Re: Re: still grappling with ISIS

On Thu, Oct 17, 2013 at 16:56 -0500, Daryl Haggard wrote:
> Okay, sorry about the attachments, I'll try to summarize where I am
> without them...
> 
> I have had more dialog with the HEASOFT folks and tried new builds.
> Now it seems that S-Lang is having trouble. Here are the tail ends

I cc'd John Davis to let him know about the S-Lang installation
problem.  

It also looks like a S-Lang installation failure may be causing
the install-isis.sh script to exit early, so maybe the two
problems are related.

Regarding the missing readline symbols, it looks like the the
linker is not finding your readline library.  Where is readline
installed?

Although I don't recommend using LD_LIBRARY_PATH (or on Macs,
DYLD_LIBRARY_PATH), you might try a simple test by providing
the path to your libreadline via DYLD_LIBRARY_PATH and then try
again to compile slang.  For example, if libreadline is in
/usr/local/lib, you might try:

   setenv DYLD_LIBRARY_PATH /usr/local/lib
   cd /usr/local/slang-2.2.4
   make

Does that fix the S-Lang build problem? If that doesn't work,
perhaps John Davis will have a better suggestion.

Thanks,
-John


> of my slang-2.2.4 configure and make attempts:
> 
> % ./configure --with-readline=gnu > & config.out &
> % tail config.out
> 
> Installation Include Dir: ${prefix}/include
> 
> See also src/sl-feat.h for various features.
> 
> The following modules that depend upon external libraries will be built:
>    pcre oniguruma png z iconv
> 
> Type 'make' to build a shared version of the library.
> Type 'make help' for more options
> 
> % make > & build.log &
> % tail build.log
> 
> cd objs && /usr/bin/gcc -m32 -c -g -O2
> -I/usr/local/slang-2.2.4/src -DSLSH_CONF_DIR='"/usr/local/etc"'
> -DSLSH_PATH='"/usr/local/share/slsh"'
> -DSLSH_CONF_DIR_ENV='"SLSH_CONF_DIR"'
> -DSLSH_LIB_DIR_ENV='"SLSH_LIB_DIR"' -DSLSH_PATH_ENV='"SLSH_PATH"'
> /usr/local/slang-2.2.4/slsh/slsh.c
> cd objs && /usr/bin/gcc -m32 -c -g -O2
> -I/usr/local/slang-2.2.4/src -DSLSH_CONF_DIR='"/usr/local/etc"'
> -DSLSH_PATH='"/usr/local/share/slsh"'
> -DSLSH_CONF_DIR_ENV='"SLSH_CONF_DIR"'
> -DSLSH_LIB_DIR_ENV='"SLSH_LIB_DIR"' -DSLSH_PATH_ENV='"SLSH_PATH"'
> -DUSE_GNU_READLINE=1 /usr/local/slang-2.2.4/slsh/readline.c
> /usr/bin/gcc -m32 -g -O2   objs/slsh.o objs/readline.o -o
> objs/slsh_exe -m32  -L/usr/local/slang-2.2.4/src/elfobjs -lslang
> -lreadline -ldl  -lm
> Undefined symbols for architecture i386:
>   "_rl_delete_text", referenced from:
>       _gnu_rl_sigint_handler in readline.o
> ld: symbol(s) not found for architecture i386
> clang: error: linker command failed with exit code 1 (use -v to see
> invocation)
> make[1]: *** [objs/slsh_exe] Error 1
> make: *** [elf] Error 2
> 
> I installed readline 6.2 (with a few recent patches), in addition to
> onig-5.9.4, pcre-8.33, and libpng-1.6.6, before attempting to
> install S-Lang.
> 
> I have also tried using the isis install script, but it doesn't seem
> to run on my machine (where I've put the source code in
> /usr/local/isis-src/):
> 
> # sh install-isis.sh /usr/local/isis-1.6.2-27
> 
> I'm about to download files into /usr/local/isis-src/isis-build
> then install into /usr/local/isis-1.6.2-27
> 
> ok? [y/N] y
> downloading slang ...
> 
> And that's it, the script creates a directory called isis-build
> within the isis-src directory but doesn't put anything in it, and
> that's all she wrote. Perhaps it's because I've already tried to
> install S-Lang? Not sure, but with no other errors or complaints to
> work with.
> 
> Thanks,
> Daryl
> 
> On 10/17/13 9:05 AM, David P. Huenemoerder wrote:
> >Note: our majordomo server doesn't like large attachements; I've
> >       stripped them to post the body of the message.  Perhaps they
> >       might fit if compressed and then attached?
> >
> >-- Dave
> >
> >David Huenemoerder   (617-253-4283)
> >MIT Kavli Institute for Astrophysics and Space Research
> >One Hampshire Street, Room NE80-6065
> >Cambridge, MA  02139
> >[Admin. Asst.: Elaine Tirrell, 617-253-7480, egt_at_email.domain.hidden> >
> >-----------------------------------------------------------------------------
> >
> >In isis-users, you wrote:
> >
