Re: Any progress with FIS GT.M?
my replies are interleaved with quotes of your email
On Tue, 19 Jun 2012, Luis Ibanez wrote:
> Here is the status of what we have
> done with Brad this afternoon.
> 1) The package for fis-gtm is now building and installing
> correctly by using the following git HEAD
yeay!
> [1]https://github.com/luisibanez/fis-gtm/commit/74aa25e0751a28a08202a13f9f13c79e532c29ab
do not use this one, but rather use straight hackathonjune2012-brad
branch + run
quilt push -a
when you extract that .orig into your packaging (or just use
svn-buildpackage if you do not care really to modify anything in
upstream sources -- it should apply patches while building the package
IIRC).
I have been pedantic and kept updating version in debian/changelog so it
points to the git treeish which I built against, e.g.:
$> head -1 debian/changelog
fis-gtm (5.5-000+git87-g5b7c3e5-1) UNRELEASED; urgency=low
so you can just look at it in the "upstream" git but cut/pasting just strip debian revision:
$> git show 5.5-000+git87-g5b7c3e5
commit 5b7c3e51e718bdeb185a8de3dbae7a415c57617b
Author: Brad King <brad.king@kitware.com>
Date: Mon Jun 18 13:36:35 2012 -0400
Make rules using 'mumps' depend on executable
This ensures they re-run if the executable changes.
;-)
> applying to it the following patch to the git sources:
> diff --git a/sr_unix/configure.gtc b/sr_unix/configure.gtc
> index 7b3a604..08a83d2 100644
> --- a/sr_unix/configure.gtc
> +++ b/sr_unix/configure.gtc
> @@ -592,7 +592,7 @@ if [ -d "$plugin_gtmcrypt" ]; then
>
> # Install gpgagent.tab
> # This is an external call table so the path to the shared library
> has to be adjusted
> - echo "$gtmdist/plugin/libgtmcrypt.so" >
> $gtmdist/$plugin/gpgagent.tab
> + echo "${gtmdist#${gtm_destdir:-}}/plugin/libgtmcrypt.so" >
> $gtmdist/$plugin/gpgagent.tab
> cat $plugin/gpgagent.tab | sed 1d >> $gtmdist/$plugin/gpgagent.tab
>
> This change above probably should be setup as a patch in Debian-med SVN
> debian-med/trunk/packages/fis-gtm/fis-gtm/trunk/debian/patches
> Yaroslav:
> Is this something that should be combined with the existing
> patch below ? :
> fis-gtm/trunk/debian/patches/up_gtm_destdir_substitution
> since this one also affects the file sr_unix/configure.gtc.
yes -- I updated the patch in revision 11397
> 2) The debian package is now created correctly, and we manage
> to install it in the destination directory /usr/lib/fis-gtm as
> expected.
I always was able to do so :-P the question always remained the same
though -- "is it usable?" and indeed we seems to be getting really close ;)
> 3) The only remaining problem is that several executables are lacking
> execution permissions. More specifically, we found that in:
> /usr/lib/fis-gtm/V5.5-000_i486
> The following files do not have execution permissions:
> ...
> Amul: Could you help us navigate the internal rules of
> gtminstall, to figure out where is it that the execution
> permissions are being lost ?
+ zhelp still doesn't work for me... installed the generated .deb's and
ran
export gtm_dist=/usr/lib/fis-gtm/V5.5-000_x86_64 ; gtmroutines=$gtm_dist/libgtmutil.so strace -fF -o /tmp/123strace5.log $gtm_dist/mumps -run %XCMD 'zhelp'
looking at strace somewhat worrisome sign:
$> grep open.*RDW /tmp/123strace5.log
1328 open("/usr/lib/fis-gtm/V5.5-000_x86_64/gtmhelp.dat", O_RDWR) = -1 EACCES (Permission denied)
1328 open("gtmhelp.dmp", O_RDWR|O_CREAT|O_NOCTTY|O_TRUNC, 0600) = 3
WHY is it trying to open gtmhelp.dat for writing? (I might now understand why
permissions had to be "sanitized" ;) )
it does open it RO later on:
open("/usr/lib/fis-gtm/V5.5-000_x86_64/gtmhelp.dat", O_RDONLY) = 3
but then it crashes at the end after:
1328 open("/usr/lib/fis-gtm/V5.5-000_x86_64/_XCMD.m", O_RDONLY) = 3
1328 open("/usr/lib/fis-gtm/V5.5-000_x86_64/GTMHELP.m", O_RDONLY) = 3
1328 open("gtmhelp.dmp", O_RDWR|O_CREAT|O_NOCTTY|O_TRUNC, 0600) = 3
1328 open("/etc/localtime", O_RDONLY) = 4
leaving me with "gtmhelp.dmp" ... so obviously I also could not run zhelp
while in any non-writable directory, e.g. /usr while not being root
+ after we resolve all the permissions and zhelp issues we should definitely
add few of those simple scripts to be ran as basic smoke tests at package build
time
+ it might be worth creating /etc/fis-gtm/APIVER/fis-gtm.sh (and a
corresponding symlink under /etc/fis-gtm for non-api-versioned fis-gtm package)
which would define all those wonderful environment variables so people could
just source it to start using fis-gtm.
+ I still think I have forgotten smth... we should have kept a TODO ;)
+ ah right -- test/fix packaging on 32bit system ;)
--
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
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