Re: [Bioc-devel] GLX extension missing on petty
On Sat, Apr 6, 2013 at 11:32 AM, Dan Tenenbaum wrote:
> On Sat, Apr 6, 2013 at 10:39 AM, Jiří Hon wrote:
>> Dne Fri, 05 Apr 2013 19:07:12 +0200 Dan Tenenbaum
>> napsal(a):
>>
>>
>>> On Fri, Apr 5, 2013 at 2:11 AM, Jiří Hon
>>> wrote:
>
> In the short term, you can disable all vignette code chunks that use
> rgl (with eval=FALSE), and do the same with examples that use rgl
> (with \dontrun{}).
Thank you a lot for tracking that down. Unfortunately all vignette code
chunks that use rgl have been always disabled with eval=FALSE. That
probably
means we have no way to workaround this problem on petty.
>>>
>>> Turns out the real problem was unescaped accented characters in the
>>> vignette. Fixing that along with two dontrun tags in example sections
>>> allows the package to build and check on Mac. I've made the changes in
>>> release and devel.
>>
>>
>> Thanks a lot for that, still it didn't pass check on Mac. So I removed the
>> work around of rgl segfault on Mac that is probably unnecessary and I hope
>> it helps. With dontrun tags around triplex.3D call no other rgl code should
>> be executed during check.
>>
>
> Thank you. I did not mean to check that in. I can confirm that the
> latest version passes check on petty.
>
Incidentally, the latest version of rgl is now available on CRAN. It
does not segfault in
example(rgl.material)
anymore. This means Snow Leopard users will be able to run triplex.
Dan
> Dan
>
>
>> Jirka
>>
>>
>>>
>>> Dan
>>>
>>>
Dne Fri, 05 Apr 2013 01:22:52 +0200 Dan Tenenbaum
napsal(a):
> On Wed, Apr 3, 2013 at 9:45 AM, Dan Tenenbaum
> wrote:
>>
>>
>> Hi Jirka,
>>
>>
>> On Wed, Apr 3, 2013 at 9:06 AM, Jiří Hon
>> wrote:
>>>
>>>
>>> Hi,
>>> the latest bioc build of my new package 'triplex' on petty ended with
>>> this
>>> error message:
>>>
>>> Warning in rgl.init(initValue) : RGL: GLX extension missing on server
>>> Warning in fun(libname, pkgname) : error in rgl_init
>>>
>>> For full report see
>>>
>>>
>>> http://bioconductor.org/checkResults/devel/bioc-LATEST/triplex/petty-buildsrc.html
>>>
>>> And I am wondering if there is anything I could do to fix this.
>>> Probably
>>> it's a build system problem, but other packages that depends on rgl
>>> and
>>> plots in 3D have no such build error (i.e. RDRToolbox) and that makes
>>> me
>>> sligthly nervous, so I would really appreciate any advice.
>>
>>
>>
>> This is a build system problem, and I am looking into it.
>> The build system runs under Xvfb, but I have no problem building your
>> package when logged into the console of petty.
>>
>
> A little more info on this.
>
> There are two problems. The first is that as mentioned before, our
> builds do not run physically logged into the console; they use a
> virtual frame buffer (Xvfb).
>
> We could look into changing this, but at present triplex seems to be
> the only package having this problem.
>
> Xvfb apparently does not have the OpenGL extensions compiled in. I
> will check with the XQuartz people. They have been responsive before.
>
> The second problem is if I do log into the actual physical console of
> the machine, I am able to build triplex but I get the following
> segfault when trying to run R CMD check on triplex:
>
>
>
>> However, do get a segfault when running R CMD check on the triplex
>> source tarball:
>>
>> $ R CMD check --no-vignettes --timings triplex_0.99.0.tar.gz
>> [...]
>> * checking examples ...sh: line 1: 41089 Segmentation fault
>> LANGUAGE=en _R_CHECK_INTERNALS2_=1
>> '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla >
>> 'triplex-Ex.Rout' 2>&1 < triplex-Ex.R
>> ERROR
>> Running examples in ?~@~Xtriplex-Ex.R?~@~Y failed
>> The error most likely occurred in:
>>
>>> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
>>> ### Name: triplex-package
>>> ### Title: Triplex search and visualization package
>>> ### Aliases: triplex-package triplex
>>> ### Keywords: package
>>>
>>> ### ** Examples
>>>
>>> seq <- DNAString("GGAAAGCAATGCCAGGCAGGG")
>>> t <- triplex.search(seq)
>>
>>
>> Searching for triplex type 0...
>> Searching for triplex type 1...
>> Searching for triplex type 2...
>> Searching for triplex type 3...
>> Searching for triplex type 4...
>> Searching for triplex type 5...
>> Searching for triplex type 6...
>> Searching for triplex type 7...
