[Bioc-devel] Build fails on windows: R_igraph_make_weak_ref not available
Ramon Diaz-Uriarte
rdiaz02 at gmail.com
Fri Apr 1 12:31:58 CEST 2016
Hi Dan,
I cannot reproduce the issue on a machine that claims to be 64-bit. I run
your two examples of igraph and graph just fine (using the 32 and 64 bit R
executables); details and output from "version" pasted below. This is a
virtual machine (my previous report for the 32 bit was another virtual
machine), the one for "MSEdge on Win10" from
https://developer.microsoft.com/en-us/microsoft-edge/tools/vms/linux/.
Windows system info shows, among others,
"System type 64-bit operating system, x64-based processor"
"Edition Windows 10 Enterprise Evaluation"
When installing packages from source, R goes through the i386 and x64
dance, and R version x64 reports arch as x86_64 . So it really seems to be
a 64 bit machine. Given that, I find it strange that "version" shows "os
mingw32" (but then, I know nothing about Windows).
*************************************
> library(graph)
> library(igraph)
Attaching package: `igraph'
The following objects are masked from `package:graph':
degree, edges, intersection, union
The following objects are masked from `package:stats':
decompose, spectrum
The following object is masked from `package:base':
union
> 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--L A--K A--I A--C A--O A--J A--D A--G A--B A--M A--F A--H A--E B--E B--D
[16] B--N B--H B--J B--I B--C B--L B--K B--M B--F B--G B--O C--E C--N C--J C--D
[31] C--F C--O C--I C--L C--G C--M C--K D--K D--H D--M D--O D--I D--E D--L D--G
[46] D--N D--J D--F E--L E--H E--N E--F E--J E--K E--I E--G F--I F--G F--L F--O
[61] F--H F--J F--M F--N F--K G--M G--K G--L G--N G--H G--I G--J G--O H--N H--I
[76] H--M H--J H--K H--O H--L I--K I--M I--O I--N I--J I--L J--K J--O J--N J--M
[91] J--L K--O K--L K--N L--M L--O L--N M--O M--N 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--D A--O A--N A--J A--F A--G A--B A--M A--L A--C A--K A--E A--H B--L
[16] B--K B--C B--F B--G B--D B--H B--J B--N B--O B--M B--I B--E C--E C--L C--N
[31] C--I C--M C--O C--D C--K C--H C--J C--F D--F D--I D--E D--G D--H D--K D--M
[46] D--O D--L D--N D--J E--L E--F E--I E--N E--M E--H E--G E--K E--O F--L F--N
[61] F--O F--H F--M F--J F--K F--I G--L G--H G--O G--N G--I G--J G--K G--M H--K
[76] H--L H--M H--I H--N H--J I--M I--N I--L I--J I--O I--K J--O J--M J--K J--N
[91] J--L K--M K--L K--O K--N L--N L--O L--M M--O M--N
> 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 x86_64-w64-mingw32
arch x86_64
os mingw32
system x86_64, 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
>
****************************************************************
> library(graph)
> library(igraph)
Attaching package: `igraph'
The following objects are masked from `package:graph':
degree, edges, intersection, union
The following objects are masked from `package:stats':
decompose, spectrum
The following object is masked from `package:base':
union
> 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--B A--G A--D A--O A--E A--M A--H A--F A--L A--J A--I A--K A--C A--N B--H
[16] B--G B--F B--I B--E B--N B--D B--O B--C B--K B--L B--M B--J C--N C--H C--I
[31] C--F C--G C--D C--K C--M C--J C--L C--O D--E D--J D--F D--I D--H D--L D--G
[46] D--N D--M D--K D--O E--G E--J E--H E--O E--L E--M E--I E--F E--K E--N F--L
[61] F--G F--N F--I F--J F--H F--K F--O G--M G--H G--N G--O G--J G--I G--K H--L
[76] H--N H--J H--M H--O H--I H--K I--O I--M I--J I--K I--L J--O J--M J--L J--N
[91] K--O K--M K--N K--L L--M L--N L--O M--N M--O N--O
> 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
>
Best,
R.
On Fri, 01-04-2016, at 01:20, Dan Tenenbaum <dtenenba at fredhutch.org> wrote:
> 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
--
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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