[Bioc-devel] Build fails on windows: R_igraph_make_weak_ref not available
Dan Tenenbaum
dtenenba at fredhutch.org
Fri Apr 1 17:25:38 CEST 2016
According to https://bugs.r-project.org/bugzilla/show_bug.cgi?id=16776 the fix for this was committed to the 3.3 branch on 3/25. The R I'm using is from 3/28 and the issue still occurs. Yours is newer, so maybe it just took a few days to percolate. I will try a newer R and report back.
Dan
----- Original Message -----
> From: "Ramon Diaz-Uriarte" <rdiaz02 at gmail.com>
> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> Cc: "Ramon Diaz-Uriarte" <rdiaz02 at gmail.com>, "Luca De Sano" <l.desano at campus.unimib.it>, "bioc-devel"
> <bioc-devel at r-project.org>
> Sent: Friday, April 1, 2016 3:31:58 AM
> Subject: Re: [Bioc-devel] Build fails on windows: R_igraph_make_weak_ref not available
> 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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