>>>
>>>
>>> triplex.diagram(t[1])
>>
>>
>> A DNAStringSet instance of length 4
>> width seq names
>> [1] 8 CCCTGCCT minus
>> [2] 8 GG
Re: [Bioc-devel] GLX extension missing on petty
On Sat, Apr 6, 2013 at 10:39 AM, Jiří Hon wrote:
> Dne Fri, 05 Apr 2013 19:07:12 +0200 Dan Tenenbaum
> napsal(a):
>
>
>> On Fri, Apr 5, 2013 at 2:11 AM, Jiří Hon
>> wrote:
In the short term, you can disable all vignette code chunks that use
rgl (with eval=FALSE), and do the same with examples that use rgl
(with \dontrun{}).
>>>
>>>
>>>
>>> Thank you a lot for tracking that down. Unfortunately all vignette code
>>> chunks that use rgl have been always disabled with eval=FALSE. That
>>> probably
>>> means we have no way to workaround this problem on petty.
>>>
>>
>> Turns out the real problem was unescaped accented characters in the
>> vignette. Fixing that along with two dontrun tags in example sections
>> allows the package to build and check on Mac. I've made the changes in
>> release and devel.
>
>
> Thanks a lot for that, still it didn't pass check on Mac. So I removed the
> work around of rgl segfault on Mac that is probably unnecessary and I hope
> it helps. With dontrun tags around triplex.3D call no other rgl code should
> be executed during check.
>
Thank you. I did not mean to check that in. I can confirm that the
latest version passes check on petty.
Dan
> Jirka
>
>
>>
>> Dan
>>
>>
>>> Dne Fri, 05 Apr 2013 01:22:52 +0200 Dan Tenenbaum
>>> napsal(a):
>>>
>>>
On Wed, Apr 3, 2013 at 9:45 AM, Dan Tenenbaum
wrote:
>
>
> Hi Jirka,
>
>
> On Wed, Apr 3, 2013 at 9:06 AM, Jiří Hon
> wrote:
>>
>>
>> Hi,
>> the latest bioc build of my new package 'triplex' on petty ended with
>> this
>> error message:
>>
>> Warning in rgl.init(initValue) : RGL: GLX extension missing on server
>> Warning in fun(libname, pkgname) : error in rgl_init
>>
>> For full report see
>>
>>
>> http://bioconductor.org/checkResults/devel/bioc-LATEST/triplex/petty-buildsrc.html
>>
>> And I am wondering if there is anything I could do to fix this.
>> Probably
>> it's a build system problem, but other packages that depends on rgl
>> and
>> plots in 3D have no such build error (i.e. RDRToolbox) and that makes
>> me
>> sligthly nervous, so I would really appreciate any advice.
>
>
>
> This is a build system problem, and I am looking into it.
> The build system runs under Xvfb, but I have no problem building your
> package when logged into the console of petty.
>
A little more info on this.
There are two problems. The first is that as mentioned before, our
builds do not run physically logged into the console; they use a
virtual frame buffer (Xvfb).
We could look into changing this, but at present triplex seems to be
the only package having this problem.
Xvfb apparently does not have the OpenGL extensions compiled in. I
will check with the XQuartz people. They have been responsive before.
The second problem is if I do log into the actual physical console of
the machine, I am able to build triplex but I get the following
segfault when trying to run R CMD check on triplex:
> However, do get a segfault when running R CMD check on the triplex
> source tarball:
>
> $ R CMD check --no-vignettes --timings triplex_0.99.0.tar.gz
> [...]
> * checking examples ...sh: line 1: 41089 Segmentation fault
> LANGUAGE=en _R_CHECK_INTERNALS2_=1
> '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla >
> 'triplex-Ex.Rout' 2>&1 < triplex-Ex.R
> ERROR
> Running examples in ?~@~Xtriplex-Ex.R?~@~Y failed
> The error most likely occurred in:
>
>> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
>> ### Name: triplex-package
>> ### Title: Triplex search and visualization package
>> ### Aliases: triplex-package triplex
>> ### Keywords: package
>>
>> ### ** Examples
>>
>> seq <- DNAString("GGAAAGCAATGCCAGGCAGGG")
>> t <- triplex.search(seq)
>
>
> Searching for triplex type 0...
> Searching for triplex type 1...
> Searching for triplex type 2...
> Searching for triplex type 3...
> Searching for triplex type 4...
> Searching for triplex type 5...
> Searching for triplex type 6...
> Searching for triplex type 7...
>>
>>
>> triplex.diagram(t[1])
>
>
> A DNAStringSet instance of length 4
> width seq names
> [1] 8 CCCTGCCT minus
> [2] 8 GGGACGGA plus
> [3] 8 CCTTTCGT para-minus
> [4] 5 GGCAT loop
>>
>>
>> triplex.3D(t[1])
>
>
>
> *** caught segfault ***
> address 0x0, cause 'memory not mapped'
>
> Traceback:
> 1: .C(rgl_material, success = FAL
Re: [Bioc-devel] GLX extension missing on petty
Dne Fri, 05 Apr 2013 19:07:12 +0200 Dan Tenenbaum
napsal(a):
On Fri, Apr 5, 2013 at 2:11 AM, Jiří Hon
wrote:
In the short term, you can disable all vignette code chunks that use
rgl (with eval=FALSE), and do the same with examples that use rgl
(with \dontrun{}).
