date:20120619

actually I think I found a way how it should be done if a utf8 locale is
required

http://www.mattfischer.com/blog/?p=105

;-) just to make sure -- utf8 local influences only utf8/* builds and has no
(negative) impact otherwise, right? ;)

On Wed, 20 Jun 2012, Yaroslav Halchenko wrote:

> Amul, Bhaskar -- question to you,

> testing installation in a clean chroot (using cowbuilder) it fails
> with
-- 
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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Re: How to proceed with EMBOSS packaging (Was: About having EMBOSS 6.4.0 in Wheezy or not.)

2012-06-19 Thread Charles Plessy

Le Tue, Jun 19, 2012 at 04:07:24PM +0200, Andreas Tille a écrit :
> 
> as you probably have noticed when watching commit logs I started working
> on EMBOSS packaging.  I was a bit unsure about some changes (perhaps
> refreshing all quilt patches might have been questionably - feel free to
> revert)

Hi Andreas,

thank you for the help.

For the quilt patches, please revert the switch to format 3.0 (quilt), as the
upstream patches are not always compatible with this format (but they are
compatible with quilt).  I would really prefer keep the original upstream patch
instead of reformatting, as it is easier to make sure that we are using the
latest one. 


> I also do have some additional question how to handle some
> lintian issues:
> 
>   1. E: emboss-lib: embedded-library usr/lib/emboss/lib/libepcre.so.7.0.9: 
> pcre3

This is a slightly modified copy of the PCRE library.  We can not use the one
from Debian.  I prefer to keep the lintian tag visible so that the issue stays
in our radar.

>  Any comment on this?
> 
>   2. W: jemboss: codeless-jar usr/share/EMBOSS/jemboss/resources/acdstore.jar
>as well as
>  W: jemboss: classpath-contains-relative-path 
> usr/share/EMBOSS/jemboss/lib/jemboss.jar: lib/jakarta-regexp-1.2.jar, 
> lib/jalviewApplet.jar
> 
>  This looks suspicious - perhaps I need to contact our Java experts
>  about this.

I can not help for this.  But if that warning was already present before, and
if JEmboss works apparently well, I would recommend to ignore it.

>   3. W: emboss: menu-command-not-in-package usr/share/menu/emboss:8 
> usr/bin/x-terminal-emulator
>  ...
> 
>  Are you *really* sure that it is necessary to call x-terminal-emulator?
>  My guess is that the reason for this is the way you want the screen
>  to remain via
>"...;echo press any key to continue"
>  If this assumption is right we probably should add an override because
>  the lintian output is that bloated to possibly oversee some relevant
>  things.
> 
>  On the other hand: Do users really call these tools via menu?
>  Wouldn't it be better to drop the menu support at all and rather
>  teach users using command line?

Let's remove these menu entries for command-line programs.

Cheers,

-- 
Charles Plessy
Debian Med packaging team,
http://www.debian.org/devel/debian-med
Tsurumi, Kanagawa, Japan


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Re: Any progress with FIS GT.M?

Amul, Bhaskar -- question to you,

testing installation in a clean chroot (using cowbuilder) it fails
with

-- Installing: 
/tmp/buildd/fis-gtm-5.5-000+git92-g81e6aa8/debian/fis-gtm-5.5.000-stage1/usr/lib/fis-gtm/V5.5-000_x86_64/GDEVERIF.o
CMake Error at cmake_install.cmake:699 (FILE):
  file INSTALL cannot find
  "/tmp/buildd/fis-gtm-5.5-000+git92-g81e6aa8/obj-x86_64-linux-gnu/utf8/GDE.o".

make[2]: *** [install] Error 1
make[2]: Leaving directory 
`/tmp/buildd/fis-gtm-5.5-000+git92-g81e6aa8/obj-x86_64-linux-gnu'
dh_auto_install: make -j1 install 
DESTDIR=/tmp/buildd/fis-gtm-5.5-000+git92-g81e6aa8/debian/fis-gtm-5.5.000-stage1
 AM_UPDATE_INFO_DIR=no returned exit code 2
make[1]: *** [override_dh_auto_install] Error 29
make[1]: Leaving directory `/tmp/buildd/fis-gtm-5.5-000+git92-g81e6aa8'

due to apparently failed build of everything under utf8/:

root@head2:~/fis-gtm-5.5-000+git92-g81e6aa8/obj-x86_64-linux-gnu# ls utf8/
GDE.m GDECHANG.m  GDEEXIT.m  GDEHELP.m  GDELOCKS.m  GDEMAP.mGDEOGET.m   
GDEPUT.m   GDERENAM.m  GDESETGD.m  GDESPAWN.m  GDEVERIF.m
GDEADD.m  GDEDELET.m  GDEGET.m   GDEINIT.m  GDELOG.mGDEMSGIN.m  GDEPARSE.m  
GDEQUIT.m  GDESCAN.m   GDESHOW.m   GDETEMPL.m


due to:

[ 92%] Generating utf8/GDE.o
cd /tmp/buildd/fis-gtm-5.5-000+git92-g81e6aa8/obj-x86_64-linux-gnu/utf8 && 
/usr/bin/cmake -D 
gtm_dist=/tmp/buildd/fis-gtm-5.5-000+git92-g81e6aa8/obj-x86_64-linux-gnu -D 
gtmroutines=. -D gtm_chset=UTF-8 -D gtm_icu_version=4.8 -D 
mumps=/tmp/buildd/fis-gtm-5.5-000+git92-g81e6aa8/obj-x86_64-linux-gnu/mumps -D 
args=/tmp/buildd/fis-gtm-5.5-000+git92-g81e6aa8/obj-x86_64-linux-gnu/utf8/GDE.m 
-P /tmp/buildd/fis-gtm-5.5-000+git92-g81e6aa8/sr_unix/mumps.cmake
%GTM-E-NONUTF8LOCALE, Locale has character encoding (ANSI_X3.4-1968) which is 
not compatible with UTF-8 character set

I needed to install locales and configure to have en.US-UTF8 -- then it
succeeded.  So I wonder -- if this requirement to have utf8 locale configured
at build time could be relaxed?  otherwise I would need to check how to assure
(if possible currently at all ;) never ran into such situation) presence of a
utf8 local in a sanitized (! ;-) ) environment.

Cheers,

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
>
> [1]https://github.com/luisibanez/fis-gtm/commit/74aa25e0751a28a08202a13f9f13c79e532c29ab
>     the Debian-med SVN revision 11396.
>     and 
>     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.
>2) The debian package is now created correctly, and we manage
>     to install it in the destination directory   /usr/lib/fis-gtm    as 
>     expected.
>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:
>-rw-r--r-- 1 root 12384036 Jun 19 15:04 gtcm_shmclean
>-rw-r--r-- 1 root 12892461 Jun 19 15:04 gtcm_play
>-rw-r--r-- 1 root 12908879 Jun 19 15:04 gtcm_server
>-rw-r--r-- 1 root 12938615 Jun 19 15:04 lke
>-rw-r--r-- 1 root 13261965 Jun 19 15:04 gtcm_gnp_server
>-rw-r--r-- 1 root 13400802 Jun 19 15:04 dse
>-rw-r--r-- 1 root 17167172 Jun 19 15:04 mupip
>  This seems to originate from a problem in
>  the way gtminstall is being run. 
>  We have verified that these files have execution permissions
>  after they have been generated by the CMake driven build.
>  They however lose the execution permissions by the time 
>   they are installed in:
>      ./debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000_i486/
>Amul:  Could you help us navigate the internal rules of 
>           gtminstall, to figure

Re: Any progress with FIS GT.M?

