[Bioc-devel] Build fails on windows: R_igraph_make_weak_ref not available: II

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]]

--
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