Thank you a lot for tracking that down. Unfortunately all vignette code
chunks that use rgl have been always disabled with eval=FALSE. That
probably
means we have no way to workaround this problem on petty.
Turns out the real problem was unescaped accented characters in the
vignette. Fixing that along with two dontrun tags in example sections
allows the package to build and check on Mac. I've made the changes in
release and devel.
Thanks a lot for that, still it didn't pass check on Mac. So I removed the
work around of rgl segfault on Mac that is probably unnecessary and I hope
it helps. With dontrun tags around triplex.3D call no other rgl code
should be executed during check.
Jirka
Dan
Dne Fri, 05 Apr 2013 01:22:52 +0200 Dan Tenenbaum
napsal(a):
On Wed, Apr 3, 2013 at 9:45 AM, Dan Tenenbaum
wrote:
Hi Jirka,
On Wed, Apr 3, 2013 at 9:06 AM, Jiří Hon
wrote:
Hi,
the latest bioc build of my new package 'triplex' on petty ended with
this
error message:
Warning in rgl.init(initValue) : RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
For full report see
http://bioconductor.org/checkResults/devel/bioc-LATEST/triplex/petty-buildsrc.html
And I am wondering if there is anything I could do to fix this.
Probably
it's a build system problem, but other packages that depends on rgl
and
plots in 3D have no such build error (i.e. RDRToolbox) and that
makes me
sligthly nervous, so I would really appreciate any advice.
This is a build system problem, and I am looking into it.
The build system runs under Xvfb, but I have no problem building your
package when logged into the console of petty.
A little more info on this.
There are two problems. The first is that as mentioned before, our
builds do not run physically logged into the console; they use a
virtual frame buffer (Xvfb).
We could look into changing this, but at present triplex seems to be
the only package having this problem.
Xvfb apparently does not have the OpenGL extensions compiled in. I
will check with the XQuartz people. They have been responsive before.
The second problem is if I do log into the actual physical console of
the machine, I am able to build triplex but I get the following
segfault when trying to run R CMD check on triplex:
However, do get a segfault when running R CMD check on the triplex
source tarball:
$ R CMD check --no-vignettes --timings triplex_0.99.0.tar.gz
[...]
* checking examples ...sh: line 1: 41089 Segmentation fault
LANGUAGE=en _R_CHECK_INTERNALS2_=1
'/Library/Frameworks/R.framework/Resources/bin/R' --vanilla >
'triplex-Ex.Rout' 2>&1 < triplex-Ex.R
ERROR
Running examples in ?~@~Xtriplex-Ex.R?~@~Y failed
The error most likely occurred in:
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: triplex-package
### Title: Triplex search and visualization package
### Aliases: triplex-package triplex
### Keywords: package
### ** Examples
seq <- DNAString("GGAAAGCAATGCCAGGCAGGG")
t <- triplex.search(seq)
Searching for triplex type 0...
Searching for triplex type 1...
Searching for triplex type 2...
Searching for triplex type 3...
Searching for triplex type 4...
Searching for triplex type 5...
Searching for triplex type 6...
Searching for triplex type 7...
triplex.diagram(t[1])
A DNAStringSet instance of length 4
width seq names
[1] 8 CCCTGCCT minus
[2] 8 GGGACGGA plus
[3] 8 CCTTTCGT para-minus
[4] 5 GGCAT loop
triplex.3D(t[1])
*** caught segfault ***
address 0x0, cause 'memory not mapped'
Traceback:
1: .C(rgl_material, success = FALSE, idata, cdata, ddata)
2: rgl.material(color = color, back = back, ...)
3: rgl.bg(color = bgr.col)
4: triplex.3D(t[1])
aborting ...
This turns out to be reproducible simply like this:
library(rgl)
example(rgl.material)
And it's caused by the following line (Material.cpp:39) in the rgl
package:
const char* version = (const char*)glGetString(GL_VERSION);
glGetString() is a function in the OpenGL library and it is
segfaulting.
Obviously that should not be happening. I'll try to track that down.
In the short term, you can disable all vignette code chunks that use
rgl (with eval=FALSE), and do the same with examples that use rgl
(with \dontrun{}).
The problem as far as I can tell is just on Snow Leopard which is what
we use on our build systems.
The package builds, checks, installs and runs OK on my Mountain Lion
laptop.
Dan
Dan
Thank you a lot for your time an
Re: [Bioc-devel] GLX extension missing on petty
On Fri, Apr 5, 2013 at 2:11 AM, Jiří Hon wrote:
>> In the short term, you can disable all vignette code chunks that use
>> rgl (with eval=FALSE), and do the same with examples that use rgl
>> (with \dontrun{}).