> + I still think I have forgotten smth... we should have kept a TODO ;)

> + ah right -- test/fix packaging on 32bit system ;)

RRIGHT -- now I remembered:

+ following Bhaskar's recommendation -- for prerm script to verify
that there is no running instances

-- 
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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Re: Any progress with FIS GT.M?


On Tue, 19 Jun 2012, Bhaskar, K.S wrote:
> >owned by root who is the one with ability to revert that anyways?
> [KSB4] Having installed files be read-only is good hygiene.  

I have heard that excessive sanitation leads to weaker immune system and
allergies ;)  but in general in Debian we just follow
http://www.debian.org/doc/debian-policy/ch-files.html#s-permissions-owners
"Files should be owned by root:root, and made writable only by the owner
and universally readable (and executable, if appropriate), that is mode
644 or 755. " and so on

> With
> the possible exception of the gtmsecshr that resides in $gtm_dist, I
> don't think any other process checks or relies on the installed
> files being read-only.

> Note that the files may be have a non-root group.

should we work toward creating/reserving a dedicated group for
fis-gtm?  I thought that for now we would just have everything
root.root... but due to the root-suid may be a dedicated group might be
a reasonable thing

> >I guess they shouldn't just be ignored, right?  but those .c's are the
> >original sources which aren't installed with the "stage1" installation --
> >is that just some legacy pieces in configure or am I missing smth?

> [KSB4] I think that is because we (maybe Amul?) changed the
> packaging of the database encryption plugin at the Hackathon.  Note
> that the plugin always goes out with full source code even in GT.M
> binary distribution because even if someone doesn't want to
> recompile GT.M (most users don't) they may want to recompile the
> encryption plugin to use openssl instead of libgrcypt, for example,
> or to tweak it to connect to their site's key management.

well, for any rebuilds they always would have an opportunity to apt-get
source and then dpkg-buildpackage after modifications... As for openssl
-- I guess we can't just provide a choice of prebuilt encryption plugins
due to openssl's license conflict with GPL (although with an additional
exception [1] that could be feasible!).  But then again -- a clear
description in README.Debian telling to do apt-get source  and taking
source.tar or just a straight source tree from there would imho be more
beneficial and reduce the size/pollution of default fis-gtm
installation.  So IMHO there is no reason for source.tar under
/usr/lib... worse come to worse and if you insist -- we could ship it
under /usr/src/fis-plugin-encryption.tar.gz ;)

[1] http://people.gnome.org/~markmc/openssl-and-the-gpl.html

-- 
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
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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 
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 Science

Re: Any progress with FIS GT.M?

2012-06-19 Thread Luis Ibanez

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

https://github.com/luisibanez/fis-gtm/commit/74aa25e0751a28a08202a13f9f13c79e532c29ab

 the Debian-med SVN revision 11396.

 and

 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 filesr_unix/configure.gtc.



2) The debian package is now created correctly, and we manage
 to install it in the destination directory   /usr/lib/fis-gtmas
 expected.


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:

-rw-r--r-- 1 root 12384036 Jun 19 15:04 gtcm_shmclean
-rw-r--r-- 1 root 12892461 Jun 19 15:04 gtcm_play
-rw-r--r-- 1 root 12908879 Jun 19 15:04 gtcm_server
-rw-r--r-- 1 root 12938615 Jun 19 15:04 lke
-rw-r--r-- 1 root 13261965 Jun 19 15:04 gtcm_gnp_server
-rw-r--r-- 1 root 13400802 Jun 19 15:04 dse
-rw-r--r-- 1 root 17167172 Jun 19 15:04 mupip



  This seems to originate from a problem in
  the way gtminstall is being run.

  We have verified that these files have execution permissions
  after they have been generated by the CMake driven build.

  They however lose the execution permissions by the time
   they are installed in:

  ./debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000_i486/


Amul:  Could you help us navigate the internal rules of
   gtminstall, to figure out where is it that the execution
   permissions are being lost ?


Thanks


  Luis

Re: Any progress with FIS GT.M?



On 06/19/12 15:01, Brad King wrote:
> On 06/19/2012 02:41 PM, Brad King wrote:
>> On 06/19/2012 02:20 PM, Amul Shah wrote:
>>> the path given to GDE should be '$gtm_dist/XYZhlp.dat'
>> Okay.  I pushed the help generation plus this fix
> Perhaps the change below is needed too for the destdir case,
> and does not hurt in the normal case?
>
> -Brad

[amul:2] Yes. That is what I meant in my last mail.


>
> diff --git a/sr_unix/configure.gtc b/sr_unix/configure.gtc
> index 0c5b54e..7b3a604 100644
> --- a/sr_unix/configure.gtc
> +++ b/sr_unix/configure.gtc
> @@ -754,7 +754,7 @@ export gtmgbldir
>
>  cat <  Do ^GDE
> -Change -segment DEFAULT-block=2048 -file=$gtmdist/gtmhelp.dat
> +Change -segment DEFAULT-block=2048 -file=\$gtm_dist/gtmhelp.dat
>  Change -region DEFAULT -record=1020-key=255
>  Exit
>  GDE.in1
> @@ -764,7 +764,7 @@ export gtmgbldir
>
>  cat <  Do ^GDE
> -Change -segment DEFAULT-block=2048 -file=$gtmdist/gdehelp.dat
> +Change -segment DEFAULT-block=2048 -file=\$gtm_dist/gdehelp.dat
>  Change -region DEFAULT -record=1020-key=255
>  Exit
>  GDE.in2

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Re: Any progress with FIS GT.M?

On 06/19/2012 02:41 PM, Brad King wrote:
> On 06/19/2012 02:20 PM, Amul Shah wrote:
>> the path given to GDE should be '$gtm_dist/XYZhlp.dat'
> 
> Okay.  I pushed the help generation plus this fix

Perhaps the change below is needed too for the destdir case,
and does not hurt in the normal case?

-Brad


diff --git a/sr_unix/configure.gtc b/sr_unix/configure.gtc
index 0c5b54e..7b3a604 100644
--- a/sr_unix/configure.gtc
+++ b/sr_unix/configure.gtc
@@ -754,7 +754,7 @@ export gtmgbldir

 cat

Re: Any progress with FIS GT.M?

On 06/19/2012 10:59 AM, Yaroslav Halchenko wrote:
> $> grep /home/yoh/deb/perspect/fis-gtm/.*debian/ -r .
> ./utf8/plugin/gpgagent.tab:/home/yoh/deb/perspect/fis-gtm/fis-gtm-gitsvn/debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_x86_64/plugin/libgtmcrypt.so
> ./plugin/gpgagent.tab:/home/yoh/deb/perspect/fis-gtm/fis-gtm-gitsvn/debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_x86_64/plugin/libgtmcrypt.so

These need an additional hunk in your gtm_destdir patch to configure.gtc.
Something like the below (untested).

-Brad


diff --git a/sr_unix/configure.gtc b/sr_unix/configure.gtc
index 0c5b54e..8b98ec9 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

# Tar the source files


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Re: Any progress with FIS GT.M?

On 06/19/2012 02:20 PM, Amul Shah wrote:
> the path given to GDE should be '$gtm_dist/XYZhlp.dat'

Okay.  I pushed the help generation plus this fix to branch

  hackathonjune2012-brad

-Brad


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Re: Any progress with FIS GT.M?

On 06/19/12 14:02, Brad King wrote:
> On 06/19/2012 01:34 PM, Brad King wrote:
>> Now the only errors I get from manually running "configure" are:
>>
>>  cp: cannot stat `gdehelp.dat': No such file or directory
>>  chown: cannot access `/home/kingb/GTM/Test2/gdehelp.dat': No such file or 
>> directory
>>  cp: cannot stat `gtmhelp.dat': No such file or directory
>>  chown: cannot access `/home/kingb/GTM/Test2/gtmhelp.dat': No such file or 
>> directory
>>  ...
>>  chmod: cannot access `/home/kingb/GTM/Test2/*.dat': No such file or 
>> directory
>>
>> Should these two files be built and installed by CMake?
> In case the answer is "yes", I pushed out branch
>
>  hackathonjune2012-brad-help-dat
>
> with commit
>
>  https://github.com/luisibanez/fis-gtm/commit/eb42ac55
>
> to do it.
>
> -Brad
[amul:4] thanks. I should have read my inbox before sending my last mail. There 
is one modification, the path given to GDE
should be '$gtm_dist/XYZhlp.dat' . GT.M will resolve the $gtm_dist to the 
correct location.

Amul

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Re: Any progress with FIS GT.M?



On 06/19/12 13:34, Brad King wrote:
> On 06/19/2012 01:21 PM, Amul Shah wrote:
>> [amul:2] Brad made the changes in CMakeLists.txt. So when you 'make install' 
>> instead of seeing the C files, you get a tarball
>> named 'source.tar' in '$gtm_dist/plugin/gtmcrypt/'. I can't find the commit 
>> for it, but its there. :)
> It was here:
>
>  https://github.com/luisibanez/fis-gtm/commit/68f30307
>
> though it was based on a commit by you which removed direct
> installation of those files.
[amul:3] Thanks. Yes, you did what I asked. :)

>> [amul:2] The CMake install directory is almost stage 2. What's missing for a 
>> complete stage2 are the help database files, all
>> the object files, and the replacements for GTM_DIST in the shell scripts. In 
>> order to let configure work as is, we should role
>> the install directory back to stage1 (my fault for bringing us past stage1).
> I pushed out a change to hackathonjune2012-brad that reverts
> this behavior and directly installs the files:
>
>  https://github.com/luisibanez/fis-gtm/commit/3b4bcd7e
>
> Now the only errors I get from manually running "configure" are:
>
>  cp: cannot stat `gdehelp.dat': No such file or directory
>  chown: cannot access `/home/kingb/GTM/Test2/gdehelp.dat': No such file or 
> directory
>  cp: cannot stat `gtmhelp.dat': No such file or directory
>  chown: cannot access `/home/kingb/GTM/Test2/gtmhelp.dat': No such file or 
> directory
>  ...
>  chmod: cannot access `/home/kingb/GTM/Test2/*.dat': No such file or directory
>
> Should these two files be built and installed by CMake?
[amul:3] Looking at the build scripts, yes. I'm going to create a separate 
cmake file for generating the help Global Directory
and Database file.

[amul:3] Is everyone generating the Unicode GDE files in the install directory? 
My machine is throwing an error, but I thought I
got past this part before without setting LC_CTYPE correctly.
%GTM-E-NONUTF8LOCALE, Locale has character encoding (ANSI_X3.4-1968) which is 
not compatible with UTF-8 character set

thanks,
Amu


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Re: Any progress with FIS GT.M?

On 06/19/2012 01:34 PM, Brad King wrote:
> Now the only errors I get from manually running "configure" are:
> 
>  cp: cannot stat `gdehelp.dat': No such file or directory
>  chown: cannot access `/home/kingb/GTM/Test2/gdehelp.dat': No such file or 
> directory
>  cp: cannot stat `gtmhelp.dat': No such file or directory
>  chown: cannot access `/home/kingb/GTM/Test2/gtmhelp.dat': No such file or 
> directory
>  ...
>  chmod: cannot access `/home/kingb/GTM/Test2/*.dat': No such file or directory
> 
> Should these two files be built and installed by CMake?

In case the answer is "yes", I pushed out branch

 hackathonjune2012-brad-help-dat

with commit

 https://github.com/luisibanez/fis-gtm/commit/eb42ac55

to do it.

-Brad


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Re: Any progress with FIS GT.M?

On 06/19/2012 01:21 PM, Amul Shah wrote:
> [amul:2] Brad made the changes in CMakeLists.txt. So when you 'make install' 
> instead of seeing the C files, you get a tarball
> named 'source.tar' in '$gtm_dist/plugin/gtmcrypt/'. I can't find the commit 
> for it, but its there. :)

It was here:

 https://github.com/luisibanez/fis-gtm/commit/68f30307

though it was based on a commit by you which removed direct
installation of those files.

> [amul:2] The CMake install directory is almost stage 2. What's missing for a 
> complete stage2 are the help database files, all
> the object files, and the replacements for GTM_DIST in the shell scripts. In 
> order to let configure work as is, we should role
> the install directory back to stage1 (my fault for bringing us past stage1).

I pushed out a change to hackathonjune2012-brad that reverts
this behavior and directly installs the files:

 https://github.com/luisibanez/fis-gtm/commit/3b4bcd7e

Now the only errors I get from manually running "configure" are:

 cp: cannot stat `gdehelp.dat': No such file or directory
 chown: cannot access `/home/kingb/GTM/Test2/gdehelp.dat': No such file or 
directory
 cp: cannot stat `gtmhelp.dat': No such file or directory
 chown: cannot access `/home/kingb/GTM/Test2/gtmhelp.dat': No such file or 
directory
 ...
 chmod: cannot access `/home/kingb/GTM/Test2/*.dat': No such file or directory

Should these two files be built and installed by CMake?

-Brad

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Re: Any progress with FIS GT.M?

2012-06-19 Thread Bhaskar, K.S

On 06/19/2012 11:36 AM, Yaroslav Halchenko wrote:

Bhaskar,

tiny questions:

- are there any internal checks/reliance on "installed" files being
read-only? what is the goal anyway behind making them read-only if
owned by root who is the one with ability to revert that anyways?

[KSB4] Having installed files be read-only is good hygiene. With the
possible exception of the gtmsecshr that resides in $gtm_dist, I don't
think any other process checks or relies on the installed files being
read-only.

Note that the files may be have a non-root group.

- shouldn't gtminstall have 'set -e' (or explicit || exit 1) so
in case configure call fails, gtminstall fails?

[KSB4] I don't know whether configure generates a valid status, but that
is a good suggestion for it to return one and for gtminstall to check for
one.

- due to above my installation 'succeeds' while configure generates quite
a bit of errors for me atm, e.g. pointing to missing gdehelp.dat etc

cp: cannot stat `gdehelp.dat': No such file or directory
chown: cannot access
`/home/yoh/deb/perspect/fis-gtm/fis-gtm-gitsvn/debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_x86_64/gdehelp.dat':
No such file or directory
cp: cannot stat `gtmhelp.dat': No such file or directory
chown: cannot access
`/home/yoh/deb/perspect/fis-gtm/fis-gtm-gitsvn/debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_x86_64/gtmhelp.dat':
No such file or directory
chmod: cannot access `gtmcrypt_ref.c': No such file or directory
chmod: cannot access `gtmcrypt_ref.h': No such file or directory
chmod: cannot access `gtmcrypt_interface.h': No such file or directory
chmod: cannot access `gtmxc_types.h': No such file or directory
chmod: cannot access `maskpass.c': No such file or directory
chmod: cannot access `gtmcrypt_dbk_ref.c': No such file or directory
...

I guess they shouldn't just be ignored, right? but those .c's are the
original sources which aren't installed with the "stage1" installation --
is that just some legacy pieces in configure or am I missing smth?

[KSB4] I think that is because we (maybe Amul?) changed the packaging of
the database encryption plugin at the Hackathon. Note that the plugin
always goes out with full source code even in GT.M binary distribution
because even if someone doesn't want to recompile GT.M (most users don't)
they may want to recompile the encryption plugin to use openssl instead
of libgrcypt, for example, or to tweak it to connect to their site's key
management.

Regards
-- Bhaskar

On Tue, 19 Jun 2012, Bhaskar, K.S wrote:

On 06/19/2012 12:03 AM, Yaroslav Halchenko wrote:

On 06/18/2012 02:42 PM, Brad King wrote:
Here is a patch series that solves this problem. I've only done
some lightweight/manual testing with this. The first patch
refactors both i386 and x86_64 code paths that emit the path to
the source file into the object file to send source file path
lookup through a common point (in obj_source.c). The second
patch modifies this common point to read a 'gtm_destdir' env var
and strip the prefix it names from source file paths.

I gave brief check to Brad's patches and adjusted Debian packaging in SVN to
make use of them (but without yet placing actual patches into quilt -- I just
grabbed the HEAD of his master for the .orig "tarball"). From the first
look (dumping strings on generated .o and .so) it did exactly what I hoped them
to do -- thanks Brad! Then I have tried to run those basic commands Bhaskar
has listed but it seems that mumps doesn't even try to load libgtmutil.so to
get access to all those pre-built .o's placed into this dynamic library on my
amd64 laptop... so anything I try fails, e.g.:

[KSB3] What is the value of $gtmroutines in the shell before you enter GT.M?
Regards
-- Bhaskar

--
GT.M - Rock solid. Lightning fast. Secure. No compromises.

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Re: Any progress with FIS GT.M?



On 06/19/12 12:41, Yaroslav Halchenko wrote:
> On Tue, 19 Jun 2012, Amul Shah wrote:
>
>>  chmod: cannot access `gtmcrypt_ref.c': No such file or directory
>>  chmod: cannot access `gtmcrypt_ref.h': No such file or directory
>>  chmod: cannot access `gtmcrypt_interface.h': No such file or directory
>>  chmod: cannot access `gtmxc_types.h': No such file or directory
>>  chmod: cannot access `maskpass.c': No such file or directory
>>  chmod: cannot access `gtmcrypt_dbk_ref.c': No such file or directory
>>  ...
>>  I guess they shouldn't just be ignored, right?  but those .c's are the
>>  original sources which aren't installed with the "stage1" installation --
>>  is that just some legacy pieces in configure or am I missing smth?
>>[amul:1] I asked Brad to tar those C files into source.tar which the
>>configure script is trying to do. If we revert that bit, the configure
>>script will work just fine. Or we fix the configure script to not package
>>the tar ball when it is already present.
> I am sorry but I am a bit lost since I do not see any relevant commits
> in those files:
>
> $> git lg sr_unix/configure.gtc sr_unix/gtminstall.sh
> * dee7100 - (5.5-000, origin/v55000, gh-yarikoptic/v55000) ENH: Version 
> 5.5000 from sourceforge. (3 months ago) [Luis Ibanez]
> * 9299623 - (origin/v54002B, origin/master, origin/HEAD, 
> gh-yarikoptic/v54002B, gh-yarikoptic/master, master) ENH: Initial import from 
> sourceforge. (5 months ago) [Luis Ibanez]
>
> anyways -- are they needed anyhow for stage2 building/installation to
> obtain the ultimate installation ? ;)
[amul:2] Brad made the changes in CMakeLists.txt. So when you 'make install' 
instead of seeing the C files, you get a tarball
named 'source.tar' in '$gtm_dist/plugin/gtmcrypt/'. I can't find the commit for 
it, but its there. :)

[amul:2] The CMake install directory is almost stage 2. What's missing for a 
complete stage2 are the help database files, all
the object files, and the replacements for GTM_DIST in the shell scripts. In 
order to let configure work as is, we should role
the install directory back to stage1 (my fault for bringing us past stage1).


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Re: Any progress with FIS GT.M?


On Tue, 19 Jun 2012, Yaroslav Halchenko wrote:
> >make: *** [binary] Error 9
> >dpkg-buildpackage: error: fakeroot debian/rules binary gave error exit
> >status 2
> >debuild: fatal error at line 1325:
> >dpkg-buildpackage -rfakeroot -d -us -uc failed
> >I'm doing this by running:
> >       debuild   -d
> >Any hints on what I might be doing wrong ?

> >or actually, to be more constructive,
> >where can Brad and I help now to move things forward ?     :-)

> please 

> * verify the permissions on binaries... either I screwed things up
> somewhere or not me:

> (git)novo:…tm-gitsvn[master]debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_x86_64
> $> file * | grep ELF | sed -e 's,:.*,,g' | xargs ls -l
> -rw-r--r-- 1 yoh yoh 2436250 Jun 19 11:19 dse
> -rw-r--r-- 1 yoh yoh   11765 Jun 19 11:19 ftok
> -rw-r--r-- 1 yoh yoh7344 Jun 19 11:19 geteuid
> -rw-r--r-- 1 yoh yoh 2616135 Jun 19 11:19 gtcm_gnp_server
> -rw-r--r-- 1 yoh yoh  320800 Jun 19 11:19 gtcm_pkdisp
> -rw-r--r-- 1 yoh yoh 2629203 Jun 19 11:19 gtcm_play
> -rw-r--r-- 1 yoh yoh 2637955 Jun 19 11:19 gtcm_server
> -rw-r--r-- 1 yoh yoh 2545944 Jun 19 11:19 gtcm_shmclean
> -rw-r--r-- 1 yoh yoh9808 Jun 19 11:19 gtmsecshr
> -rw-r--r-- 1 yoh yoh 2079480 Jun 19 11:19 libgtmshr.so
> -rw-r--r-- 1 yoh yoh 1003616 Jun 19 11:19 libgtmutil.so
> -rw-r--r-- 1 yoh yoh 2619251 Jun 19 11:19 lke
> -rwxr-xr-x 1 yoh yoh6792 Jun 19 11:19 mumps
> -rw-r--r-- 1 yoh yoh 3053950 Jun 19 11:19 mupip
> -rw-r--r-- 1 yoh yoh9674 Jun 19 11:19 semstat2

> * we should aim to make configure not report any error so we could make it set
> -e to robustify building - so whatever is reported in .err (e.g. those missing
> *help.dat should be fixed)

> * so we could harmonize things -- I will commit those Brad's patches into
> quilt in a minute and then we would work based on on the 'upstream' git branch

+ if you could work on that path adjustment (probably within
debian/rules or as a (quilt) patch to sr_unix/configure.gtc to fix up
paths in those *help* files

I need to wash off my hands for now and will look at it in the evening
for what would be left TODO

-- 
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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Re: Any progress with FIS GT.M?

