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 <dtene...@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" <rdia...@gmail.com> >> To: "Dan Tenenbaum" <dtene...@fredhutch.org> >> Cc: "Luca De Sano" <l.des...@campus.unimib.it>, "bioc-devel" >> <bioc-devel@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 <dtene...@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.des...@campus.unimib.it> >>>> To: "bioc-devel" <bioc-devel@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.des...@campus.unimib.it >>>> PEC: luca.des...@pec.it >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioc-devel@r-project.org mailing list >>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel >>> >>> _______________________________________________ >>> Bioc-devel@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: rdia...@gmail.com >> ramon.d...@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: rdia...@gmail.com ramon.d...@iib.uam.es http://ligarto.org/rdiaz _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel