Awful lot of spam coming through this list lately!

2018-02-27 Thread David Mathog
Can the list maintainer please (try) do something about the spam 
relaying through this list?  There were 5 copies of the last one, about 
skin tag removal.


Thanks,

David Mathog
mat...@caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech

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Re: Spurious pastes

2018-02-07 Thread David Mathog

On 07-Feb-2018 06:26, Jon Turney wrote:

On 02/02/2018 22:26, David Mathog wrote:
In the last few days nedit on those remote machines has been doing 
spurious pastes. That is, whatever is currently in the X11 paste 
buffer (not the program's paste buffer) is ending up dropped into 
whatever file is being edited. Unclear why they are landing where they 
do, I have not actually seen it happen, just found it when diff 
indicated these odd insertions. My best guess is that these happen 
while I am scrolling over these regions. Needless to say, this is 
really not a good thing.


There have been only two changes recently.

1. I cleaned my mouse. 2. yum on 1/27/18 automatically installed on 
those servers: xorg-x11-server-common-1.17.4-16.el6.centos.1.x86_64


To eliminate (1) the mouse was swapped with another one. Too soon to
 know if that did anything.


I wonder if you aren't somehow accidentally clicking the middle mouse
button whilst scrolling?


That seems to be what caused it.  Those errant pastes have not happened 
again with the 2nd mouse.  My best guess is that somehow putting the 
mouse back together decreased the "click distance" on the scroll wheel, 
so that now and then in the middle of a scroll motion there was also a 
click.  I would never see it when it happened because the scroll actions 
on either side of the click would move it off the screen.





On 02-Feb-2018 13:13, David Mathog wrote:

I seem to recall that before this if I highlighted a region in an
xterm window, then moved to another X11 application window, and 
center
clicked, it would paste the highlighted text.  However, if nothing 
was
highlighted in the last window, nothing would paste.  My memory may 
be

faulty on this issue though, as I never paid a lot of attention to it
before it started misbehaving.


That wasn't right, but cut/paste is slightly different between "on the 
console" and "over putty ssh tunnel with X11 Server on Windows".


On an XFCE4 ubuntu system console this is what happens:


I'm guessing this means a non-X terminal?


That is a regular X11 server, xorg 1.15.1.  It just acts differently in 
that it was possible to "select nothing".



Is there a standard way to clear this buffer?


I was going to suggest 'xsel -c' or 'xclip -i /dev/null', but that
doesn't work (in this case) for obscure reasons to do with cut
buffers...


Too bad.  Sometimes I cut and paste hundreds of lines of text and those 
are always a mistaken center click in an xterm away from hundreds of 
bogus commands trying to run.


If you have any control of this issue a standard key stroke combination 
to clear would be wonderful.  Failing that, control-shift-center click 
(or something like that) to paste and then clear would be nearly as 
good.



For future issues, can I ask you to use the cygwin list, per [1]

[1] https://cygwin.com/ml/cygwin-xfree-announce/2015-03/msg1.html


I will try to remember that.

Thanks,

David Mathog
mat...@caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech

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Re: Spurious pastes

2018-02-02 Thread David Mathog

On 02-Feb-2018 13:13, David Mathog wrote:

I seem to recall that before this if I highlighted a region in an
xterm window, then moved to another X11 application window, and center
clicked, it would paste the highlighted text.  However, if nothing was
highlighted in the last window, nothing would paste.  My memory may be
faulty on this issue though, as I never paid a lot of attention to it
before it started misbehaving.


That wasn't right, but cut/paste is slightly different between "on the 
console" and "over putty ssh tunnel with X11 Server on Windows".


On an XFCE4 ubuntu system console this is what happens:

1.  type "pwd" into an uxterm window
2.  highlight "pwd" on the line at the preceding prompt, center
click once at the current prompt.  "pwd" is pasted.
Press "enter".
3.  left click once on the still highlighted "pwd", now 2 lines up.
The highlight goes away.  Center click once at the prompt.
"pwd" is still pasted. Press "enter".
4.  With the left mouse button drag across any letter and back
to the original position.  So nothing is highlighted.  This can
be on any text anywhere in the window.  Center click
at the prompt.  Nothing is pasted - the paste buffer is now
empty.

So on the console it is possible to select "nothing".

On the X11 server ssh to the Ubuntu system and it is the same for the 
first 3 steps, but the 4th still pastes "pwd".  The rule seems to be 
"paste buffer can be replaced by anything selected, but not by a select 
operation which ends with nothing highlighted."


On the X11 server ssh to the Centos system, it behaves just like a 
similar connection to the Centos system.


The operations do the same thing when going between two uxterm windows 
on any of these tests.


Which is right?  Is "nothing" a valid thing to load into the paste 
buffer or no?


Is there a standard way to clear this buffer?

Thanks,

David Mathog
mat...@caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech

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Spurious pastes

2018-02-02 Thread David Mathog

Greetings,

I do most of my work on remote CentOS machines from a Windows box using 
a putty ssh tunnel and Cygwin X Server (1.14.1-1).