>
>
> Thank you a lot for tracking that down. Unfortunately all vignette code
> chunks that use rgl have been always disabled with eval=FALSE. That probably
> means we have no way to workaround this problem on petty.
>
Turns out the real problem was unescaped accented characters in the
vignette. Fixing that along with two dontrun tags in example sections
allows the package to build and check on Mac. I've made the changes in
release and devel.
Dan
> Dne Fri, 05 Apr 2013 01:22:52 +0200 Dan Tenenbaum
> napsal(a):
>
>
>> On Wed, Apr 3, 2013 at 9:45 AM, Dan Tenenbaum wrote:
>>>
>>> Hi Jirka,
>>>
>>>
>>> On Wed, Apr 3, 2013 at 9:06 AM, Jiří Hon
>>> wrote:
Hi,
the latest bioc build of my new package 'triplex' on petty ended with
this
error message:
Warning in rgl.init(initValue) : RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
For full report see
http://bioconductor.org/checkResults/devel/bioc-LATEST/triplex/petty-buildsrc.html
And I am wondering if there is anything I could do to fix this. Probably
it's a build system problem, but other packages that depends on rgl and
plots in 3D have no such build error (i.e. RDRToolbox) and that makes me
sligthly nervous, so I would really appreciate any advice.
>>>
>>>
>>> This is a build system problem, and I am looking into it.
>>> The build system runs under Xvfb, but I have no problem building your
>>> package when logged into the console of petty.
>>>
>>
>> A little more info on this.
>>
>> There are two problems. The first is that as mentioned before, our
>> builds do not run physically logged into the console; they use a
>> virtual frame buffer (Xvfb).
>>
>> We could look into changing this, but at present triplex seems to be
>> the only package having this problem.
>>
>> Xvfb apparently does not have the OpenGL extensions compiled in. I
>> will check with the XQuartz people. They have been responsive before.
>>
>> The second problem is if I do log into the actual physical console of
>> the machine, I am able to build triplex but I get the following
>> segfault when trying to run R CMD check on triplex:
>>
>>
>>
>>> However, do get a segfault when running R CMD check on the triplex
>>> source tarball:
>>>
>>> $ R CMD check --no-vignettes --timings triplex_0.99.0.tar.gz
>>> [...]
>>> * checking examples ...sh: line 1: 41089 Segmentation fault
>>> LANGUAGE=en _R_CHECK_INTERNALS2_=1
>>> '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla >
>>> 'triplex-Ex.Rout' 2>&1 < triplex-Ex.R
>>> ERROR
>>> Running examples in ?~@~Xtriplex-Ex.R?~@~Y failed
>>> The error most likely occurred in:
>>>
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: triplex-package
### Title: Triplex search and visualization package
### Aliases: triplex-package triplex
### Keywords: package
### ** Examples
seq <- DNAString("GGAAAGCAATGCCAGGCAGGG")
t <- triplex.search(seq)
>>>
>>> Searching for triplex type 0...
>>> Searching for triplex type 1...
>>> Searching for triplex type 2...
>>> Searching for triplex type 3...
>>> Searching for triplex type 4...
>>> Searching for triplex type 5...
>>> Searching for triplex type 6...
>>> Searching for triplex type 7...
triplex.diagram(t[1])
>>>
>>> A DNAStringSet instance of length 4
>>> width seq names
>>> [1] 8 CCCTGCCT minus
>>> [2] 8 GGGACGGA plus
>>> [3] 8 CCTTTCGT para-minus
>>> [4] 5 GGCAT loop
triplex.3D(t[1])
>>>
>>>
>>> *** caught segfault ***
>>> address 0x0, cause 'memory not mapped'
>>>
>>> Traceback:
>>> 1: .C(rgl_material, success = FALSE, idata, cdata, ddata)
>>> 2: rgl.material(color = color, back = back, ...)
>>> 3: rgl.bg(color = bgr.col)
>>> 4: triplex.3D(t[1])
>>> aborting ...
>>>
>>
>> This turns out to be reproducible simply like this:
>>
>> library(rgl)
>> example(rgl.material)
>>
>> And it's caused by the following line (Material.cpp:39) in the rgl
>> package:
>>
>> const char* version = (const char*)glGetString(GL_VERSION);
>>
>> glGetString() is a function in the OpenGL library and it is segfaulting.
>>
>>
>> Obviously that should not be happening. I'll try to track that down.
>>
>> In the short term, you can disable all vignette code chunks that use
>> rgl (with eval=FALSE), and do the same with examples that use rgl
>> (with \dontrun{}).
>>
>> The problem as far as I can tell is just on Snow Leopard which is what
>> we use on our build systems.