On Tue, 19 Jun 2012, Yaroslav Halchenko wrote:
> > >tar: ./usr/lib/fis-gtm/V5.5-000+git80-g211bd16_i486/utf8/_utf2hex.m: 
> > > file
> > >changed as we read it
> > >dpkg-deb: subprocess tar -cf returned error exit status 1
> > >dh_builddeb: dpkg-deb --build debian/fis-gtm-5.5.000 .. returned exit 
> > > code
> > >2
> > >make: *** [binary] Error 9
> > >dpkg-buildpackage: error: fakeroot debian/rules binary gave error exit
> > >status 2
> > >debuild: fatal error at line 1325:
> > >dpkg-buildpackage -rfakeroot -d -us -uc failed
> > >I'm doing this by running:
> > >       debuild   -d
> > >Any hints on what I might be doing wrong ?

> ah -- I just wanted to say something silly obvious like -- verify that
> you do not have two processes running somehow ;)... and then realized
> that I haven't yet went through the full build process (just did
> debian/rules binary) for a while -- I will see if it replicates for me
> and will report back (I SVN committed those patches + some other minor
> changes now)

* nope -- it built just fine for me but I did it from clean
since we are working now with packaging in SVN I did

from "upstream git":
git archive --format=tar --prefix=fis-gtm-5.5-000+git87-g5b7c3e5/ 
origin/hackathonjune2012-brad | gzip -9 >| 
../fis-gtm_5.5-000+git87-g5b7c3e5.orig.tar.gz

to get the .orig tarball, and then in that SVN packaging repo (cloned
via git svn into GIT):

git clean -dfx; tar --strip-components=1 -xzvf 
../fis-gtm_5.5-000+git87-g5b7c3e5.orig.tar.gz && quilt push -a && 
PATH=/usr/lib/ccache:$PATH dpkg-buildpackage -uc -us -rfakeroot

and it built just fine.  I also did a round of 

PATH=/usr/lib/ccache:$PATH fakeroot debian/rules clean
PATH=/usr/lib/ccache:$PATH fakeroot debian/rules binary

and it seems to be fine


* Lintian is screaming again about non-fortified (not
necessary but desired) build flags,  which is due to:

,---
| $> git show d6506e286ac536a56ae4f8229fb075dcd6d16862
| commit d6506e286ac536a56ae4f8229fb075dcd6d16862
| Author: luisibanez-guest 

| Date:   Fri Jun 15 20:17:06 2012 +
|
| ENH: Reverting to version 8 to match VM.
|
| git-svn-id: 
svn+ssh://svn.debian.org/svn/debian-med/trunk/packages/fis-gtm/fis-gtm/trunk@11360
 d8681a01-af0d-0410-a158-b4166a59cfaa
|
| diff --git a/debian/compat b/debian/compat
| index ec63514..45a4fb7 100644
| --- a/debian/compat
| +++ b/debian/compat
| @@ -1 +1 @@
| -9
| +8
`---

which I would recommend to revert and update your VM to Debian sid since that
is our target ATM from what I understood ;)

-- 
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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Re: Any progress with FIS GT.M?

On Tue, 19 Jun 2012, Yaroslav Halchenko wrote:
> >tar: ./usr/lib/fis-gtm/V5.5-000+git80-g211bd16_i486/utf8/_utf2hex.m: file
> >changed as we read it
> >dpkg-deb: subprocess tar -cf returned error exit status 1
> >dh_builddeb: dpkg-deb --build debian/fis-gtm-5.5.000 .. returned exit 
> > code
> >2
> >make: *** [binary] Error 9
> >dpkg-buildpackage: error: fakeroot debian/rules binary gave error exit
> >status 2
> >debuild: fatal error at line 1325:
> >dpkg-buildpackage -rfakeroot -d -us -uc failed
> >I'm doing this by running:
> >       debuild   -d
> >Any hints on what I might be doing wrong ?

ah -- I just wanted to say something silly obvious like -- verify that
you do not have two processes running somehow ;)... and then realized
that I haven't yet went through the full build process (just did
debian/rules binary) for a while -- I will see if it replicates for me
and will report back (I SVN committed those patches + some other minor
changes now)

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Re: Any progress with FIS GT.M?


On Tue, 19 Jun 2012, Amul Shah wrote:

>  chmod: cannot access `gtmcrypt_ref.c': No such file or directory
>  chmod: cannot access `gtmcrypt_ref.h': No such file or directory
>  chmod: cannot access `gtmcrypt_interface.h': No such file or directory
>  chmod: cannot access `gtmxc_types.h': No such file or directory
>  chmod: cannot access `maskpass.c': No such file or directory
>  chmod: cannot access `gtmcrypt_dbk_ref.c': No such file or directory
>  ...

>  I guess they shouldn't just be ignored, right?  but those .c's are the
>  original sources which aren't installed with the "stage1" installation --
>  is that just some legacy pieces in configure or am I missing smth?

>[amul:1] I asked Brad to tar those C files into source.tar which the
>configure script is trying to do. If we revert that bit, the configure
>script will work just fine. Or we fix the configure script to not package
>the tar ball when it is already present.

I am sorry but I am a bit lost since I do not see any relevant commits
in those files:

$> git lg sr_unix/configure.gtc sr_unix/gtminstall.sh
* dee7100 - (5.5-000, origin/v55000, gh-yarikoptic/v55000) ENH: Version 5.5000 
from sourceforge. (3 months ago) [Luis Ibanez]
* 9299623 - (origin/v54002B, origin/master, origin/HEAD, gh-yarikoptic/v54002B, 
gh-yarikoptic/master, master) ENH: Initial import from sourceforge. (5 months 
ago) [Luis Ibanez]

anyways -- are they needed anyhow for stage2 building/installation to
obtain the ultimate installation ? ;)

-- 
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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Re: Any progress with FIS GT.M?


On Tue, 19 Jun 2012, Luis Ibanez wrote:
>tar: ./usr/lib/fis-gtm/V5.5-000+git80-g211bd16_i486/utf8/_utf2hex.m: file
>changed as we read it
>dpkg-deb: subprocess tar -cf returned error exit status 1
>dh_builddeb: dpkg-deb --build debian/fis-gtm-5.5.000 .. returned exit code
>2
>make: *** [binary] Error 9
>dpkg-buildpackage: error: fakeroot debian/rules binary gave error exit
>status 2
>debuild: fatal error at line 1325:
>dpkg-buildpackage -rfakeroot -d -us -uc failed
>I'm doing this by running:
>       debuild   -d
>Any hints on what I might be doing wrong ?

