R devel - May 2011 - R crashes if "toFile" given "~/" in Linux envirnonment

I was running some sample code from a help page tonight and wished to
redirect the sample output to my Desktop under Linux (Mint-Debian 64 if it
makes a different). I was surprised to find that file name expansion using
the ubuquitious "~/" was not recognized, in fact it caused R to crash.
Is
this expected behavior? See my output below and sessionInfo().  Also, not
shown, but 'setwd("~/Desktop")' works just fine.  Thanks, Mark

# sample code from Rgraphviz clusterData help page
library(graph)
library(Rgraphviz)
g1_gz <-
gzfile(system.file("GXL/graphExample-01.gxl.gz",package="graph"),
open="rb")
g11_gz <-
gzfile(system.file("GXL/graphExample-11.gxl.gz",package="graph"),
open="rb")
g1 <- fromGXL(g1_gz)
g11 <- fromGXL(g11_gz)
g1_11 <- join(g1, g11)
sgl <- vector(mode="list", length=2)
sgl[[1]] <- list(graph=g1, cluster=TRUE)
sgl[[2]] <- list(graph=g11, cluster=TRUE)
ng <- agopenSimple(g1_11, "tmpsg", subGList=sgl)
clusterData(ng, 1, c("bgcolor")) <- c("blue")
clusterData(ng, 2, c("bgcolor")) <- c("red")
############################################
# and now 2 usually equivalent ways to specify the location for output file,
with the second way crashing:
toFile(ng, layoutType="dot",
filename="/home/mkimpel/Desktop/g1_11_dot.ps",
fileType="ps")
NULL
toFile(ng, layoutType="dot",
filename="~/Desktop/g1_11_dot.ps",
fileType="ps")
~/Desktop/g1_11_dot.ps: No such file or directory

Process R exited abnormally with code 1 at Mon May 16 22:42:12 2011
#################################################
# and my sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8     LC_MONETARY=C

 [6] LC_MESSAGES=en_US.utf8    LC_PAPER=en_US.utf8
LC_NAME=C                 LC_ADDRESS=C              LC_TELEPHONE=C

[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base
####################################################
Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
Indiana University School of Medicine

15032 Hunter Court, Westfield, IN  46074

(317) 490-5129 Work, & Mobile & VoiceMail
(317) 399-1219 Skype No Voicemail please

	[[alternative HTML version deleted]]

Mark,

I think you have the wrong list - this has nothing to do with R. to File() is a
function in Rgraphviz and it doesn't crash, it simply exits R. Obviously it
doesn't support path expansion (I suppose it should consider calling
path.expand()) and it should also consider using R_error() instead of quitting
-- but both issues should be best addressed to the Rgraphviz maintainers.

Cheers,
Simon


On May 16, 2011, at 10:50 PM, Mark Kimpel wrote:
> I was running some sample code from a help page tonight and wished to
> redirect the sample output to my Desktop under Linux (Mint-Debian 64 if it
> makes a different). I was surprised to find that file name expansion using
> the ubuquitious "~/" was not recognized, in fact it caused R to
crash. Is
> this expected behavior? See my output below and sessionInfo().  Also, not
> shown, but 'setwd("~/Desktop")' works just fine.  Thanks,
Mark
> 
> # sample code from Rgraphviz clusterData help page
> library(graph)
> library(Rgraphviz)
> g1_gz <-
gzfile(system.file("GXL/graphExample-01.gxl.gz",package="graph"),
> open="rb")
> g11_gz <-
gzfile(system.file("GXL/graphExample-11.gxl.gz",package="graph"),
> open="rb")
> g1 <- fromGXL(g1_gz)
> g11 <- fromGXL(g11_gz)
> g1_11 <- join(g1, g11)
> sgl <- vector(mode="list", length=2)
> sgl[[1]] <- list(graph=g1, cluster=TRUE)
> sgl[[2]] <- list(graph=g11, cluster=TRUE)
> ng <- agopenSimple(g1_11, "tmpsg", subGList=sgl)
> clusterData(ng, 1, c("bgcolor")) <- c("blue")
> clusterData(ng, 2, c("bgcolor")) <- c("red")
> ############################################
> # and now 2 usually equivalent ways to specify the location for output
file,
> with the second way crashing:
> toFile(ng, layoutType="dot",
filename="/home/mkimpel/Desktop/g1_11_dot.ps",
> fileType="ps")
> NULL
> toFile(ng, layoutType="dot",
filename="~/Desktop/g1_11_dot.ps",
> fileType="ps")
> ~/Desktop/g1_11_dot.ps: No such file or directory
> 
> Process R exited abnormally with code 1 at Mon May 16 22:42:12 2011
> #################################################
> # and my sessionInfo()
> R version 2.13.0 (2011-04-13)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> locale:
> [1] LC_CTYPE=en_US.utf8       LC_NUMERIC=C
> LC_TIME=en_US.utf8        LC_COLLATE=en_US.utf8     LC_MONETARY=C
> 
> [6] LC_MESSAGES=en_US.utf8    LC_PAPER=en_US.utf8
> LC_NAME=C                 LC_ADDRESS=C              LC_TELEPHONE=C
> 
> [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices datasets  utils     methods   base
> ####################################################
> Mark W. Kimpel MD  ** Neuroinformatics ** Dept. of Psychiatry
> Indiana University School of Medicine
> 
> 15032 Hunter Court, Westfield, IN  46074
> 
> (317) 490-5129 Work, & Mobile & VoiceMail
> (317) 399-1219 Skype No Voicemail please
> 
> 	[[alternative HTML version deleted]]
> 
> ______________________________________________
> R-devel at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel
> 
>