>> The package bu
Re: [Bioc-devel] GLX extension missing on petty
In the short term, you can disable all vignette code chunks that use
rgl (with eval=FALSE), and do the same with examples that use rgl
(with \dontrun{}).
Thank you a lot for tracking that down. Unfortunately all vignette code
chunks that use rgl have been always disabled with eval=FALSE. That
probably means we have no way to workaround this problem on petty.
Dne Fri, 05 Apr 2013 01:22:52 +0200 Dan Tenenbaum
napsal(a):
On Wed, Apr 3, 2013 at 9:45 AM, Dan Tenenbaum wrote:
Hi Jirka,
On Wed, Apr 3, 2013 at 9:06 AM, Jiří Hon
wrote:
Hi,
the latest bioc build of my new package 'triplex' on petty ended with
this
error message:
Warning in rgl.init(initValue) : RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
For full report see
http://bioconductor.org/checkResults/devel/bioc-LATEST/triplex/petty-buildsrc.html
And I am wondering if there is anything I could do to fix this.
Probably
it's a build system problem, but other packages that depends on rgl and
plots in 3D have no such build error (i.e. RDRToolbox) and that makes
me
sligthly nervous, so I would really appreciate any advice.
This is a build system problem, and I am looking into it.
The build system runs under Xvfb, but I have no problem building your
package when logged into the console of petty.
A little more info on this.
There are two problems. The first is that as mentioned before, our
builds do not run physically logged into the console; they use a
virtual frame buffer (Xvfb).
We could look into changing this, but at present triplex seems to be
the only package having this problem.
Xvfb apparently does not have the OpenGL extensions compiled in. I
will check with the XQuartz people. They have been responsive before.
The second problem is if I do log into the actual physical console of
the machine, I am able to build triplex but I get the following
segfault when trying to run R CMD check on triplex:
However, do get a segfault when running R CMD check on the triplex
source tarball:
$ R CMD check --no-vignettes --timings triplex_0.99.0.tar.gz
[...]
* checking examples ...sh: line 1: 41089 Segmentation fault
LANGUAGE=en _R_CHECK_INTERNALS2_=1
'/Library/Frameworks/R.framework/Resources/bin/R' --vanilla >
'triplex-Ex.Rout' 2>&1 < triplex-Ex.R
ERROR
Running examples in ?~@~Xtriplex-Ex.R?~@~Y failed
The error most likely occurred in:
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: triplex-package
### Title: Triplex search and visualization package
### Aliases: triplex-package triplex
### Keywords: package
### ** Examples
seq <- DNAString("GGAAAGCAATGCCAGGCAGGG")
t <- triplex.search(seq)
Searching for triplex type 0...
Searching for triplex type 1...
Searching for triplex type 2...
Searching for triplex type 3...
Searching for triplex type 4...
Searching for triplex type 5...
Searching for triplex type 6...
Searching for triplex type 7...
triplex.diagram(t[1])
A DNAStringSet instance of length 4
width seq names
[1] 8 CCCTGCCT minus
[2] 8 GGGACGGA plus
[3] 8 CCTTTCGT para-minus
[4] 5 GGCAT loop
triplex.3D(t[1])
*** caught segfault ***
address 0x0, cause 'memory not mapped'
Traceback:
1: .C(rgl_material, success = FALSE, idata, cdata, ddata)
2: rgl.material(color = color, back = back, ...)
3: rgl.bg(color = bgr.col)
4: triplex.3D(t[1])
aborting ...
This turns out to be reproducible simply like this:
library(rgl)
example(rgl.material)
And it's caused by the following line (Material.cpp:39) in the rgl
package:
const char* version = (const char*)glGetString(GL_VERSION);
glGetString() is a function in the OpenGL library and it is segfaulting.
Obviously that should not be happening. I'll try to track that down.
In the short term, you can disable all vignette code chunks that use
rgl (with eval=FALSE), and do the same with examples that use rgl
(with \dontrun{}).
The problem as far as I can tell is just on Snow Leopard which is what
we use on our build systems.
The package builds, checks, installs and runs OK on my Mountain Lion
laptop.
Dan
Dan
Thank you a lot for your time and patience,
Jirka
___
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___
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Re: [Bioc-devel] GLX extension missing on petty
On Thu, Apr 4, 2013 at 4:22 PM, Dan Tenenbaum wrote:
> On Wed, Apr 3, 2013 at 9:45 AM, Dan Tenenbaum wrote:
>> Hi Jirka,
>>
>>
>> On Wed, Apr 3, 2013 at 9:06 AM, Jiří Hon wrote:
>>> Hi,
>>> the latest bioc build of my new package 'triplex' on petty ended with this
>>> error message:
>>>
>>> Warning in rgl.init(initValue) : RGL: GLX extension missing on server
>>> Warning in fun(libname, pkgname) : error in rgl_init
>>>
>>> For full report see
>>> http://bioconductor.org/checkResults/devel/bioc-LATEST/triplex/petty-buildsrc.html
>>>
>>> And I am wondering if there is anything I could do to fix this. Probably
>>> it's a build system problem, but other packages that depends on rgl and
>>> plots in 3D have no such build error (i.e. RDRToolbox) and that makes me
>>> sligthly nervous, so I would really appreciate any advice.
