R SIG Fedora - Jan 2016 - rgl.snapshot only captures a small portion what's visible in the RGL device window on CentOS 7

Hello,

As an example, I ran the following code:

library("rgl")
example(plot3d)                                                                 
rgl.snapshot("test.png")

The full plot is visible in the window titled RGL device 1 [Focus], but only a
small portion of the upper left part of the plot is visible in test.png (see
attached test.png, if the list server attaches it. Otherwise, email me if you
like and I'll send it directly to you.)

The output of sessionInfo() is as follows:

R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

locale:
 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C             
 [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8    
 [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8   
 [7] LC_PAPER=en_US.utf8       LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C      

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rgl_0.95.1441

loaded via a namespace (and not attached):
[1] tools_3.2.3

In addition to the CentOS 7 machine, I have a CentOS 5.3 machine, which has R
3.0.2 and rgl 0.93.996. I tried the code above on it and it captured the full
window in the output of rgl.snapshot (i.e., it worked properly).

To see whether the difference could be attributed to the CentOS version or the
R/rgl version, I put R 3.0.2 with rgl 0.93.996 on the CentOS 7 machine and ran
the code above. As with the earlier CentOS 7 run, only a small portion of the
plot was visible in the output of rgl.snapshot. So it seems the difference is
due to a difference in the CentOS versions and not the R/rgl versions.

Thanks in advance for any help.

-Ben




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addressed. If you believe this e-mail was sent to you in error and the e-mail
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On 08/01/2016 4:13 PM, Wittner, Ben, Ph.D. wrote:
> Hello,
>
> As an example, I ran the following code:
>
> library("rgl")
> example(plot3d)
> rgl.snapshot("test.png")
>
> The full plot is visible in the window titled RGL device 1 [Focus], but
only a small portion of the upper left part of the plot is visible in test.png
(see attached test.png, if the list server attaches it. Otherwise, email me if
you like and I'll send it directly to you.)
>
> The output of sessionInfo() is as follows:
>
> R version 3.2.3 (2015-12-10)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: CentOS Linux 7 (Core)
>
> locale:
>   [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
>   [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8
>   [7] LC_PAPER=en_US.utf8       LC_NAME=C
>   [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] rgl_0.95.1441
>
> loaded via a namespace (and not attached):
> [1] tools_3.2.3
>
> In addition to the CentOS 7 machine, I have a CentOS 5.3 machine, which has
R 3.0.2 and rgl 0.93.996. I tried the code above on it and it captured the full
window in the output of rgl.snapshot (i.e., it worked properly).
>
> To see whether the difference could be attributed to the CentOS version or
the R/rgl version, I put R 3.0.2 with rgl 0.93.996 on the CentOS 7 machine and
ran the code above. As with the earlier CentOS 7 run, only a small portion of
the plot was visible in the output of rgl.snapshot. So it seems the difference
is due to a difference in the CentOS versions and not the R/rgl versions.
>
> Thanks in advance for any help.
>
I think you'll need to contact CentOS about this.  That code hasn't 
changed in rgl in a long time.  It's possible that rgl is wrong, but I'd
need more information from them to convince me.

Duncan Murdoch

Dear Duncan, Thanks very much for your reply. I guess I'll start with
R-SIG-Fedora. I'll keep you cc'd unless you tell me you would rather I
not. -Ben

-----Original Message-----
From: Duncan Murdoch [mailto:murdoch.duncan at gmail.com] 
Sent: Friday, January 08, 2016 8:13 PM
To: Wittner, Ben, Ph.D.; r-help at r-project.org
Subject: Re: [R] rgl.snapshot only captures a small portion what's visible
in the RGL device window on CentOS 7

On 08/01/2016 4:13 PM, Wittner, Ben, Ph.D. wrote:
> Hello,
>
> As an example, I ran the following code:
>
> library("rgl")
> example(plot3d)
> rgl.snapshot("test.png")
>
> The full plot is visible in the window titled RGL device 1 [Focus], 
> but only a small portion of the upper left part of the plot is visible 
> in test.png (see attached test.png, if the list server attaches it. 
> Otherwise, email me if you like and I'll send it directly to you.)
>
> The output of sessionInfo() is as follows:
>
> R version 3.2.3 (2015-12-10)
> Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 
> (Core)
>
> locale:
>   [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
>   [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8
>   [7] LC_PAPER=en_US.utf8       LC_NAME=C
>   [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] rgl_0.95.1441
>
> loaded via a namespace (and not attached):
> [1] tools_3.2.3
>
> In addition to the CentOS 7 machine, I have a CentOS 5.3 machine, which has
R 3.0.2 and rgl 0.93.996. I tried the code above on it and it captured the full
window in the output of rgl.snapshot (i.e., it worked properly).
>
> To see whether the difference could be attributed to the CentOS version or
the R/rgl version, I put R 3.0.2 with rgl 0.93.996 on the CentOS 7 machine and
ran the code above. As with the earlier CentOS 7 run, only a small portion of
the plot was visible in the output of rgl.snapshot. So it seems the difference
is due to a difference in the CentOS versions and not the R/rgl versions.
>
> Thanks in advance for any help.
>
I think you'll need to contact CentOS about this.  That code hasn't
changed in rgl in a long time.  It's possible that rgl is wrong, but I'd
need more information from them to convince me.

Duncan Murdoch



The information in this e-mail is intended only for the ...{{dropped:11}}

Dear R-SIG-Fedora,

I'm finding that on CentOS 7, rgl.snapshot (a function in the R package rgl,
which provides an R interface to the OpenGL 3-d graphics library) only captures
a small portion what's visible in the RGL device window. This does not
happen with the same R and rgl versions on CentOS 5.3 (see details below).

The maintainer of rgl, Duncan Murdoch, responded (see below) that the rgl code
has not changed in a long time, so it's likely, although not certain, that
the problem lies with CentOS 7.

I know very little about graphics, but it seems to me from looking at the rgl
source code that the fundamental work of rgl.snapshot is done by calls to
glReadBuffer, glPixelStorei, and glReadPixels, which seem to be functions in the
OpenGL library.

Can anyone take a look at this or advise me on how to proceed?

Thanks very much in advance.

-Ben

-----Original Message-----
From: Duncan Murdoch [mailto:murdoch.duncan at gmail.com] 
Sent: Friday, January 08, 2016 8:13 PM
To: Wittner, Ben, Ph.D.; r-help at r-project.org
Subject: Re: [R] rgl.snapshot only captures a small portion what's visible
in the RGL device window on CentOS 7

On 08/01/2016 4:13 PM, Wittner, Ben, Ph.D. wrote:
> Hello,
>
> As an example, I ran the following code:
>
> library("rgl")
> example(plot3d)
> rgl.snapshot("test.png")
>
> The full plot is visible in the window titled RGL device 1 [Focus], 
> but only a small portion of the upper left part of the plot is visible 
> in test.png (see attached test.png, if the list server attaches it. 
> Otherwise, email me if you like and I'll send it directly to you.)
>
> The output of sessionInfo() is as follows:
>
> R version 3.2.3 (2015-12-10)
> Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 
> (Core)
>
> locale:
>   [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
>   [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8
>   [7] LC_PAPER=en_US.utf8       LC_NAME=C
>   [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] rgl_0.95.1441
>
> loaded via a namespace (and not attached):
> [1] tools_3.2.3
>
> In addition to the CentOS 7 machine, I have a CentOS 5.3 machine, which has
R 3.0.2 and rgl 0.93.996. I tried the code above on it and it captured the full
window in the output of rgl.snapshot (i.e., it worked properly).
>
> To see whether the difference could be attributed to the CentOS version or
the R/rgl version, I put R 3.0.2 with rgl 0.93.996 on the CentOS 7 machine and
ran the code above. As with the earlier CentOS 7 run, only a small portion of
the plot was visible in the output of rgl.snapshot. So it seems the difference
is due to a difference in the CentOS versions and not the R/rgl versions.
>
> Thanks in advance for any help.
>
I think you'll need to contact CentOS about this.  That code hasn't
changed in rgl in a long time.  It's possible that rgl is wrong, but I'd
need more information from them to convince me.

Duncan Murdoch



The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
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The problem discussed below was fixed on my computer with much help from Tom
Callaway, of RedHat.
My computer has an NVIDIA graphics card and CentOS 7 comes with an open-source
driver for NVIDIA graphic cards called nouveau. When I replaced the nouveau
driver with a driver from NVIDIA, the problem went away.

To see whether your machine has an NVIDIA graphics card, execute the command
lspci -v
and search in the output for VGA. The top of that block of output will tell you
what graphics card you have and the last line of the block will tell you what
driver is in use.
In my case the top of that block of output was the following:

07:00.0 VGA compatible controller: NVIDIA Corporation G84GL [Quadro FX 370] (rev
a1)

So I knew I had an NVIDIA graphics card and that the model was Quadro FX 370,
which was important when trying to determine which driver to download from
http://www.nvidia.com/object/unix.html .

After downloading the driver, I was not able to get it installed just using the
instructions from the NVIDIA download page. The key for me was to follow the
instructions in http://www.dedoimedo.com/computers/centos-7-nvidia.html .

Good luck!

