Installing staden-2.0.0b7 or b6 on OSX

Forster
2010-11-25
2013-04-18
  • Forster
    Forster
    2010-11-25

    I've read the previous posts describing the installation of tcl and tk using macports.  I've done this and then use the command
    ../configure -with-tcl=/opt/local/lib -with-tk=/opt/local/lib

    Configure stops with the error

    checking for Tcl private include files… Using -I"/opt/local/var/macports/build/_opt_local_var_macports_sources_www.macports.org_files_ports_lang_tcl/work/tcl8.5.9/generic" -I"/opt/local/var/macports/build/_opt_local_var_macports_sources_www.macports.org_files_ports_lang_tcl/work/tcl8.5.9/unix"
    checking for Tk public headers… /opt/local/include
    checking for Tk private include files… Using -I"/opt/local/var/macports/build/_opt_local_var_macports_sources_www.macports.org_files_ports_x11_tk/work/tk8.5.9/generic" -I"/opt/local/var/macports/build/_opt_local_var_macports_sources_www.macports.org_files_ports_x11_tk/work/tk8.5.9/unix"
    checking tklib directory… no
    configure: error: Abort: no tklib package found, use -with-tklib=DIR

    I tried putting -with-tklib=/opt/local/lib  but that doesn't help.  libtk.dylib is present in this directory if that is what it is looking for. Configure found tclConfig.sh and tkConfig.sh

    What should I be doing to get staden built?  I'm looking to use GAP5

     
  • James Bonfield
    James Bonfield
    2010-11-26

    It's a bit confusing, but there is a difference between -with-tk and -with-tklib. So latter is the tklib tcl package of various tk extensions. It can be found at https://sourceforge.net/projects/tcllib/files/ along with tcllib.

    There may also be issues with tcl/tk 8.5. I'm not sure yet as we haven't done much testing on those releases yet. (Nor do we test much on MacOS X as I only have access to an aging iMac.) I do plan on another round of portability testing sometime soon though.

     
  • Forster
    Forster
    2010-11-26

    I was able to get a bit further yesterday.  I downloaded and installed through macports tk, tcl, itcl, tcllib itcl and iwidgets.  I still got the tklib error so I followed the above link and downloaded and installed tklib.  The only thing I was missing was itk. It wouldn't install through macports. Reading that it wasn't really necessary I went through the staden configure files and took out all the code referring to itk. It then configured and built and I could get GAP5 to start.

    I'm now trying to import  some result files from MIRA and I'm having trouble compiling the CAF2GAP program.  It looks like I have to edit the makefile so it points to the proper staden src and other directories on my mac. I'm just hacking my way through this with very little programming knowledge. Hopefully I can get it to work!

    cheers

     
  • Dear forsterb,

    Any update on your progress? You are key to many forum readers!

    good luck!

     
  • caf2gap is a part of caftools now.

    wget ftp://ftp.sanger.ac.uk/pub/PRODUCTION_SOFTWARE/src/caftools-2.0.tar.gz
    gzip -dc caftools-2.0.tar.gz | tar xvf -
    cd caftools-2.0
    sed -i 's#prefix = /usr#prefix = $(DESTDIR)/usr#' Makefile
    sed -i 's#prefix = /usr#\#prefix = $(DESTDIR)/usr#' src/Makefile

    patch -p0 < EOF
    -- src/Makefile.in.ori 2010-12-05 22:08:50.000000000 +0100
    +++ src/Makefile.in     2010-12-05 22:10:07.000000000 +0100
    @@ -18,7 +18,7 @@
    srcdir = @srcdir@
    top_srcdir = @top_srcdir@
    VPATH = @srcdir@
    -prefix = @prefix@
    +prefix = $(DESTDIR)/@prefix@
    exec_prefix = @exec_prefix@

    bindir = @bindir@
    @@ -394,14 +394,14 @@
    binPROGRAMS_INSTALL = $(INSTALL_PROGRAM)
    install-binPROGRAMS: $(bin_PROGRAMS)
            @$(NORMAL_INSTALL)
    -       $(mkinstalldirs) $(DESTDIR)$(bindir)
    +       $(mkinstalldirs) $(bindir)
            @list='$(bin_PROGRAMS)'; for p in $$list; do \
              p1=`echo $$p|sed 's/$(EXEEXT)$$//'`; \
              if test -f $$p \
              ; then \
                f=`echo "$$p1" | sed 's,^.*/,,;$(transform);s/$$/$(EXEEXT)/'`; \
    -          echo " $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(DESTDIR)$(bindir)/$$f"; \
    -          $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(DESTDIR)$(bindir)/$$f; \
    +          echo " $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(bindir)/$$f"; \
    +          $(INSTALL_PROGRAM_ENV) $(binPROGRAMS_INSTALL) $$p $(bindir)/$$f; \
              else :; fi; \
            done

    @@ -409,8 +409,8 @@
            @$(NORMAL_UNINSTALL)
            @list='$(bin_PROGRAMS)'; for p in $$list; do \
              f=`echo "$$p" | sed 's,^.*/,,;s/$(EXEEXT)$$//;$(transform);s/$$/$(EXEEXT)/'`; \
    -         echo " rm -f $(DESTDIR)$(bindir)/$$f"; \
    -         rm -f $(DESTDIR)$(bindir)/$$f; \
    +         echo " rm -f $(bindir)/$$f"; \
    +         rm -f $(bindir)/$$f; \
            done

    clean-binPROGRAMS:
    @@ -663,7 +663,7 @@
    all-am: Makefile $(PROGRAMS) config.h
    installdirs: installdirs-recursive
    installdirs-am:
    -       $(mkinstalldirs) $(DESTDIR)$(bindir)
    +       $(mkinstalldirs) $(bindir)

    install: install-recursive
    install-exec: install-exec-recursive
    EOF

     
  • sir,
    while i was installing staden package i receive following error

    make: Entering directory `/home/du/Downloads/staden-2.0.0b7-src/src/gap5'
    /home/du/Downloads/staden-2.0.0b7-src/src/../gap5/Makefile:6: system.mk: No such file or directory
    make: *** No rule to make target `system.mk'.  Stop.
    make: Leaving directory `/home/du/Downloads/staden-2.0.0b7-src/src/gap5'
    make: ***  Error 2
    root@du-CELSIUS-R670-2:/home/du/Downloads/staden-2.0.0b7-src/src#

    please tell me what i need to do to over cum this error, so that i can install the package for utilization.
    also i am attaching the full terminal out put which was generated  so that you can get some clue where i was wrung or what need to be done for installing staden

    thank you
    regards
    -
    Vineet Jha
    Institute of Genomics and Integrative Biology (CSIR)

     
  • Hello Vineet,

    Could you give me more information on what you were doing and what version of the operating  you are using?  The full terminal output you attached does not show up on SourceForge.  If it is too big to paste here you can send it to me at aw7 at sanger ac uk.

    regards,

    Andrew