In the last few days nedit on those remote machines has been doing 
spurious pastes. That is, whatever is currently in the X11 paste buffer 
(not the program's paste buffer) is ending up dropped into whatever file 
is being edited.  Unclear why they are landing where they do, I have not 
actually seen it happen, just found it when diff indicated these odd 
insertions.  My best guess is that these happen while I am scrolling 
over these regions.  Needless to say, this is really not a good thing.


There have been only two changes recently.

1.  I cleaned my mouse.
2.  yum on 1/27/18 automatically installed on those servers:
 xorg-x11-server-common-1.17.4-16.el6.centos.1.x86_64

To eliminate (1) the mouse was swapped with another one.  Too soon to 
know if that did anything.


Part, maybe the whole issue, seems to be a change in how the X11 paste 
buffer is working.


I seem to recall that before this if I highlighted a region in an xterm 
window, then moved to another X11 application window, and center 
clicked, it would paste the highlighted text.  However, if nothing was 
highlighted in the last window, nothing would paste.  My memory may be 
faulty on this issue though, as I never paid a lot of attention to it 
before it started misbehaving.


Now the paste buffer seems to remember forever the last thing that was 
loaded into it.  This is the X11 paste buffer, not the one in nedit.  
The latter can be cleared by clicking once in any document and doing 
copy.  However, that does not clear the X11 paste buffer, just the 
applications.


In order to minimize these spurious X11 window into nedit pastes I would 
like to be able to clear the X11 paste buffer.  How would one do so?  I 
mean, other than shutting down and restarting the X11 server!


Thanks,

David Mathog
mat...@caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech

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Re: new start method questions

2016-06-10 Thread mathog

On 09-Jun-2016 17:55, mathog wrote:

Last time around the start bat script was just:

@echo off
set CYGXTOP=%~dp0
C:
chdir "%CYGXTOP%\var\log\xwin"
move XWin.0.log.1 XWin.0.log.2
move XWin.0.log XWin.0.log.1
chdir "%CYGXTOP%\bin"
start Xwin :0 -multiwindow

Is there some reason that a similar cut down bat file would not work
with the current cygwin X11 server? (With "-listen tcp" plus a windows
firewall rule to only let it talk to localhost.)


In a regular CMD shell navigated to the bin directory and did:

start Xwin :0 -multiwindow -listen tcp

and it worked.  So none of the current start script seems to be 
necessary if the only
goal is to start the X11 server.  It seems to work normally, at least by 
the criterion that xdpyinfo returns the same information as for the 
other starts.


On a related note - are there any situations where the X11 server itself 
(not something in its startup script) will start a subprocess and run a 
different binary?  For instance, some sort of font search operation, or 
perhaps some conditional load of an X11 feature which isn't normally 
started, or some funny kind of cut and paste operation on the Window 
side?


Thanks,

David Mathog
mat...@caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech

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Re: new start method questions

2016-06-09 Thread mathog

On 09-Jun-2016 16:32, mathog wrote:

With an older version of Cygwin I had constructed a cut down
distribution which included only the minimum pieces needed to run X11.
 It was about 40Mb, installed.


This approach is not working well at all for the current release.  Last 
time around I just tossed things into a folder to temporarily hide them, 
and by process of elimination winnowed it down to that small size.  This 
time there are many, many, MANY more dll's that are required for the 
server to start, at least  via this method:


C:\cygwinX\bin\run.exe --quote /usr/bin/bash.exe -l -c "cd; exec 
/usr/bin/startxwin"


For instance, cyggtk-x11-2.0.0.dll.  Take it out and the X11 server does 
not start.
That dll, according to "ldd" has everything but the kitchen sink linked 
into it.  It isn't linked directly into the server though, it is needed 
for "xwin-xdg-menu.exe",
an accessory program, which if removed from /usr/bin, also results in 
the server not starting.


Last time around the start bat script was just:

@echo off
set CYGXTOP=%~dp0
C:
chdir "%CYGXTOP%\var\log\xwin"
move XWin.0.log.1 XWin.0.log.2
move XWin.0.log XWin.0.log.1
chdir "%CYGXTOP%\bin"
start Xwin :0 -multiwindow

Is there some reason that a similar cut down bat file would not work 
with the current cygwin X11 server? (With "-listen tcp" plus a windows 
firewall rule to only let it

talk to localhost.)

Thanks,

David Mathog
mat...@caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech

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new start method questions

2016-06-09 Thread mathog

Hi,

With an older version of Cygwin I had constructed a cut down 
distribution which included only the minimum pieces needed to run X11.  
It was about 40Mb, installed.


Since the X11 server update the start method changed.  The .bat file 
which starts things now has this as its active line:


C:\cygwinX\bin\run.exe --quote /usr/bin/bash.exe -l -c "cd; exec 
/usr/bin/startxwin"


Unfortunately this method creates a "/home/username" directory.  The 
startxwin part

isn't the culprit, just starting bash does it.  This is sufficient:

C:\cygwinX\bin\run.exe --quote /usr/bin/bash.exe -l -c "cd; ls"

Is there a way to run startxwin without allowing bash to make a new home 
directory? Leaving off the "-l" does not create the home directory - it 
also does not start the X11 server.


