[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__> #'
> 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.



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

Phone: +34-91-497-2412

Email: rdiaz02 at gmail.com
       ramon.diaz at iib.uam.es


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