>or actually, to be more constructive,
>where can Brad and I help now to move things forward ?     :-)

please 

* verify the permissions on binaries... either I screwed things up
somewhere or not me:

(git)novo:…tm-gitsvn[master]debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_x86_64
$> file * | grep ELF | sed -e 's,:.*,,g' | xargs ls -l
-rw-r--r-- 1 yoh yoh 2436250 Jun 19 11:19 dse
-rw-r--r-- 1 yoh yoh   11765 Jun 19 11:19 ftok
-rw-r--r-- 1 yoh yoh7344 Jun 19 11:19 geteuid
-rw-r--r-- 1 yoh yoh 2616135 Jun 19 11:19 gtcm_gnp_server
-rw-r--r-- 1 yoh yoh  320800 Jun 19 11:19 gtcm_pkdisp
-rw-r--r-- 1 yoh yoh 2629203 Jun 19 11:19 gtcm_play
-rw-r--r-- 1 yoh yoh 2637955 Jun 19 11:19 gtcm_server
-rw-r--r-- 1 yoh yoh 2545944 Jun 19 11:19 gtcm_shmclean
-rw-r--r-- 1 yoh yoh9808 Jun 19 11:19 gtmsecshr
-rw-r--r-- 1 yoh yoh 2079480 Jun 19 11:19 libgtmshr.so
-rw-r--r-- 1 yoh yoh 1003616 Jun 19 11:19 libgtmutil.so
-rw-r--r-- 1 yoh yoh 2619251 Jun 19 11:19 lke
-rwxr-xr-x 1 yoh yoh6792 Jun 19 11:19 mumps
-rw-r--r-- 1 yoh yoh 3053950 Jun 19 11:19 mupip
-rw-r--r-- 1 yoh yoh9674 Jun 19 11:19 semstat2

* we should aim to make configure not report any error so we could make it set
-e to robustify building - so whatever is reported in .err (e.g. those missing
*help.dat should be fixed)

* so we could harmonize things -- I will commit those Brad's patches into
quilt in a minute and then we would work based on on the 'upstream' git branch

-- 
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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Re: Any progress with FIS GT.M?


On Tue, 19 Jun 2012, Bhaskar, K.S wrote:



> On 06/19/2012 10:59 AM, Yaroslav Halchenko wrote:
> >>>$>  strace -fF -o /tmp/123strace2.log $gtm_dist/mumps -direct
> >>It works for me if I add
> >>  gtmroutines=$gtm_dist/libgtmutil.so
> >>to the environment.
> >rright -- forgot about this one ;-)  so many hidden precious env
> >variables without any punishing me-forgetful error messages ;)

> [KSB] Actually, GT.M did issue an error message saying it couldn't
> find the routine!

do you mean:
$> gtm_dist=/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_x86_64 
/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_x86_64/mumps -run %XCMD 'write 
$text(^%RSEL)' 
%GTM-E-ZLINKFILE, Error while zlinking "%XCMD"
%GTM-E-FILENOTFND, File %XCMD not found

this one?  I was just whining that it was not as as descriptive for a silly me 
as

%GTM-E-FILENOTFND, File %XCMD not found.  Use gtmroutines environment variable 
to define the path to routines

;-)

> >so whenever help files and gpgagent.tab is composed we should strip prefix as
> >well.   Is there a clean "fix"? ;)

> [KSB] Yes, there is.  The GDE program is used to maintain the global
> directory (gtmhelp.gld) which in turn points to the help database.
> This is easily fixed as follows:

> # export gtm_dist=
> # export gtmroutines=$gtm_dist/libgtmutil.so
> # export gtmgbldir=$gtm_dist/gdehelp.gld
> # $gtm_dist/mumps -run GDE
> >...<
> This should make both ZHELP and the HELP command in GDE work.

COOL -- I will give it a shout

> >dpkg-shlibdeps: warning: 
> >debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_x86_64/plugin/libgtmcrypt.so
> > contains an unresolvable reference to symbol gtm_ci: it's probably a plugin.
> [KSB] The database encryption plugin always runs in the context of a
> mumps process, which should provide the gtm_* functions.

coolio -- less TODO then ;)

-- 
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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Re: Any progress with FIS GT.M?

2012-06-19 Thread Bhaskar, K.S




On 06/19/2012 10:59 AM, Yaroslav Halchenko wrote:

$>  strace -fF -o /tmp/123strace2.log $gtm_dist/mumps -direct

It works for me if I add
  gtmroutines=$gtm_dist/libgtmutil.so
to the environment.

rright -- forgot about this one ;-)  so many hidden precious env
variables without any punishing me-forgetful error messages ;)


[KSB] Actually, GT.M did issue an error message saying it couldn't find 
the routine!



also we need to adjust/patch configure so it strips the gtm_destdir
during s|GTMDIST|$gtmdist|g, i.e.

$>  quilt diff
--- a/sr_unix/configure.gtc
+++ b/sr_unix/configure.gtc
@@ -371,7 +371,7 @@ fi
  cat<<  SEDSCRIPT>  sedin$$
  s|ARCH|$arch|g
  s|ECHO|"$echo"|g
-s|GTMDIST|$gtmdist|g
+s|GTMDIST|${gtmdist#${gtm_destdir:-}}|g
  s|SERVERID|$server_id|g
  SEDSCRIPT
  for i in $pathmods

I have pushed that into SVN for packaging (to be bundled with of
gtm_destdir patches from Brad)

But there is tiny bit left

$>  grep /home/yoh/deb/perspect/fis-gtm/.*debian/ -r .
Binary file ./utf8/gdehelp.gld matches
./utf8/plugin/gpgagent.tab:/home/yoh/deb/perspect/fis-gtm/fis-gtm-gitsvn/debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_x86_64/plugin/libgtmcrypt.so
Binary file ./utf8/gtmhelp.gld matches
Binary file ./gdehelp.gld matches
./plugin/gpgagent.tab:/home/yoh/deb/perspect/fis-gtm/fis-gtm-gitsvn/debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_x86_64/plugin/libgtmcrypt.so
Binary file ./gtmhelp.gld matches

so whenever help files and gpgagent.tab is composed we should strip prefix as
well.   Is there a clean "fix"? ;)


[KSB] Yes, there is.  The GDE program is used to maintain the global 
directory (gtmhelp.gld) which in turn points to the help database.  This 
is easily fixed as follows:


# export gtm_dist=
# export gtmroutines=$gtm_dist/libgtmutil.so
# export gtmgbldir=$gtm_dist/gdehelp.gld
# $gtm_dist/mumps -run GDE
%GDE-I-LOADGD, Loading Global Directory file
/usr/lib/fis-gtm/V5.5-000_x86_64/gdehelp.gld
%GDE-I-VERIFY, Verification OK


GDE> change -segment DEFAULT -file=$gtm_dist/gdehelp.dat
GDE> exit
%GDE-I-VERIFY, Verification OK

%GDE-I-GDUPDATE, Updating Global Directory file
/usr/lib/fis-gtm/V5.5-000_x86_64/gdehelp.gld
# export gtmgbldir=$gtm_dist/gtmhelp.gld
# $gtm_dist/mumps -run GDE
%GDE-I-LOADGD, Loading Global Directory file
/usr/lib/fis-gtm/V5.5-000_x86_64/gtmhelp.gld
%GDE-I-VERIFY, Verification OK


GDE> change -segment DEFAULT -file=$gtm_dist/gtmhelp.dat
GDE> exit
%GDE-I-VERIFY, Verification OK

%GDE-I-GDUPDATE, Updating Global Directory file
/usr/lib/fis-gtm/V5.5-000_x86_64/gtmhelp.gld
#

This should make both ZHELP and the HELP command in GDE work.


