[Bioc-devel] Build fails on windows: R_igraph_make_weak_ref not available
Dan Tenenbaum
dtenenba at fredhutch.org
Fri Apr 1 01:20:29 CEST 2016
I can also run the example on i386. Seems to just affect x64; let me know if your experience is different when you try this on a 64-bit machine.
I'll add this data point to the issue.
Dan
----- Original Message -----
> From: "Ramon Diaz-Uriarte" <rdiaz02 at gmail.com>
> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> Cc: "Luca De Sano" <l.desano at campus.unimib.it>, "bioc-devel" <bioc-devel at r-project.org>
> Sent: Thursday, March 31, 2016 4:13:49 PM
> Subject: Re: [Bioc-devel] Build fails on windows: R_igraph_make_weak_ref not available
> 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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