Re: Any progress with FIS GT.M?

[Yaroslav Halchenko <debian@onerussian.com>]

Luis,  I have inlined my answers ... I do not have a "working" checkout
of fis-gtm since there was some restructuring you guys were talking
about -- please commit them.

On Mon, 02 Jul 2012, Shah, Amul wrote:
> I did not see this email in the debian-med mailing list archive, so I'm re-sending.
> my comments marked as [amul:1].

> >W: fis-gtm source: newer-standards-version 3.9.3 (current is 3.9.1)

use the freshiest lintian ;-) better use Debian sid (unstable)
altogether (e.g. in VM) for the working environment to test it
appropriately

> >W: fis-gtm-5.5.000: executable-not-elf-or-script ./usr/lib/fis-gtm/V5.5-000_x86_64/gtmprofile
> >W: fis-gtm-5.5.000: executable-not-elf-or-script ./usr/lib/fis-gtm/V5.5-000_x86_64/gtmprofile_preV54000
> >W: fis-gtm-5.5.000: executable-not-elf-or-script ./usr/lib/fis-gtm/V5.5-000_x86_64/gtmstart
> >W: fis-gtm-5.5.000: executable-not-elf-or-script ./usr/lib/fis-gtm/V5.5-000_x86_64/gtcm_run
> >W: fis-gtm-5.5.000: executable-not-elf-or-script ./usr/lib/fis-gtm/V5.5-000_x86_64/gtmstop
> >W: fis-gtm-5.5.000: executable-not-elf-or-script ./usr/lib/fis-gtm/V5.5-000_x86_64/gtmcshrc
> >W: fis-gtm-5.5.000: executable-not-elf-or-script ./usr/lib/fis-gtm/V5.5-000_x86_64/gtcm_slist

> [amul:1] I'm going to hazard a guess that that lintian expects file extensions
> or shebang on the first line to identify what the file is doing.
> ...
> The others are bourne shell scripts that lack the shebang. I'm going
> to look into their usage and see if we can add that into them.

yeap -- all executables scripts must have shebang to guarantee proper
environment to be chosen.

> Of the scripts
> above, gtmprofile* and gtmcshrc are bourne shell and C-shell scripts for users
> to source.

if they are to be sourced they should not be executable... we might
altogether place them under /etc/fis-gtm/5.5.000/ since they sound like
environment configuration files.  Are they supposed to be sourced by any
fis-gtm's script? then we might like to symlink them back under
/usr/lib/fis-gtm/V5.5-000_x86_64/


> >W: fis-gtm-5.5.000: extra-license-file usr/lib/fis-gtm/V5.5-000_x86_64/COPYING
> [amul:1] Is this because it is also in ./usr/share/doc/fis-gtm-5.5.000/copyright?

most probably.  if no internal scripts/binaries rely on it to be there:
rm after installation (in debian/rules).  If they are needed -- lintian
override is needed with a description for that

> >W: fis-gtm-5.5.000: shlib-with-executable-stack usr/lib/fis-gtm/V5.5-000_x86_64/libgtmshr.so
> [amul:1] This is expected. Ignore it

weird -- that should have been ignored since I added creation of an
override in debian/rules... may be that old lintian did not understand
the '*' in the file pattern... test with  a fresh one

> >W: fis-gtm-5.5.000: shared-lib-without-dependency-information ./usr/lib/fis-gtm/V5.5-000_x86_64/libgtmutil.so
> >W: fis-gtm-5.5.000: shared-lib-without-dependency-information ./usr/lib/fis-gtm/V5.5-000_x86_64/utf8/libgtmutil.so

> [amul:1] This is expected. The installation builds there shared libraries from
> compiled M code. Ignore it

we better then have an override (adjust debian/rules which generates it
) with such a comment 


> >                          gtmsecshr
> [amul:1] Not knowing anything about debuild or cowbuilder, I assume that you
> run the commands as a normal user. I would no expect gtmsecshr to have setuid
> permissions. Nor would I expect gtmsecshr to have setuid root permissions until
> the file is installed.

kinda resolved in my other comment -- need override_dh_fixperms.

> [amul:1] This is the only thing that I could find that resembles a post install script.
> ls -l ../build/luisibanez-fis-gtm-4077ab8/debian/fis-gtm-5.5.000/usr/share/lintian/overrides/fis-gtm-5.5.000
> -rw-r--r-- 1 ibanez ibanez 83 Jun 30 17:34 ../build/luisibanez-fis-gtm-4077ab8/debian/fis-gtm-5.5.000/usr/share/lintian/overrides/fis-gtm-5.5.000

that is those lintian overrides which get installed


> >So.. something is unfolding differently in the cowbuilder environment.
> >One thing that comes to mind is that in the CMakeList.txt file we
> >are expecting to find CMake 2.8.5 (or higher).

that is ok -- we have 2.8.8 in sid

> >(with debuild ) I have been building a local cmake (from the source
> >in the Git repository of CMake) and then running "debuild -d" so
> >it ignores the fact that the cmake dependency is not preset (as an
> >installed debian package).

evil you! ;) (see my comment about sid a as working environment)

> >It would look like something in the cowbuilder environment is preventing
> >the installation scripts from setting the right permissions, or maybe
> >from knowing that it has to modify the permissions....

those non-executable permissions are a bit weird to me to say the
truth -- may be another gift from dh_fixperms?... and I am lost
already either it was resolved or not ;)

Hope this helps
-- 
Yaroslav O. Halchenko
Postdoctoral Fellow,   Department of Psychological and Brain Sciences
Dartmouth College, 419 Moore Hall, Hinman Box 6207, Hanover, NH 03755
Phone: +1 (603) 646-9834                       Fax: +1 (603) 646-1419
WWW:   http://www.linkedin.com/in/yarik