But also zhelp doesn't work since there is no gtmhelp.dat
installed which should come from:

sr_unix/comlist.mk:../gtmhelp.dat: ../mumps.hlp

I guess -- is it me somehow missing it or it is a generic TODO for
cmakification?

Also I recalled that we spotted with Bhaskar following missing
symbols and he said that it looks like absent needed linking

dpkg-shlibdeps: warning: 
debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_x86_64/plugin/libgtmcrypt.so
 contains an unresolvable reference to symbol gtm_free: it's probably a plugin.
dpkg-shlibdeps: warning: 
debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_x86_64/plugin/libgtmcrypt.so
 contains an unresolvable reference to symbol gtm_xcfileid_free: it's probably 
a plugin.
dpkg-shlibdeps: warning: 
debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_x86_64/plugin/libgtmcrypt.so
 contains an unresolvable reference to symbol gtm_is_file_identical: it's 
probably a plugin.
dpkg-shlibdeps: warning: 
debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_x86_64/plugin/libgtmcrypt.so
 contains an unresolvable reference to symbol gtm_filename_to_id: it's probably 
a plugin.
dpkg-shlibdeps: warning: 
debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_x86_64/plugin/libgtmcrypt.so
 contains an unresolvable reference to symbol gtm_zstatus: it's probably a 
plugin.
dpkg-shlibdeps: warning: 
debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_x86_64/plugin/libgtmcrypt.so
 contains an unresolvable reference to symbol gtm_malloc: it's probably a 
plugin.
dpkg-shlibdeps: warning: 
debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_x86_64/plugin/libgtmcrypt.so
 contains an unresolvable reference to symbol gtm_ci: it's probably a plugin.


[KSB] The database encryption plugin always runs in the context of a 
mumps process, which should provide the gtm_* functions.


Regards
-- Bhaskar

--
GT.M - Rock solid. Lightning fast. Secure. No compromises.

_
The information contained in this message is proprietary and/or confidential. 
If you are not the intended recipient, please: (i) delete the message and all 
copies; (ii) do not disclose, distribute or use the message in any manner; and 
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Re: Any progress with FIS GT.M?

2012-06-19 Thread Luis Ibanez

Yaroslav,

Thanks for configuring the Debian files to take
advantage of Brad's recent modifications.

I'm trying to replicate the process and run in the following message:


...

I: Fixing up permissions for removed write rights -- we aren't done yet!
chmod +w -R
/home/ibanez/src/fis-gtm-packaged/fis-gtm_5.5-000/debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_i486
make[1]: Leaving directory
`/home/ibanez/src/fis-gtm-packaged/fis-gtm_5.5-000'
   dh_install
   dh_installdocs
   debian/rules override_dh_installchangelogs
make[1]: Entering directory
`/home/ibanez/src/fis-gtm-packaged/fis-gtm_5.5-000'
dh_installchangelogs debian/upstream-files/GTM_V5.5-000_Release_Notes.html
make[1]: Leaving directory
`/home/ibanez/src/fis-gtm-packaged/fis-gtm_5.5-000'
   dh_installexamples
   dh_installman
   dh_installcatalogs
   dh_installcron
   dh_installdebconf
   dh_installemacsen
   dh_installifupdown
   dh_installinfo
   dh_pysupport
   dh_installinit
   dh_installmenu
   dh_installmime
   dh_installmodules
   dh_installlogcheck
   dh_installlogrotate
   dh_installpam
   dh_installppp
   dh_installudev
   dh_installwm
   dh_installxfonts
   dh_bugfiles
   debian/rules override_dh_lintian
make[1]: Entering directory
`/home/ibanez/src/fis-gtm-packaged/fis-gtm_5.5-000'
echo "fis-gtm-5.5.000 binary: shlib-with-executable-stack
usr/lib/fis-gtm/*/libgtmshr.so" > debian/fis-gtm-5.5.000.lintian-overrides
dh_lintian
make[1]: Leaving directory
`/home/ibanez/src/fis-gtm-packaged/fis-gtm_5.5-000'
   dh_gconf
   dh_icons
   dh_perl
   dh_usrlocal
   debian/rules override_dh_link
make[1]: Entering directory
`/home/ibanez/src/fis-gtm-packaged/fis-gtm_5.5-000'
echo '/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_i486
/usr/lib/fis-gtm/current' > debian/fis-gtm.links
dh_link
make[1]: Leaving directory
`/home/ibanez/src/fis-gtm-packaged/fis-gtm_5.5-000'
   dh_compress
   dh_fixperms
   dh_strip
   dh_makeshlibs
   dh_shlibdeps
dpkg-shlibdeps: warning:
debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_i486/plugin/libgtmcrypt.so
contains an unresolvable reference to symbol gtm_free: it's probably a
plugin.
dpkg-shlibdeps: warning: 6 other similar warnings have been skipped (use -v
to see them all).
dpkg-shlibdeps: warning: dependency on libelf.so.1 could be avoided if
"debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_i486/mumps
debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_i486/libgtmshr.so"
were not uselessly linked against it (they use none of its symbols).
dpkg-shlibdeps: warning: dependency on libgpg-error.so.0 could be avoided
if
"debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_i486/plugin/libgtmcrypt.so
debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_i486/plugin/gtmcrypt/maskpass"
were not uselessly linked against it (they use none of its symbols).
   dh_installdeb
   dh_gencontrol
   dh_md5sums
   dh_builddeb
dpkg-deb: building package `fis-gtm' in
`../fis-gtm_5.5-000+git80-g211bd16-1_all.deb'.
dpkg-deb: building package `fis-gtm-5.5.000' in
`../fis-gtm-5.5.000_5.5-000+git80-g211bd16-1_i386.deb'.
tar: ./usr/lib/fis-gtm/V5.5-000+git80-g211bd16_i486/utf8/_utf2hex.m: file
changed as we read it
dpkg-deb: subprocess tar -cf returned error exit status 1
dh_builddeb: dpkg-deb --build debian/fis-gtm-5.5.000 .. returned exit code 2
make: *** [binary] Error 9
dpkg-buildpackage: error: fakeroot debian/rules binary gave error exit
status 2
debuild: fatal error at line 1325:
dpkg-buildpackage -rfakeroot -d -us -uc failed



I'm doing this by running:

   debuild   -d


Any hints on what I might be doing wrong ?


or actually, to be more constructive,
where can Brad and I help now to move things forward ? :-)


Thanks


 Luis

Re: Any progress with FIS GT.M?

Bhaskar,

tiny questions:

- are there any internal checks/reliance on "installed" files being
read-only?   what is the goal anyway behind making them read-only if
owned by root who is the one with ability to revert that anyways?

- shouldn't  gtminstall have 'set -e' (or explicit || exit 1) so
  in case configure call fails, gtminstall fails?

- due to above my installation 'succeeds' while configure generates quite
  a bit of errors for me atm, e.g. pointing to missing gdehelp.dat etc

cp: cannot stat `gdehelp.dat': No such file or directory
chown: cannot access 
`/home/yoh/deb/perspect/fis-gtm/fis-gtm-gitsvn/debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_x86_64/gdehelp.dat':
 No such file or directory
cp: cannot stat `gtmhelp.dat': No such file or directory
chown: cannot access 
`/home/yoh/deb/perspect/fis-gtm/fis-gtm-gitsvn/debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_x86_64/gtmhelp.dat':
 No such file or directory
chmod: cannot access `gtmcrypt_ref.c': No such file or directory
chmod: cannot access `gtmcrypt_ref.h': No such file or directory
chmod: cannot access `gtmcrypt_interface.h': No such file or directory
chmod: cannot access `gtmxc_types.h': No such file or directory
chmod: cannot access `maskpass.c': No such file or directory
chmod: cannot access `gtmcrypt_dbk_ref.c': No such file or directory
...

