[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]]
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--
Ramon Diaz-Uriarte
Department of Biochemistry, Lab B-25
Facultad de Medicina
Universidad Aut?noma 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 Aut?noma 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