This distribution is intended to work with putty's ssh, not the ssh in 
cygwin.  To get putty to work these changes were made to startxwin:


defaultserverargs=""
to
defaultserverargs=" -listen tcp"

and

eval xinit \"$client\" $clientargs -- \"$server\" $display $serverargs

to

#rotate the log files, keep 2 older ones
cp -f /var/log/xwin/XWin.0.log.1 /var/log/xwin/XWin.0.log.2
cp -f /var/log/xwin/XWin.0.log /var/log/xwin/XWin.0.log.1
(sleep 5; export DISPLAY=$defaultdisplay; xhost +localhost)&
eval xinit \"$client\" $clientargs -- \"$server\" $display $serverargs

I really don't like the cludgy way xhost is started.  However, it does 
work, or at least it works the "most of the time" when the X11 server 
starts within 5 seconds. Ideally it would be more like this:


(xinit \"$client\" $clientargs -- \"$server\" $display $serverargs)&
export DISPLAY=$defaultdisplay;
xhost +localhost
wait

This doesn't work though.  The first line throws an error with that 
syntax, the part within the parens doesn't just use eval, it apparently 
requires it.  Anybody know the correct syntax for this variant?  xhost 
might fail because it starts before the X11 server is working, but I can 
deal with that once the background start is going.


Thanks,

David Mathog
mat...@caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech

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Re: Magic Cookie - SSH Secure Shell

2015-04-21 Thread mathog

On 19/04/2015 22:08, Nicholas Fitzkee wrote:
Ultimately, I have graduate and undergraduate students who need to be 
able
to quickly set up their own Windows systems to run X11 apps on my 
linux
server.  These students are often not particularly tech-saavy, so I'd 
like
my tutorial for them to be as simple as posslble.  As an example, you 
can

see what I wrote for the old xinit at this link:


If you don't mind using a slightly older version of the Cygwin X11 
server you might point your students to this instead:


http://sourceforge.net/projects/minimalcygwinx/

This was put together for exactly your stated purpose. It is a Cygwin 
installation pruned down to just the parts needed for X11 to run with 
Putty.  Since it uses the older X11 server it doesn't have any of the 
features (ie, problems from the perspective of your intended users) 
that the current X11 server does.


Regards,

David Mathog
mat...@caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech


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Re: startxwin.exe no longer exists?

2014-12-17 Thread mathog

On 16-Dec-2014 15:39, Erik Soderquist wrote:

My best guess (and this is only a guess) is that
something is causing X to crash as it shuts down on your system,
causing the lock files to be left behind.


There is no reason that should happen unless the startxwin script also 
crashes - and that basically should never happen.  The script should 
clean up any mess that the binary might leave, and it should handle all 
conditions that might result from some process it has started crashing.  
That is, in the script (pseudocode):


# If there is an existing lock file:
#   Test is there also an existing X11 binary process?
# yes - abort with message: X11 server already running
# no  - remove lock file
##
# do whatever housekeeping is needed
#   then start binary
/path/X11_server_binary $args
#no matter how binary exits...
rm /path/.X*lock

The only time a script might not have a chance to run the last command 
is if it starts the server via nohup binary , assuming such a thing 
is even possible in cygwin, and then exits without waiting around for 
the binary to exit.  Or, of course, if the whole system crashes, but 
that isn't the issue the end users are having.


Regards,

David Mathog
mat...@caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech

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Re: startxwin.exe no longer exists?

2014-12-17 Thread mathog

On 17-Dec-2014 09:40, Erik Soderquist wrote:

snip

There is no reason that should happen unless the startxwin script also
crashes - and that basically should never happen.  The script should 
clean
up any mess that the binary might leave, and it should handle all 
conditions
that might result from some process it has started crashing.  That is, 
in

the script (pseudocode):

# If there is an existing lock file:
#   Test is there also an existing X11 binary process?
# yes - abort with message: X11 server already running
# no  - remove lock file
##
# do whatever housekeeping is needed
#   then start binary
/path/X11_server_binary $args
#no matter how binary exits...
rm /path/.X*lock

The only time a script might not have a chance to run the last command 
is if
it starts the server via nohup binary , assuming such a thing is 
even
possible in cygwin, and then exits without waiting around for the 
binary to
exit.  Or, of course, if the whole system crashes, but that isn't the 
issue

the end users are having.


So you want your script to completely mask and/or destroy any evidence
that something crashed??


No, that is the log file, this is the lock file.  It should rotate the 
log file from the previous run and delete the lock file.




Also, as the X server is not bound to a tty, it forks to the
background on its own anyway, so your pseudocode example would delete
the lock file just after the X server started.


