ./bootstrap
    

    Message:

    + rm -rf install-sh missing mkinstalldirs depcomp aclocal.m4 config.cache config.log config.status configure autom4te.cache io_lib_config.h.in config.sub config.guess Makefile.in progs/Makefile.in progs/Makefile read/Makefile.in read/Makefile tests/Makefile tests/Makefile.in dependencies io_lib-config
    + libtoolize -force -copy
    libtoolize: putting auxiliary files in `.'.
    libtoolize: copying file `./ltmain.sh'
    libtoolize: You should add the contents of the following files to `aclocal.m4':
    libtoolize:   `/opt/local/share/aclocal/libtool.m4'
    libtoolize:   `/opt/local/share/aclocal/ltoptions.m4'
    libtoolize:   `/opt/local/share/aclocal/ltversion.m4'
    libtoolize:   `/opt/local/share/aclocal/ltsugar.m4'
    libtoolize:   `/opt/local/share/aclocal/lt~obsolete.m4'
    libtoolize: Consider adding `AC_CONFIG_MACRO_DIR()' to configure.in and
    libtoolize: rerunning libtoolize, to keep the correct libtool macros in-tree.
    libtoolize: Consider adding `-I m4' to ACLOCAL_AMFLAGS in Makefile.am.
    + aclocal -I .
    aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in'
    configure.in:3: error: 'AM_CONFIG_HEADER': this macro is obsolete.
        You should use the 'AC_CONFIG_HEADERS' macro instead.
    /opt/local/share/aclocal-1.13/obsolete-err.m4:12: AM_CONFIG_HEADER is expanded from…
    configure.in:3: the top level
    autom4te: /opt/local/bin/gm4 failed with exit status: 1
    aclocal: error: echo failed with exit status: 1

    We are all used to warning messages from 'bootstrap' and ignoring them, but in this case, it dies.

    Solution:

    Edit 'config.in'. On the third line, replace:
    AM_CONFIG_HEADER(io_lib_config.h)
    with:
    AC_CONFIG_HEADERS(io_lib_config.h)

    Result:

    + rm -rf install-sh missing mkinstalldirs depcomp aclocal.m4 config.cache config.log config.status configure autom4te.cache io_lib_config.h.in config.sub config.guess Makefile.in progs/Makefile.in progs/Makefile read/Makefile.in read/Makefile tests/Makefile tests/Makefile.in dependencies io_lib-config
    + libtoolize -force -copy
    libtoolize: putting auxiliary files in `.'.
    libtoolize: copying file `./ltmain.sh'
    libtoolize: You should add the contents of the following files to `aclocal.m4':
    libtoolize:   `/opt/local/share/aclocal/libtool.m4'
    libtoolize:   `/opt/local/share/aclocal/ltoptions.m4'
    libtoolize:   `/opt/local/share/aclocal/ltversion.m4'
    libtoolize:   `/opt/local/share/aclocal/ltsugar.m4'
    libtoolize:   `/opt/local/share/aclocal/lt~obsolete.m4'
    libtoolize: Consider adding `AC_CONFIG_MACRO_DIR()' to configure.in and
    libtoolize: rerunning libtoolize, to keep the correct libtool macros in-tree.
    libtoolize: Consider adding `-I m4' to ACLOCAL_AMFLAGS in Makefile.am.
    + aclocal -I .
    aclocal: warning: autoconf input should be named 'configure.ac', not 'configure.in'
    configure.in:83: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
    ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from…
    ../../lib/autoconf/general.m4:2661: _AC_LINK_IFELSE is expanded from…
    ../../lib/autoconf/general.m4:2678: AC_LINK_IFELSE is expanded from…
    ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from…
    ../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from…
    ../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from…
    acinclude.m4:40: LIBCURL_CHECK_CONFIG is expanded from…
    configure.in:83: the top level
    + autoheader
    configure.in:83: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
    ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from…
    ../../lib/autoconf/general.m4:2661: _AC_LINK_IFELSE is expanded from…
    ../../lib/autoconf/general.m4:2678: AC_LINK_IFELSE is expanded from…
    ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from…
    ../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from…
    ../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from…
    acinclude.m4:40: LIBCURL_CHECK_CONFIG is expanded from…
    configure.in:83: the top level
    + automake -foreign -add-missing -copy
    automake: warning: autoconf input should be named 'configure.ac', not 'configure.in'
    configure.in:83: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
    ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from…
    ../../lib/autoconf/general.m4:2661: _AC_LINK_IFELSE is expanded from…
    ../../lib/autoconf/general.m4:2678: AC_LINK_IFELSE is expanded from…
    ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from…
    ../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from…
    ../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from…
    acinclude.m4:40: LIBCURL_CHECK_CONFIG is expanded from…
    configure.in:83: the top level
    configure.in:66: installing './config.guess'
    configure.in:66: installing './config.sub'
    configure.in:4: installing './install-sh'
    configure.in:4: installing './missing'
    io_lib/Makefile.am:86: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
    automake: warning: autoconf input should be named 'configure.ac', not 'configure.in'
    io_lib/Makefile.am: installing './depcomp'
    progs/Makefile.am:95: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
    + autoconf
    configure.in:83: warning: AC_LANG_CONFTEST: no AC_LANG_SOURCE call detected in body
    ../../lib/autoconf/lang.m4:193: AC_LANG_CONFTEST is expanded from…
    ../../lib/autoconf/general.m4:2661: _AC_LINK_IFELSE is expanded from…
    ../../lib/autoconf/general.m4:2678: AC_LINK_IFELSE is expanded from…
    ../../lib/m4sugar/m4sh.m4:639: AS_IF is expanded from…
    ../../lib/autoconf/general.m4:2031: AC_CACHE_VAL is expanded from…
    ../../lib/autoconf/general.m4:2052: AC_CACHE_CHECK is expanded from…
    acinclude.m4:40: LIBCURL_CHECK_CONFIG is expanded from…
    configure.in:83: the top level

    i.e. Lots of warnings but it configures, makes and installs.

     
  • Andrew Whitwham

    Andrew Whitwham - 2013-01-18

    Thank you.  Our lack of a development Mac here at work means we just don't catch these things.

     
  • James Bonfield

    James Bonfield - 2013-01-18

    Fixed in SVN - thanks.

    You may notice some new CRAM development things appearing in there too. It's a work in progress so don't get too excited, but (for now at least) I've moving my next-gen format handling code into io_lib too.

    James

     

Log in to post a comment.

Get latest updates about Open Source Projects, Conferences and News.

Sign up for the SourceForge newsletter:





No, thanks