> >>Sender: Daryl Haggard <darylhaggard_at_email.domain.hidden> >>Message-ID: <525F141D.4050301_at_email.domain.hidden> >>Date: Wed, 16 Oct 2013 17:33:01 -0500
> >>From: Daryl Haggard <dhaggard_at_email.domain.hidden> >>User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10.8; rv:24.0) Gecko/20100101 Thunderbird/24.0.1
> >>MIME-Version: 1.0
> >>To: "isis-users_at_email.domain.hidden> >>Subject: still grappling with ISIS
> >>Content-Type: multipart/mixed;
> >>  boundary="------------060203040503020004010303"
> >>
> >>This is a multi-part message in MIME format.
> >>--------------060203040503020004010303
> >>Content-Type: text/plain; charset=ISO-8859-1; format=flowed
> >>Content-Transfer-Encoding: 7bit
> >>
> >>Hi folks,
> >>
> >>I have stripped my software down and rebuilt HEASOFT/XSPEC (also S-Lang,
> >>GNU Readline, SLIRP), but now can't get ISIS to build/initialize
> >>properly. Note that the HEASOFT/XSPEC build required a patch for XCode
> >>5, and a lot of email support from
> >>not-to-be-named-folks-who-know-a-lot-about-XSPEC.
> >>
> >>I attach my ISIS config.out, build.log, and install.log files here (Mac
> >>OS X 10.8.5). There are no errors that I see and the 'make' completes,
> >>but clearly there are issues. It looks like there's something wrong with
> >>the modules I have in ISIS and/or HEADAS. E.g., when I call
> >>
> >>% isis
> >>
> >>*** isis initialization failed; using ISIS_SRCDIR = /usr/local/isis/1.6.2
> >>
> >>Error linking to /usr/local/isis/1.6.2/lib/modules/pgplot-module.so:
> >>dlopen(/usr/local/isis/1.6.2/lib/modules/pgplot-module.so, 10): Symbol
> >>not found: _cpgconf
> >>    Referenced from: /usr/local/isis/1.6.2/lib/modules/pgplot-module.so
> >>    Expected in: flat namespace
> >>   in /usr/local/isis/1.6.2/lib/modules/pgplot-module.so
> >>Traceback: import
> >>/usr/local/isis/1.6.2/share/pgplot.sl:1:<top-level>:Import Error
> >>Traceback: evalfile
> >>Traceback: evalfile
> >>*** isis initialization failed
> >>
> >>I get similar complaints if I call 'make check' before 'make install'.
> >>And there are similar warnings (but not errors?) in the attached files.
> >>E.g., in the config.out file
> >>
> >>ls: /usr/local/heasoft-6.14/i386-apple-darwin12.5.0/lib/libpgplot*.so:
> >>No such file or directory
> >>
> >>You'll also note in the config.out file that there is a warning about
> >>using mismatched versions of my compilers
> >>
> >>WARNING: possibly mismatched C and Fortran compilers:
> >>          CC version = Configured with:
> >>--prefix=/Applications/Xcode.app/Contents/Developer/usr
> >>--with-gxx-include-dir=/usr/include/c++/4.2.1
> >>          FC version = GNU Fortran (GCC) 4.8.1
> >>
> >>I do have matched compilers in /usr/local/bin, but could not use the
> >>4.8.1 versions of gcc and g++ during my HEASOFT install (some XCode
> >>problem, those compilers MUST be in /usr/bin). I can change these for
> >>the ISIS installation, but wasn't sure whether it would be bad to use
> >>different compilers for installing XSPEC and ISIS, and that may not
> >>resolve the issue with the missing modules anyway.
> >>
> >>Thanks for any help you can offer.
> >>
> >>All the best,
> >>Daryl
> >>
> >>--
> >>Dr. Daryl Haggard
> >>CIERA Fellow, Northwestern University
> >>Dearborn Observatory
> >>2131 Tech Drive
> >>Evanston, IL 60208-2900
> >>http://ciera.northwestern.edu/dhaggard
> >>
> >
> >
> >[ attachments deleted due to size ]
> >
> >----
> >You received this message because you are
> >subscribed to the isis-users list.
> >To unsubscribe, send a message to
> >isis-users-request_at_email.domain.hidden> >with the first line of the message as:
> >unsubscribe
> >
> 
> -- 
> Dr. Daryl Haggard
> CIERA Fellow, Northwestern University
> Dearborn Observatory
> 2131 Tech Drive
> Evanston, IL 60208-2900
> http://ciera.northwestern.edu/dhaggard
> ----
> You received this message because you are
> subscribed to the isis-users list.
> To unsubscribe, send a message to
> isis-users-request_at_email.domain.hidden> with the first line of the message as:
> unsubscribe

----
You received this message because you are
subscribed to the isis-users list.
To unsubscribe, send a message to
isis-users-request_at_email.domain.hiddenwith the first line of the message as:
unsubscribe