In that case the the script needs to retrieve the PID of the forked 
process and wait for it to exit.


Regards,

David Mathog
mat...@caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech

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Re: startxwin.exe no longer exists?

2014-12-17 Thread mathog

On 17-Dec-2014 10:35, Erik Soderquist wrote:


How often do you check your log files for crashes when you have your
script hiding the fact that it crashed from you?


Fine, have the script emit a warning when this situation is encountered. 
 Personally I have never seen the X11 server crash between shut down 
and removing the lock file.  I have seen it crash while running - and 
that was pretty evident since all my X11 windows disappeared, no need to 
look for a lock file!






Also, as the X server is not bound to a tty, it forks to the
background on its own anyway, so your pseudocode example would delete
the lock file just after the X server started.



In that case the the script needs to retrieve the PID of the forked 
process

and wait for it to exit.



I would much rather have the binary process clean up after itself like
it is supposed to, and figure out why the binary process is failing to
do so when it doesn't than have a script that hides such failures from
me.


Sure, the binary SHOULD work like that, but what others have said is 
that it is not always doing so.  Hence, the script should pick up the 
pieces if the binary failed to do so.  The script need not hide 
anything, it can emit warning messages on any and all conditions.  At 
start up:


  Found orphan lock file and removed it.  Possible crash during 
previous X11 server session.  Starting X11 server normally.


at shut down:

  X11 server process exited abnormally.  Orphan lock file removed.

etc.

Regards,

David Mathog
mat...@caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech

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Re: Clipboard interaction issues - breaks after awhile

2014-10-07 Thread mathog

On 07-Oct-2014 06:14, Jon TURNEY wrote:
It always overwrites the Xwin.0.log file when it starts.  Is there 
some
change we could make to this .bat script that would cause it to at 
least

save one previous version?


I guess you could add to the above something like:

move C:\cygwin\var\log\XWin.0.log C:\cygwin\var\log\XWin.0.log.old

but yes, there is actually some code in the server to do that, but
it's not turned on in XWin for unknown reasons...


Good idea.  Changed it to the following and tested. It keeps the last 
two versions.


==after this line
@echo off
set CYGXTOP=%~dp0

C:
chdir %CYGXTOP%\var\log\xwin
move XWin.0.log.1 XWin.0.log.2
move XWin.0.log XWin.0.log.1
chdir %CYGXTOP%\bin

start Xwin :0 -multiwindow
==before this line

Regards,

David Mathog
mat...@caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech

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Re: Clipboard interaction issues - breaks after awhile

2014-10-03 Thread mathog

Today I ran into an interesting variant of this.

1.  putty   ssh -X session from XP to a remote Centos 6.5 system.
2.  on the remote system: xterm 
3.  copy a line of text on remote system
4.  paste it into a roundcube compose window on XP system.  The 
browser is

Seamonkey 2.29.

It works fine for a while and then the _browser_ locks.  It is 
definitely an X11
issue because this unlocked the browser: exit all xterms, exit the putty 
session, kill

the X11 server.  The browser didn't unlock until the last step.

This lock up happened twice within half an hour.  Now I can't reproduce 
it.


That is the only system I have used recently that uses xterm instead of 
uxterm.


The clipboard problems I have seen previously were all in the other 
direction, where clip going into an X11 application would fail.


Unfortunately I didn't save the X server log file.  Which, brings up 
another point.
The X11 server is started by clicking on start_server.bat which 
contains:


@echo off
set CYGXTOP=%~dp0
C:
chdir %CYGXTOP%\bin
start Xwin :0 -multiwindow

It always overwrites the Xwin.0.log file when it starts.  Is there some 
change we could make to this .bat script that would cause it to at least 
save one previous version?


Regards,

David Mathog
mat...@caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech

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Re: Clipboard interaction issues - breaks after awhile

2014-09-10 Thread mathog

On 10-Sep-2014 09:33, Nem W Schlecht wrote:

After the latest update to xorg-server (1.16.0-1), I've been having
issues with clipboard interaction between my xterm windows and Windows
apps.  Bi-directional copy/paste works initially, but at some unknown
point stops working.  Anybody else seeing this as well?  What can I do
to help debug this issue?


Look in the X11 server log file for error messages after you experience 
a

failed paste.

I see something like that inside nedit.

   http://www.cygwin.com/ml/cygwin-xfree/2013-06/msg0.html

The crash problem in that post was resolved with a later version of the 
X11 server, but

the paste and window degradation problems are still around.

I hardly ever do a copy/paste from an X11 app to windows app or vice 
versa, so

no idea if the nedit issue is related to what you are seeing.

Regards,

David Mathog
mat...@caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech

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Re: Clipboard interaction issues - breaks after awhile

2014-09-10 Thread mathog

On 10-Sep-2014 10:57, Nem W Schlecht wrote:

That 'nedit' thread looks pretty old.


Sadly, yes.  Fixing it seems to be nobody's priority.

