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" <rdia...@gmail.com> > To: "Dan Tenenbaum" <dtene...@fredhutch.org> > Cc: "Ramon Diaz-Uriarte" <rdia...@gmail.com>, "Luca De Sano" > <l.des...@campus.unimib.it>, "bioc-devel" > <bioc-devel@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 <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
