[Bioc-devel] Build fails on windows: R_igraph_make_weak_ref not available
Ramon Diaz-Uriarte
rdiaz02 at gmail.com
Fri Apr 1 01:13:49 CEST 2016
Hi Dan,
OncoSimulR is also afflicted by this
(https://www.bioconductor.org/checkResults/devel/bioc-LATEST/OncoSimulR/moscato2-buildsrc.html). However,
like Luca, I cannot reproduce the issue: I followed your instructions, and I
was able to build (and check) the package without problem.
Moreover, I can run the examples you report in the github issue without
problems. Here is the output:
****************
> library(igraph)
> g1 = randomEGraph(LETTERS[1:15], edges=100)
> graph_from_graphnel(g1)
IGRAPH UNW- 15 100 --
+ attr: name (v/c), weight (e/n)
+ edges (vertex names):
[1] A--G A--C A--H A--N A--K A--F A--L A--M A--I A--B A--O A--J A--E B--D
[15] B--L B--H B--E B--O B--J B--G B--K B--M B--N B--F B--I B--C C--H C--I
[29] C--M C--K C--N C--J C--E C--L C--F C--D C--G C--O D--M D--K D--N D--L
[43] D--E D--I D--O D--J D--F D--H E--M E--G E--F E--L E--O E--I E--N E--K
[57] E--J F--H F--N F--I F--L F--M F--G F--K F--J F--O G--L G--J G--N G--O
[71] G--I G--H G--M G--K H--K H--O H--N H--I H--M H--J I--M I--K I--O I--J
[85] I--L I--N J--L J--M J--N J--K J--O K--L K--M K--O K--N L--O L--M M--N
[99] M--O N--O
>
>
> library(graph)
> library(igraph)
> g1 = randomEGraph(LETTERS[1:15], edges=100)
> graph_from_graphnel(g1)
IGRAPH UNW- 15 100 --
+ attr: name (v/c), weight (e/n)
+ edges (vertex names):
[1] A--I A--G A--D A--J A--K A--B A--O A--M A--F A--H A--E A--N A--L B--M
[15] B--H B--G B--N B--L B--O B--F B--I B--C B--J B--D B--E C--F C--O C--I
[29] C--J C--L C--G C--M C--H C--E C--N C--D C--K D--K D--O D--G D--I D--M
[43] D--N D--H D--L D--E D--J D--F E--G E--K E--H E--J E--N E--I E--L E--F
[57] E--M F--O F--I F--H F--J F--N F--K F--L F--M F--G G--L G--N G--K G--M
[71] G--O G--J G--I H--K H--L H--M H--O H--J H--N H--I I--N I--L I--K I--M
[85] I--O I--J J--M J--O J--N J--K K--L K--O K--M K--N L--O L--M L--N M--N
[99] M--O N--O
> library(igraph)
> example(graph_from_graphnel, run.dontrun=TRUE)
grph__> ## Undirected
grph__> g <- make_ring(10)
grph__> V(g)$name <- letters[1:10]
grph__> GNEL <- as_graphnel(g)
grph__> g2 <- graph_from_graphnel(GNEL)
grph__> g2
IGRAPH UNW- 10 10 -- Ring graph
+ attr: name (g/c), mutual (g/l), circular (g/l), name (v/c),
| weight (e/n)
+ edges (vertex names):
[1] a--b a--j b--c c--d d--e e--f f--g g--h h--i i--j
grph__> ## Directed
grph__> g3 <- make_star(10, mode="in")
grph__> V(g3)$name <- letters[1:10]
grph__> GNEL2 <- as_graphnel(g3)
grph__> g4 <- graph_from_graphnel(GNEL2)
grph__> g4
IGRAPH DNW- 10 9 -- In-star
+ attr: name (g/c), mode (g/c), center (g/n), name (v/c), weight
| (e/n)
+ edges (vertex names):
[1] b->a c->a d->a e->a f->a g->a h->a i->a j->a
grph__> #'
grph__>
grph__>
grph__>
>
>
> version
_
platform i386-w64-mingw32
arch i386
os mingw32
system i386, mingw32
status beta
major 3
minor 3.0
year 2016
month 03
day 30
svn rev 70404
language R
version.string R version 3.3.0 beta (2016-03-30 r70404)
nickname Supposedly Educational
>
*******************************
If I can tomorrow, I'll try using a 64-bit machine.
Best,
R.
On Thu, 31-03-2016, at 22:21, Dan Tenenbaum <dtenenba at fredhutch.org> wrote:
> I think it's a problem with igraph (a CRAN package) under the new toolchain. I was just in the process of filing a github issue with that package maintainer. Watch for it at https://github.com/igraph/igraph/issues/ .
>
> Dan
>
>
> ----- Original Message -----
>> From: "Luca De Sano" <l.desano at campus.unimib.it>
>> To: "bioc-devel" <bioc-devel at r-project.org>
>> Sent: Thursday, March 31, 2016 1:17:59 PM
>> Subject: [Bioc-devel] Build fails on windows: R_igraph_make_weak_ref not available
>
>> Hi all,
>> the build of our package TRONCO fails with this error on the Windows test
>> machine:
>>
>> Error: processing vignette 'vignette.Rnw' failed with diagnostics:
>> "R_igraph_make_weak_ref" not available for .Call() for package "igraph"
>> Execution halted
>>
>> as reported in
>> http://bioconductor.org/checkResults/devel/bioc-LATEST/TRONCO/moscato2-buildsrc.html
>>
>> After a rapid check I've found other packages with the same problem:
>>
>> http://bioconductor.org/checkResults/devel/bioc-LATEST/BiRewire/moscato2-buildsrc.html
>> http://bioconductor.org/checkResults/devel/bioc-LATEST/cellTree/moscato2-buildsrc.html
>> http://bioconductor.org/checkResults/devel/bioc-LATEST/clipper/moscato2-buildsrc.html
>> ...
>>
>> I can't reproduce the error. Any suggestion on how to solve this?
>>
>> Thanks
>>
>> --
>> Luca De Sano
>> Research Associate
>>
>> Department of Informatics, Systems and Communication
>> University of Milan Bicocca
>>
>> Institute of Biomembranes and Bioenergetics of the Italian National
>> Research Council (IBBE-CNR)
>>
>> email: l.desano at campus.unimib.it
>> PEC: luca.desano at pec.it
>>
>> [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/bioc-devel
--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Autónoma de Madrid
Arzobispo Morcillo, 4
28029 Madrid
Spain
Phone: +34-91-497-2412
Email: rdiaz02 at gmail.com
ramon.diaz at iib.uam.es
http://ligarto.org/rdiaz
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