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 <dtene...@fhcrc.org>
napsal(a):
Hi Jirka,
On Wed, Apr 3, 2013 at 9:06 AM, Jiří Hon <xhonj...@stud.fit.vutbr.cz>
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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