>>
>> This is a build system problem, and I am looking into it.
>> The build system runs under Xvfb, but I have no problem building your
>> package when logged into the console of petty.
>>
>
> A little more info on this.
>
> There are two problems. The first is that as mentioned before, our
> builds do not run physically logged into the console; they use a
> virtual frame buffer (Xvfb).
>
> We could look into changing this, but at present triplex seems to be
> the only package having this problem.
>
> Xvfb apparently does not have the OpenGL extensions compiled in. I
> will check with the XQuartz people. They have been responsive before.
>
> The second problem is if I do log into the actual physical console of
> the machine, I am able to build triplex but I get the following
> segfault when trying to run R CMD check on triplex:
>
>
>
>> However, do get a segfault when running R CMD check on the triplex
>> source tarball:
>>
>> $ R CMD check --no-vignettes --timings triplex_0.99.0.tar.gz
>> [...]
>> * checking examples ...sh: line 1: 41089 Segmentation fault
>> LANGUAGE=en _R_CHECK_INTERNALS2_=1
>> '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla >
>> 'triplex-Ex.Rout' 2>&1 < triplex-Ex.R
>> ERROR
>> Running examples in ?~@~Xtriplex-Ex.R?~@~Y failed
>> The error most likely occurred in:
>>
>>> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
>>> ### Name: triplex-package
>>> ### Title: Triplex search and visualization package
>>> ### Aliases: triplex-package triplex
>>> ### Keywords: package
>>>
>>> ### ** Examples
>>>
>>> seq <- DNAString("GGAAAGCAATGCCAGGCAGGG")
>>> t <- triplex.search(seq)
>> Searching for triplex type 0...
>> Searching for triplex type 1...
>> Searching for triplex type 2...
>> Searching for triplex type 3...
>> Searching for triplex type 4...
>> Searching for triplex type 5...
>> Searching for triplex type 6...
>> Searching for triplex type 7...
>>> triplex.diagram(t[1])
>> A DNAStringSet instance of length 4
>> width seq names
>> [1] 8 CCCTGCCT minus
>> [2] 8 GGGACGGA plus
>> [3] 8 CCTTTCGT para-minus
>> [4] 5 GGCAT loop
>>> triplex.3D(t[1])
>>
>> *** caught segfault ***
>> address 0x0, cause 'memory not mapped'
>>
>> Traceback:
>> 1: .C(rgl_material, success = FALSE, idata, cdata, ddata)
>> 2: rgl.material(color = color, back = back, ...)
>> 3: rgl.bg(color = bgr.col)
>> 4: triplex.3D(t[1])
>> aborting ...
>>
>
> This turns out to be reproducible simply like this:
>
> library(rgl)
> example(rgl.material)
>
Duncan Murdoch has pointed me towards a workaround. If you call
another rgl function first (probably one that opens a window), this
segfault won't happen, suggesting some intiialization problem in rgl.
For example, if you do:
example(plot3d)
before the call to rgl.material() there will be no segfault.
However, because of the problem with rgl extensions not being compiled
into Xvfb, this will not totally solve your problem. You'll still need
to disable all vignette chunks and examples that call rgl code.
Hopefully a fix is forthcoming in the rgl package which will at least
take care of the segfault issue.
Thanks,
Dan
> And it's caused by the following line (Material.cpp:39) in the rgl package:
>
> const char* version = (const char*)glGetString(GL_VERSION);
>
> glGetString() is a function in the OpenGL library and it is segfaulting.
>
>
> Obviously that should not be happening. I'll try to track that down.
>
> In the short term, you can disable all vignette code chunks that use
> rgl (with eval=FALSE), and do the same with examples that use rgl
> (with \dontrun{}).
>
> The problem as far as I can tell is just on Snow Leopard which is what
> we use on our build systems.
> The package builds, checks, installs and runs OK on my Mountain Lion laptop.
>
> Dan
>
>
>> Dan
>>
>>
>>>
>>> Thank you a lot for your time and patience,
>>> Jirka
>>>
>>> ___
>>> Bioc-d
Re: [Bioc-devel] GLX extension missing on petty
On Wed, Apr 3, 2013 at 9:45 AM, Dan Tenenbaum wrote:
> Hi Jirka,
>
>
> On Wed, Apr 3, 2013 at 9:06 AM, Jiří Hon wrote:
>> Hi,
>> the latest bioc build of my new package 'triplex' on petty ended with this
>> error message:
>>
>> Warning in rgl.init(initValue) : RGL: GLX extension missing on server
>> Warning in fun(libname, pkgname) : error in rgl_init
>>
>> For full report see
>> http://bioconductor.org/checkResults/devel/bioc-LATEST/triplex/petty-buildsrc.html
>>
>> And I am wondering if there is anything I could do to fix this. Probably
>> it's a build system problem, but other packages that depends on rgl and
>> plots in 3D have no such build error (i.e. RDRToolbox) and that makes me
>> sligthly nervous, so I would really appreciate any advice.