I guess they shouldn't just be ignored, right?  but those .c's are the
original sources which aren't installed with the "stage1" installation -- 
is that just some legacy pieces in configure or am I missing smth?

On Tue, 19 Jun 2012, Bhaskar, K.S wrote:
> On 06/19/2012 12:03 AM, Yaroslav Halchenko wrote:
> >>On 06/18/2012 02:42 PM, Brad King wrote:
> >>  Here is a patch series that solves this problem.  I've only done
> >>  some lightweight/manual testing with this.  The first patch
> >>  refactors both i386 and x86_64 code paths that emit the path to
> >>  the source file into the object file to send source file path
> >>  lookup through a common point (in obj_source.c).  The second
> >>  patch modifies this common point to read a 'gtm_destdir' env var
> >>  and strip the prefix it names from source file paths.
> >I gave brief check to Brad's patches and adjusted Debian packaging in SVN to
> >make use of them (but without yet placing actual patches into quilt -- I just
> >grabbed the HEAD of his master for the .orig "tarball").  From the first
> >look (dumping strings on generated .o and .so) it did exactly what I hoped 
> >them
> >to do -- thanks Brad!  Then I have tried to run those basic commands Bhaskar
> >has listed but it seems that mumps doesn't even try to load libgtmutil.so to
> >get access to all those pre-built .o's placed into this dynamic library on my
> >amd64 laptop...  so anything I try fails, e.g.:

> [KSB3] What is the value of $gtmroutines in the shell before you enter GT.M?

> Regards
> -- Bhaskar
-- 
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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Re: Any progress with FIS GT.M?

> > $> strace -fF -o /tmp/123strace2.log $gtm_dist/mumps -direct
> It works for me if I add
>  gtmroutines=$gtm_dist/libgtmutil.so
> to the environment.

rright -- forgot about this one ;-)  so many hidden precious env
variables without any punishing me-forgetful error messages ;)

also we need to adjust/patch configure so it strips the gtm_destdir
during s|GTMDIST|$gtmdist|g, i.e.

$> quilt diff
--- a/sr_unix/configure.gtc
+++ b/sr_unix/configure.gtc
@@ -371,7 +371,7 @@ fi
 cat << SEDSCRIPT > sedin$$
 s|ARCH|$arch|g
 s|ECHO|"$echo"|g
-s|GTMDIST|$gtmdist|g
+s|GTMDIST|${gtmdist#${gtm_destdir:-}}|g
 s|SERVERID|$server_id|g
 SEDSCRIPT
 for i in $pathmods

I have pushed that into SVN for packaging (to be bundled with of
gtm_destdir patches from Brad)

But there is tiny bit left

$> grep /home/yoh/deb/perspect/fis-gtm/.*debian/ -r .
Binary file ./utf8/gdehelp.gld matches
./utf8/plugin/gpgagent.tab:/home/yoh/deb/perspect/fis-gtm/fis-gtm-gitsvn/debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_x86_64/plugin/libgtmcrypt.so
Binary file ./utf8/gtmhelp.gld matches
Binary file ./gdehelp.gld matches
./plugin/gpgagent.tab:/home/yoh/deb/perspect/fis-gtm/fis-gtm-gitsvn/debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_x86_64/plugin/libgtmcrypt.so
Binary file ./gtmhelp.gld matches

so whenever help files and gpgagent.tab is composed we should strip prefix as
well.   Is there a clean "fix"? ;)

But also zhelp doesn't work since there is no gtmhelp.dat
installed which should come from:

sr_unix/comlist.mk:../gtmhelp.dat: ../mumps.hlp

I guess -- is it me somehow missing it or it is a generic TODO for
cmakification?

Also I recalled that we spotted with Bhaskar following missing
symbols and he said that it looks like absent needed linking

dpkg-shlibdeps: warning: 
debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_x86_64/plugin/libgtmcrypt.so
 contains an unresolvable reference to symbol gtm_free: it's probably a plugin.
dpkg-shlibdeps: warning: 
debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_x86_64/plugin/libgtmcrypt.so
 contains an unresolvable reference to symbol gtm_xcfileid_free: it's probably 
a plugin.
dpkg-shlibdeps: warning: 
debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_x86_64/plugin/libgtmcrypt.so
 contains an unresolvable reference to symbol gtm_is_file_identical: it's 
probably a plugin.
dpkg-shlibdeps: warning: 
debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_x86_64/plugin/libgtmcrypt.so
 contains an unresolvable reference to symbol gtm_filename_to_id: it's probably 
a plugin.
dpkg-shlibdeps: warning: 
debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_x86_64/plugin/libgtmcrypt.so
 contains an unresolvable reference to symbol gtm_zstatus: it's probably a 
plugin.
dpkg-shlibdeps: warning: 
debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_x86_64/plugin/libgtmcrypt.so
 contains an unresolvable reference to symbol gtm_malloc: it's probably a 
plugin.
dpkg-shlibdeps: warning: 
debian/fis-gtm-5.5.000/usr/lib/fis-gtm/V5.5-000+git80-g211bd16_x86_64/plugin/libgtmcrypt.so
 contains an unresolvable reference to symbol gtm_ci: it's probably a plugin.


-- 
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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How to proceed with EMBOSS packaging (Was: About having EMBOSS 6.4.0 in Wheezy or not.)

2012-06-19 Thread Andreas Tille

Hi Charles,

as you probably have noticed when watching commit logs I started working
on EMBOSS packaging.  I was a bit unsure about some changes (perhaps
refreshing all quilt patches might have been questionably - feel free to
revert) and I also do have some additional question how to handle some
lintian issues:

  1. E: emboss-lib: embedded-library usr/lib/emboss/lib/libepcre.so.7.0.9: pcre3

 Any comment on this?

  2. W: jemboss: codeless-jar usr/share/EMBOSS/jemboss/resources/acdstore.jar
   as well as
 W: jemboss: classpath-contains-relative-path 
usr/share/EMBOSS/jemboss/lib/jemboss.jar: lib/jakarta-regexp-1.2.jar, 
lib/jalviewApplet.jar

 This looks suspicious - perhaps I need to contact our Java experts
 about this.

  3. W: emboss: menu-command-not-in-package usr/share/menu/emboss:8 
usr/bin/x-terminal-emulator
 ...

 Are you *really* sure that it is necessary to call x-terminal-emulator?
 My guess is that the reason for this is the way you want the screen
 to remain via
   "...;echo press any key to continue"
 If this assumption is right we probably should add an override because
 the lintian output is that bloated to possibly oversee some relevant
 things.

 On the other hand: Do users really call these tools via menu?
 Wouldn't it be better to drop the menu support at all and rather
 teach users using command line?

Please explain how you would deal these issues to enable me continue to
work on this in a way you would regard reasonable.

Kind regards

Andreas.

-- 
http://fam-tille.de


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Re: Any progress with FIS GT.M?