Regards,

David Mathog
mat...@caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech

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Possible X11 server bug

2014-09-05 Thread mathog
I have run into an issue which _may_ indicate a bug in the cygwin X11 
server.  The issue is documented here:


   https://bugs.launchpad.net/inkscape/+bug/1365153

In brief, for certain test files viewed in Inkscape (current trunk at 
least) over a putty ssh tunnel from an Ubuntu 12.04lts system to the 
cygwin 1.14.1.0 X11 server there are glitches in the image when it is 
zoomed in and out.  This does not occur if the same program is run 
locally on the console of the test machine.  It also does not happen if 
I run a native Windows version (not cygwin, not X11) of Inkscape on the 
same PC which hosts that X11 server on the same test files.  The glitch 
does not occur with a huge number of other test files I have looked at 
over the years.  It seems there is something specific to the clipping 
code in Inkscape and this particular X11 transport path/server 
combination.  Moreover, it looks like the problem is only manifested (or 
only manifested frequently) when the clipping path consists of two (or 
more?) disjoint sections.


When the glitches occur nothing is added to XWin.0.log.

Also this X11 server is not running in the full cygwin environment, but 
rather in one edited down to just the minimum needed to run the X11 
server.  I distribute this version here:


   http://sourceforge.net/projects/minimalcygwinx/

I don't think this is a factor though, since all of the action is going 
on inside the X11 server process(es).


Thanks,

David Mathog
mat...@caltech.edu
Manager, Sequence Analysis Facility, Biology Division, CaltechWelcome to the XWin X Server
Vendor: The Cygwin/X Project
Release: 1.14.1.0
OS: CYGWIN_NT-5.1 SAF00 1.7.20(0.266/5/3) 2013-06-07 11:11 i686
OS: Windows XP Service Pack 3 [Windows NT 5.1 build 2600] (Win32)
Package: version 1.14.1-1 built 2013-05-07

XWin was started with the following command line:

Xwin :0 -multiwindow 

ddxProcessArgument - Initializing default screens
winInitializeScreenDefaults - primary monitor w 1280 h 1024
winInitializeScreenDefaults - native DPI x 96 y 96
_XSERVTransSocketOpenCOTSServer: Unable to open socket for inet6
_XSERVTransOpen: transport open failed for inet6/SAF00:0
_XSERVTransMakeAllCOTSServerListeners: failed to open listener for inet6
Initializing built-in extension Generic Event Extension
[   119.468] Initializing built-in extension Generic Event Extension
Initializing built-in extension SHAPE
[   119.468] Initializing built-in extension SHAPE
Initializing built-in extension MIT-SHM
[   119.468] Initializing built-in extension MIT-SHM
Initializing built-in extension XInputExtension
[   119.468] Initializing built-in extension XInputExtension
Initializing built-in extension XTEST
[   119.468] Initializing built-in extension XTEST
Initializing built-in extension BIG-REQUESTS
[   119.468] Initializing built-in extension BIG-REQUESTS
Initializing built-in extension SYNC
[   119.468] Initializing built-in extension SYNC
Initializing built-in extension XKEYBOARD
[   119.468] Initializing built-in extension XKEYBOARD
Initializing built-in extension XC-MISC
[   119.468] Initializing built-in extension XC-MISC
Initializing built-in extension XINERAMA
[   119.468] Initializing built-in extension XINERAMA
Initializing built-in extension XFIXES
[   119.468] Initializing built-in extension XFIXES
Initializing built-in extension XFree86-Bigfont
[   119.468] Initializing built-in extension XFree86-Bigfont
Initializing built-in extension RENDER
[   119.468] Initializing built-in extension RENDER
Initializing built-in extension RANDR
[   119.468] Initializing built-in extension RANDR
Initializing built-in extension COMPOSITE
[   119.468] Initializing built-in extension COMPOSITE
Initializing built-in extension DAMAGE
[   119.468] Initializing built-in extension DAMAGE
Initializing built-in extension MIT-SCREEN-SAVER
[   119.468] Initializing built-in extension MIT-SCREEN-SAVER
Initializing built-in extension DOUBLE-BUFFER
[   119.468] Initializing built-in extension DOUBLE-BUFFER
Initializing built-in extension RECORD
[   119.468] Initializing built-in extension RECORD
Initializing built-in extension DPMS
[   119.468] Initializing built-in extension DPMS
Initializing built-in extension X-Resource
[   119.468] Initializing built-in extension X-Resource
Initializing built-in extension GLX
[   119.468] Initializing built-in extension GLX
(II) xorg.conf is not supported
[   119.468] (II) xorg.conf is not supported
(II) See http://x.cygwin.com/docs/faq/cygwin-x-faq.html for more information
[   119.468] (II) See http://x.cygwin.com/docs/faq/cygwin-x-faq.html for more 
information
LoadPreferences: /home/david/.XWinrc not found
[   119.500] LoadPreferences: /home/david/.XWinrc not found
LoadPreferences: /etc/X11/system.XWinrc not found
[   119.500] LoadPreferences: /etc/X11/system.XWinrc not found
LoadPreferences: See man XWinrc to customize the XWin menu.
[   119.500] LoadPreferences: See man XWinrc to customize the XWin menu.
LoadPreferences: Loading built

Nedit bugs: paste and server crash

2013-06-06 Thread mathog

Hi,

I am using Cygwin/X Xserver with nedit from a remote client.  Most of 
the time
it works but there are 3 bugs that have been getting on my nerves 
enough so that
I now want to track them down.  Is there a prepackaged debug version of 
the X11 server
that I can load (for the 3rd problem below)?  I don't want to have to 
assemble a

complete build environment for cygwin just for this one problem?

