[Bioc-devel] Build fails on windows: R_igraph_make_weak_ref not available: II
Dan Tenenbaum
dtenenba at fredhutch.org
Fri Apr 1 18:01:25 CEST 2016
OK, this is solved (by Jim Hester at https://github.com/RcppCore/Rcpp/issues/442#issuecomment-190848342 ).
I didn't even need to upgrade R, though I will do that soon.
Since today's builds are almost done, and there will be no builds tonight, the results will be available Sunday morning.
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 5:13:09 AM
> Subject: Re: [Bioc-devel] Build fails on windows: R_igraph_make_weak_ref not available: II
> And on that same machine ("System type 64-bit operating system, x64-based
> processor", "Edition Windows 10 Enterprise Evaluation", MSEdge
> Win10 virtual machine), I can confirm R CMD build (and check) of OncoSimulR work
> without problems (which also means the igraph issue is not showing there).
>
>
>
>
>
>
> On Fri, 01-04-2016, at 12:31, Ramon Diaz-Uriarte <rdiaz02 at gmail.com> wrote:
>> 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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