>
> This is a build system problem, and I am looking into it.
> The build system runs under Xvfb, but I have no problem building your
> package when logged into the console of petty.
>
A little more info on this.
There are two problems. The first is that as mentioned before, our
builds do not run physically logged into the console; they use a
virtual frame buffer (Xvfb).
We could look into changing this, but at present triplex seems to be
the only package having this problem.
Xvfb apparently does not have the OpenGL extensions compiled in. I
will check with the XQuartz people. They have been responsive before.
The second problem is if I do log into the actual physical console of
the machine, I am able to build triplex but I get the following
segfault when trying to run R CMD check on triplex:
> However, do get a segfault when running R CMD check on the triplex
> source tarball:
>
> $ R CMD check --no-vignettes --timings triplex_0.99.0.tar.gz
> [...]
> * checking examples ...sh: line 1: 41089 Segmentation fault
> LANGUAGE=en _R_CHECK_INTERNALS2_=1
> '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla >
> 'triplex-Ex.Rout' 2>&1 < triplex-Ex.R
> ERROR
> Running examples in ?~@~Xtriplex-Ex.R?~@~Y failed
> The error most likely occurred in:
>
>> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
>> ### Name: triplex-package
>> ### Title: Triplex search and visualization package
>> ### Aliases: triplex-package triplex
>> ### Keywords: package
>>
>> ### ** Examples
>>
>> seq <- DNAString("GGAAAGCAATGCCAGGCAGGG")
>> t <- triplex.search(seq)
> Searching for triplex type 0...
> Searching for triplex type 1...
> Searching for triplex type 2...
> Searching for triplex type 3...
> Searching for triplex type 4...
> Searching for triplex type 5...
> Searching for triplex type 6...
> Searching for triplex type 7...
>> triplex.diagram(t[1])
> A DNAStringSet instance of length 4
> width seq names
> [1] 8 CCCTGCCT minus
> [2] 8 GGGACGGA plus
> [3] 8 CCTTTCGT para-minus
> [4] 5 GGCAT loop
>> triplex.3D(t[1])
>
> *** caught segfault ***
> address 0x0, cause 'memory not mapped'
>
> Traceback:
> 1: .C(rgl_material, success = FALSE, idata, cdata, ddata)
> 2: rgl.material(color = color, back = back, ...)
> 3: rgl.bg(color = bgr.col)
> 4: triplex.3D(t[1])
> aborting ...
>
This turns out to be reproducible simply like this:
library(rgl)
example(rgl.material)
And it's caused by the following line (Material.cpp:39) in the rgl package:
const char* version = (const char*)glGetString(GL_VERSION);
glGetString() is a function in the OpenGL library and it is segfaulting.
Obviously that should not be happening. I'll try to track that down.
In the short term, you can disable all vignette code chunks that use
rgl (with eval=FALSE), and do the same with examples that use rgl
(with \dontrun{}).
The problem as far as I can tell is just on Snow Leopard which is what
we use on our build systems.
The package builds, checks, installs and runs OK on my Mountain Lion laptop.
Dan
> Dan
>
>
>>
>> Thank you a lot for your time and patience,
>> Jirka
>>
>> ___
>> Bioc-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] GLX extension missing on petty
This is a build system problem, and I am looking into it.
The build system runs under Xvfb, but I have no problem building your
package when logged into the console of petty.
Thank you a lot for your immediate reaction and please let me know if I
could help with anything.
Jirka
Dne Wed, 03 Apr 2013 18:45:31 +0200 Dan Tenenbaum
napsal(a):
Hi Jirka,
On Wed, Apr 3, 2013 at 9:06 AM, Jiří Hon
wrote:
Hi,
the latest bioc build of my new package 'triplex' on petty ended with
this
error message:
Warning in rgl.init(initValue) : RGL: GLX extension missing on server
Warning in fun(libname, pkgname) : error in rgl_init
For full report see
http://bioconductor.org/checkResults/devel/bioc-LATEST/triplex/petty-buildsrc.html
And I am wondering if there is anything I could do to fix this. Probably
it's a build system problem, but other packages that depends on rgl and
plots in 3D have no such build error (i.e. RDRToolbox) and that makes me
sligthly nervous, so I would really appreciate any advice.
However, do get a segfault when running R CMD check on the triplex
source tarball:
$ R CMD check --no-vignettes --timings triplex_0.99.0.tar.gz
[...]