These are the three problems with this configuration:

1.  Cut from a windows application, paste into a nedit window. Works 
99.8% of the
time - until it doesn't.  This one is likely going to be horrible to 
figure out since
it only shows up intermittently. Once it goes bad it locks up nedit 
(does not respond to mouse
or keyboard input) for seconds to minutes, and then it comes alive 
again.  Once this
happens subsequent pastes also tend to lock.  The only way to 
completely clear this
situation seems to be to shut down nedit and X11, then restart X11 and 
then nedit.  Very inconvenient.

This message appears on the terminal that started nedit:

XmClipboardInquireLength() failed: clipboard locked.

I have never seen a similar paste error when using Nedit on the console 
of remote workstation.  Due
to the length of time it takes to appear, that may be just a 
statistical effect, since
I never work there for 4 hours at a time, as I do normally with Cygwin 
X11 and the remote
nedit.  It is my impression that one factor that helps to trigger this 
bug is when the
cut paste remains highlighted in the original windows application - 
but it is inconvenient
to do select text, cut, deselect text  then paste, as the 3rd 
step is not

normally required.


2.  In long editing sessions (hours) draw errors tend to accumulate in 
nedit.
For instance, the save as dialog will come up with none of the 
buttons (like save!)
visible.  Other times divots will appear on parts of the screen outside 
of the text
editing region, and/or parts of the pull down menu list will disappear. 
Possibly
related to the preceding bug since, again, it only shows up 
intermittently and after

long periods.

3.  The X11 server will crash, taking all sessions from various 
machines,
with nedit or not, with it.  I do not recall the log file containing 
anything

useful, for instance, a backtrace from the point of the crash.

Details:

Cygwin/X Xserver package version 1.11.1-1 built 2011-10-05

Nedit from Ubuntu 12.04.1 LTS.  That nedit package is:

1:5.6~cvs20081118-7

and ldd shows that it is linked ot /usr/lib/libXm.so.2 which is
the one from lesstif2 (1:0.95.2-1), even though libmotif4 
(2.3.3-5ubuntu) is

installed (so libXm.so.4 is present as well).

Connection is over ssh using putty.

Thanks,

David Mathog
mat...@caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech

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Re: Nedit bugs: paste and server crash

2013-06-06 Thread mathog

On 06-Jun-2013 09:41, mathog wrote:

3.  The X11 server will crash, taking all sessions from various 
machines,
with nedit or not, with it.  I do not recall the log file containing 
anything

useful, for instance, a backtrace from the point of the crash.


Here is the log file from such a crash.  There is nothing in it that I 
find useful, perhaps

it means something to one of you:

Welcome to the XWin X Server
Vendor: The Cygwin/X Project
Release: 1.11.1.0
OS: Windows XP Service Pack 3 [Windows NT 5.1 build 2600] (Win32)
Package: version 1.11.1-1 built 2011-10-05

XWin was started with the following command line:

Xwin :0 -multiwindow

ddxProcessArgument - Initializing default screens
winInitializeScreenDefaults - primary monitor w 1280 h 1024
winInitializeDefaultScreens - native DPI x 96 y 96
_XSERVTransSocketOpenCOTSServer: Unable to open socket for inet6
_XSERVTransOpen: transport open failed for inet6/SAF00:0
_XSERVTransMakeAllCOTSServerListeners: failed to open listener for 
inet6

_XSERVTransmkdir: Mode of /tmp/.X11-unix should be set to 1777
_XSERVTransmkdir: this may cause subsequent errors
[75.937] (II) xorg.conf is not supported
[75.937] (II) See http://x.cygwin.com/docs/faq/cygwin-x-faq.html 
for more information

[75.937] LoadPreferences: /home/david/.XWinrc not found
[75.937] LoadPreferences: /etc/X11/system.XWinrc not found
[75.937] LoadPreferences: See man XWinrc to customize the XWin 
menu.