-Ben

-----Original Message-----
From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Wittner, Ben,
Ph.D.
Sent: Friday, January 08, 2016 4:13 PM
To: r-help at r-project.org
Subject: [R] rgl.snapshot only captures a small portion what's visible in
the RGL device window on CentOS 7

Hello,

As an example, I ran the following code:

library("rgl")
example(plot3d)                                                                 
rgl.snapshot("test.png")

The full plot is visible in the window titled RGL device 1 [Focus], but only a
small portion of the upper left part of the plot is visible in test.png (see
attached test.png, if the list server attaches it. Otherwise, email me if you
like and I'll send it directly to you.)

The output of sessionInfo() is as follows:

R version 3.2.3 (2015-12-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

locale:
 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C             
 [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8    
 [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8   
 [7] LC_PAPER=en_US.utf8       LC_NAME=C                
 [9] LC_ADDRESS=C              LC_TELEPHONE=C           
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C      

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] rgl_0.95.1441

loaded via a namespace (and not attached):
[1] tools_3.2.3

In addition to the CentOS 7 machine, I have a CentOS 5.3 machine, which has R
3.0.2 and rgl 0.93.996. I tried the code above on it and it captured the full
window in the output of rgl.snapshot (i.e., it worked properly).

To see whether the difference could be attributed to the CentOS version or the
R/rgl version, I put R 3.0.2 with rgl 0.93.996 on the CentOS 7 machine and ran
the code above. As with the earlier CentOS 7 run, only a small portion of the
plot was visible in the output of rgl.snapshot. So it seems the difference is
due to a difference in the CentOS versions and not the R/rgl versions.

Thanks in advance for any help.

-Ben



The information in this e-mail is intended only for the ...{{dropped:11}}

On 11/01/2016 5:39 PM, Wittner, Ben, Ph.D. wrote:
> The problem discussed below was fixed on my computer with much help from
Tom Callaway, of RedHat.
> My computer has an NVIDIA graphics card and CentOS 7 comes with an
open-source driver for NVIDIA graphic cards called nouveau. When I replaced the
nouveau driver with a driver from NVIDIA, the problem went away.
>
> To see whether your machine has an NVIDIA graphics card, execute the
command
> lspci -v
> and search in the output for VGA. The top of that block of output will tell
you what graphics card you have and the last line of the block will tell you
what driver is in use.
> In my case the top of that block of output was the following:
>
> 07:00.0 VGA compatible controller: NVIDIA Corporation G84GL [Quadro FX 370]
(rev a1)
>
> So I knew I had an NVIDIA graphics card and that the model was Quadro FX
370, which was important when trying to determine which driver to download from
http://www.nvidia.com/object/unix.html .
>
> After downloading the driver, I was not able to get it installed just using
the instructions from the NVIDIA download page. The key for me was to follow the
instructions in http://www.dedoimedo.com/computers/centos-7-nvidia.html .
Thanks for following up on this.  If I get any other similar reports, 
I'll be able to point them to your message.

Duncan Murdoch
> Good luck!
>
> -Ben
>
> -----Original Message-----
> From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of Wittner,
Ben, Ph.D.
> Sent: Friday, January 08, 2016 4:13 PM
> To: r-help at r-project.org
> Subject: [R] rgl.snapshot only captures a small portion what's visible
in the RGL device window on CentOS 7
>
> Hello,
>
> As an example, I ran the following code:
>
> library("rgl")
> example(plot3d)
> rgl.snapshot("test.png")
>
> The full plot is visible in the window titled RGL device 1 [Focus], but
only a small portion of the upper left part of the plot is visible in test.png
(see attached test.png, if the list server attaches it. Otherwise, email me if
you like and I'll send it directly to you.)
>
> The output of sessionInfo() is as follows:
>
> R version 3.2.3 (2015-12-10)
> Platform: x86_64-pc-linux-gnu (64-bit)
> Running under: CentOS Linux 7 (Core)
>
> locale:
>   [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
>   [3] LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8
>   [5] LC_MONETARY=en_US.utf8    LC_MESSAGES=en_US.utf8
>   [7] LC_PAPER=en_US.utf8       LC_NAME=C
>   [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] rgl_0.95.1441
>
> loaded via a namespace (and not attached):
> [1] tools_3.2.3
>
> In addition to the CentOS 7 machine, I have a CentOS 5.3 machine, which has
R 3.0.2 and rgl 0.93.996. I tried the code above on it and it captured the full
window in the output of rgl.snapshot (i.e., it worked properly).
>
> To see whether the difference could be attributed to the CentOS version or
the R/rgl version, I put R 3.0.2 with rgl 0.93.996 on the CentOS 7 machine and
ran the code above. As with the earlier CentOS 7 run, only a small portion of
the plot was visible in the output of rgl.snapshot. So it seems the difference
is due to a difference in the CentOS versions and not the R/rgl versions.
>
> Thanks in advance for any help.
>
> -Ben
>
>
>
> The information in this e-mail is intended only for the ...{{dropped:11}}
>
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