* checking examples ...sh: line 1: 41089 Segmentation fault
LANGUAGE=en _R_CHECK_INTERNALS2_=1
'/Library/Frameworks/R.framework/Resources/bin/R' --vanilla >
'triplex-Ex.Rout' 2>&1 < triplex-Ex.R
ERROR
Running examples in ?~@~Xtriplex-Ex.R?~@~Y failed
The error most likely occurred in:
base::assign(".ptime", proc.time(), pos = "CheckExEnv")
### Name: triplex-package
### Title: Triplex search and visualization package
### Aliases: triplex-package triplex
### Keywords: package
### ** Examples
seq <- DNAString("GGAAAGCAATGCCAGGCAGGG")
t <- triplex.search(seq)
Searching for triplex type 0...
Searching for triplex type 1...
Searching for triplex type 2...
Searching for triplex type 3...
Searching for triplex type 4...
Searching for triplex type 5...
Searching for triplex type 6...
Searching for triplex type 7...
triplex.diagram(t[1])
A DNAStringSet instance of length 4
width seq names
[1] 8 CCCTGCCT minus
[2] 8 GGGACGGA plus
[3] 8 CCTTTCGT para-minus
[4] 5 GGCAT loop
triplex.3D(t[1])
*** caught segfault ***
address 0x0, cause 'memory not mapped'
Traceback:
1: .C(rgl_material, success = FALSE, idata, cdata, ddata)
2: rgl.material(color = color, back = back, ...)
3: rgl.bg(color = bgr.col)
4: triplex.3D(t[1])
aborting ...
Dan
Thank you a lot for your time and patience,
Jirka
___
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___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
Re: [Bioc-devel] GLX extension missing on petty
Hi Jirka,
On Wed, Apr 3, 2013 at 9:06 AM, Jiří Hon wrote:
> Hi,
> the latest bioc build of my new package 'triplex' on petty ended with this
> error message:
>
> Warning in rgl.init(initValue) : RGL: GLX extension missing on server
> Warning in fun(libname, pkgname) : error in rgl_init
>
> For full report see
> http://bioconductor.org/checkResults/devel/bioc-LATEST/triplex/petty-buildsrc.html
>
> And I am wondering if there is anything I could do to fix this. Probably
> it's a build system problem, but other packages that depends on rgl and
> plots in 3D have no such build error (i.e. RDRToolbox) and that makes me
> sligthly nervous, so I would really appreciate any advice.
This is a build system problem, and I am looking into it.
The build system runs under Xvfb, but I have no problem building your
package when logged into the console of petty.
However, do get a segfault when running R CMD check on the triplex
source tarball:
$ R CMD check --no-vignettes --timings triplex_0.99.0.tar.gz
[...]
* checking examples ...sh: line 1: 41089 Segmentation fault
LANGUAGE=en _R_CHECK_INTERNALS2_=1
'/Library/Frameworks/R.framework/Resources/bin/R' --vanilla >
'triplex-Ex.Rout' 2>&1 < triplex-Ex.R
ERROR
Running examples in ?~@~Xtriplex-Ex.R?~@~Y failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: triplex-package
> ### Title: Triplex search and visualization package
> ### Aliases: triplex-package triplex
> ### Keywords: package
>
> ### ** Examples
>
> seq <- DNAString("GGAAAGCAATGCCAGGCAGGG")
> t <- triplex.search(seq)
Searching for triplex type 0...
Searching for triplex type 1...
Searching for triplex type 2...
Searching for triplex type 3...
Searching for triplex type 4...
Searching for triplex type 5...
Searching for triplex type 6...
Searching for triplex type 7...
> triplex.diagram(t[1])
A DNAStringSet instance of length 4
width seq names
[1] 8 CCCTGCCT minus
[2] 8 GGGACGGA plus
[3] 8 CCTTTCGT para-minus
[4] 5 GGCAT loop
> triplex.3D(t[1])
*** caught segfault ***
address 0x0, cause 'memory not mapped'
Traceback:
1: .C(rgl_material, success = FALSE, idata, cdata, ddata)
2: rgl.material(color = color, back = back, ...)
3: rgl.bg(color = bgr.col)
4: triplex.3D(t[1])
aborting ...
Dan
>
> Thank you a lot for your time and patience,
> Jirka
>
> ___
> Bioc-devel@r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
___
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
[Bioc-devel] GLX extension missing on petty
Hi, the latest bioc build of my new package 'triplex' on petty ended with this error message: Warning in rgl.init(initValue) : RGL: GLX extension missing on server Warning in fun(libname, pkgname) : error in rgl_init For full report see http://bioconductor.org/checkResults/devel/bioc-LATEST/triplex/petty-buildsrc.html And I am wondering if there is anything I could do to fix this. Probably it's a build system problem, but other packages that depends on rgl and plots in 3D have no such build error (i.e. RDRToolbox) and that makes me sligthly nervous, so I would really appreciate any advice. Thank you a lot for your time and patience, Jirka ___ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