[75.937] LoadPreferences: Loading built-in default
[75.953] winDetectSupportedEngines - DirectDraw installed, allowing 
ShadowDD

[75.953] winDetectSupportedEngines - Windows NT, allowing PrimaryDD
[75.953] winDetectSupportedEngines - DirectDraw4 installed, 
allowing ShadowDDNL
[75.953] winDetectSupportedEngines - Returning, supported engines 
001f
[75.953] winTaskbarInit - Could not get SHGetPropertyStoreForWindow 
address

[75.968] winSetEngine - Multi Window or Rootless = ShadowGDI
[75.968] winScreenInit - Using Windows display depth of 32 bits per 
pixel
[75.984] winAllocateFBShadowGDI - Creating DIB with width: 1280 
height: 1024 depth: 32

[75.984] winFinishScreenInitFB - Masks: 00ff ff00 00ff
[75.984] winInitVisualsShadowGDI - Masks 00ff ff00 00ff 
BPRGB 8 d 24 bpp 32

[76.031] winMultiWindowXMsgProc - Calling pthread_mutex_lock ()
[76.031] Screen 0 added at virtual desktop coordinate (0,0).
[76.046] winInitMultiWindowWM - Calling pthread_mutex_lock ()
[76.140] MIT-SHM extension disabled due to lack of kernel support
[76.218] XFree86-Bigfont extension local-client optimization 
disabled due to lack of shared memory support in the kernel

[77.328] (II) AIGLX: Loaded and initialized swrast
[77.328] (II) GLX: Initialized DRISWRAST GL provider for screen 0
[77.609] [dix] Could not init font path element 
/usr/share/fonts/TTF/, removing from list!
[77.609] [dix] Could not init font path element 
/usr/share/fonts/OTF/, removing from list!

[81.750] winPointerWarpCursor - Discarding first warp: 640 512
[81.750] (--) 5 mouse buttons found
[81.750] (--) Setting autorepeat to delay=500, rate=31
[81.750] (--) Windows keyboard layout: 0409 (0409) US, 
type 4

[81.750] (--) Found matching XKB configuration English (USA)
[81.750] (--) Model = pc105 Layout = us Variant = none 
Options = none
[81.750] Rules = base Model = pc105 Layout = us Variant = 
none Options = none

[81.750] winBlockHandler - pthread_mutex_unlock()
[81.750] winMultiWindowXMsgProc - pthread_mutex_lock () returned.
[81.750] winMultiWindowXMsgProc - pthread_mutex_unlock () returned.
[81.750] winInitMultiWindowWM - pthread_mutex_lock () returned.
[81.750] winMultiWindowXMsgProc - DISPLAY=:0.0
[81.750] winInitMultiWindowWM - pthread_mutex_unlock () returned.
[81.781] winProcEstablishConnection - winInitClipboard returned.
[81.781] winInitMultiWindowWM - DISPLAY=:0.0
[81.781] winClipboardProc - DISPLAY=:0.0
[81.812] winMultiWindowXMsgProc - XOpenDisplay () returned and 
successfully opened the display.
[81.812] winInitMultiWindowWM - XOpenDisplay () returned and 
successfully opened the display.
[81.828] winClipboardProc - XOpenDisplay () returned and 
successfully opened the display.

[   506.921] winAboutDlgProc - WM_CLOSE
[  1040.625] winAboutDlgProc - WM_COMMAND - IDOK or IDCANCEL
[  5247.750] Segmentation fault at address 0x1
[  5247.750]
Fatal server error:
[  5247.750] Caught signal 11 (Segmentation fault). Server aborting
[  5247.750]
[  5247.750] Server terminated with error (1). Closing log file.

Regarding the 1777 warning about /tmp/.X11-unix, that file (as seen in 
Mingw) has
protection flags 755 and is owned by the same program running the X11 
server and
putty.  (Unclear to me what 1777 means on Windows XP + Cygwin, since 
Windows does not

have the 1000 protection bit like Unix does.)

Thanks,

David Mathog
mat

Nedit bugs: paste and server crash

2013-06-06 Thread mathog
[Apologies if this is a duplicate post.  The first one did not come 
back through the mailing

list, even though a reply to it did.]

Hi,

I am using Cygwin/X Xserver with nedit from a remote client.  Most of 
the time
it works but there are 3 bugs that have been getting on my nerves 
enough so that
I now want to track them down.  Is there a prepackaged debug version of 
the X11 server
that I can load (for the 3rd problem below)?  I don't want to have to 
assemble a

complete build environment for cygwin just for this one problem?

These are the three problems with this configuration:

1.  Cut from a windows application, paste into a nedit window. Works 
99.8% of the
time - until it doesn't.  This one is likely going to be horrible to 
figure out since
it only shows up intermittently. Once it goes bad it locks up nedit 
(does not respond to mouse
or keyboard input) for seconds to minutes, and then it comes alive 
again.  Once this
happens subsequent pastes also tend to lock.  The only way to 
completely clear this
situation seems to be to shut down nedit and X11, then restart X11 and 
then nedit.  Very inconvenient.

This message appears on the terminal that started nedit:

XmClipboardInquireLength() failed: clipboard locked.

I have never seen a similar paste error when using Nedit on the console 
of remote workstation.  Due
to the length of time it takes to appear, that may be just a 
statistical effect, since
I never work there for 4 hours at a time, as I do normally with Cygwin 
X11 and the remote
nedit.  It is my impression that one factor that helps to trigger this 
bug is when the
cut paste remains highlighted in the original windows application - 
but it is inconvenient
to do select text, cut, deselect text  then paste, as the 3rd 
step is not

normally required.


2.  In long editing sessions (hours) draw errors tend to accumulate in 
nedit.
For instance, the save as dialog will come up with none of the 
buttons (like save!)
visible.  Other times divots will appear on parts of the screen outside 
of the text
editing region, and/or parts of the pull down menu list will disappear. 
Possibly
related to the preceding bug since, again, it only shows up 
intermittently and after

long periods.

3.  The X11 server will crash, taking all sessions from various 
machines,
with nedit or not, with it.  I do not recall the log file containing 
anything

useful, for instance, a backtrace from the point of the crash.

Details:

Cygwin/X Xserver package version 1.11.1-1 built 2011-10-05

Nedit from Ubuntu 12.04.1 LTS.  That nedit package is:

1:5.6~cvs20081118-7

and ldd shows that it is linked ot /usr/lib/libXm.so.2 which is
the one from lesstif2 (1:0.95.2-1), even though libmotif4 
(2.3.3-5ubuntu) is

installed (so libXm.so.4 is present as well).

Connection is over ssh using putty.

Thanks,

David Mathog
mat...@caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech


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font question, xfs locally on cygwin?

2012-01-17 Thread mathog

Short version:

Can somebody please point me to instructions for setting up xfs on 
Cygwin/X?  I especially need to know how
to set this up so that Courier fonts work properly for sizes for which 
there is no corresponding pcf file.  Is
xfs really needed, or is putting in the right libfreetype bits and 
pieces enough?  The files that go in

/usr/share/fonts/default/Type1 on Mandriva, for instance?

Long version:

Two machines both running Xorg, one is an old Mandriva 2008.0 machine 
with Xorg 7.2
on the console, and the other is a Cygwin machine using whatever Xorg 
version is current

on Cygwin/X.

In nedit they handle the following font differently:

-*-courier-medium-r-normal--17-120-*-*-*-iso8859-1

That works fine on the Mandriva machine X11 server, but uses some other 
font on the Cygwin X11
server (in both cases the Nedit client is on the Mandriva machine).  I 
don't know what font is actually
being used, but it isn't fixed (no error messages relating to this show 
up in the X.0.log file).


I looked through the fonts on the Mandriva machine and it does not 
actually have a 17 point Courier
font in the 75dpi directory, so it is coming up with that size on the 
fly, presumably through xfs, which is running there. Change to 14 pt 
(for which a pcf font file exists) then it is fixed width.  
Unfortunately that
font is much too small on the monitor in question.  Seems like font use 
on the Mandriva server is through xfs, but Cygwin/X client cannot use 
it, and isn't running its own copy.


The main server has in /usr/share/fonts:


100dpi/  75dpi/  cyrillic/  default/  fluxbox-artwiz-fonts/  misc/  
OTF/  Speedo/  ttf/  TTF/  Type1/


whereas the Cygwin variant has only the first two, and only the 75dpi 
has any fonts in it.


Presumably the Cygwin X11 server could be aimed at the Mandriva xfs, 
but for reasons I don't want to go into

here it would be much better if the Cygwin machine ran its own xfs.

How is this done?  (Pointer to instructions?)
Also, which part of xfs is coming up with the nice 17 point courier?  
What else, if anything, needs to

be added to get that functionality?

Or is xfs irrelevant and this is done through libfreetype?  The 
Mandriva machine definitely loads that, and
the Cygwin does not.  Moreover on the Mandriva machine there is a 
/usr/share/fonts/default/Type1/adobestd35/ directory with a .dir file 
that does include a Courier entry.


Thank you,

David Mathog
mat...@caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech

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Re: font question, xfs locally on cygwin?

2012-01-17 Thread mathog

On 17-Jan-2012 11:07, mathog wrote:

Is
xfs really needed, or is putting in the right libfreetype bits and
pieces enough?  The files that go in
/usr/share/fonts/default/Type1 on Mandriva, for instance?


So I tried copying the files from Mandriva over and dropping them into 
the
Cygwin distro.  That actually worked, in that the fonts then appeared 
and they looked
good on the screen.  Looks like xfs isn't needed.  However, there was a 
problem with the naming conventions.


This one works on the Mandriva X11 server

 -*-courier-medium-r-normal--17-120-*-*-*-iso8859-1

but it doesn't work on the Cygwin X11 server.  The file name there must 
be


-*-courier-medium-r-normal--17-120-*-*-*-*-iso8859-13

The problem seems to be that the font naming convention is slightly 
different.  There
are 3 fields between 120 and iso8859 on the Mandriva machine, but 4 on 
Cygwin/X.  Change in

the font naming conventions between different Xorg versions???

Which Cygwin package would install /usr/share/fonts/Type1 properly?

Thanks,

David Mathog
mat...@caltech.edu
Manager, Sequence Analysis Facility, Biology Division, Caltech

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