I have compiled R version 2.12.1 (2010-12-16) for my system (CentOS), and afterwards I installed Cairo_1.4-5.
I'd like use Cairo to produce PNG (and maybe PDF) output of my graphs when I batch-invoke my scripts, but this gives me difficulties when I am using X (I am tunneling X through ssh and it often disconnects while the R scripts are running...), so this is why I want to use Cairo.
(I do not have root access btw).
Although it's installed according to sessionInfo
> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
I can not call CairoPDF:
> CairoPDF()
Error: could not find function "CairoPDF"
Weirdly, I can invoke a function called cairo_pdf
> cairo_pdf()
>
I can not call CairoPNG, cairo_PNG or cairo_png:
> CairoPNG()
Error: could not find function "CairoPNG"
> cairo_PNG()
Error: could not find function "cairo_PNG"
> cairo_png()
Error: could not find function "cairo_png"
Is something wrong withmy installation? Frankly I have no idea how to proceed from here, why can't I even call CairoPNG()?
On Ubuntu I have:
> sessionInfo()
R version 2.12.1 (2010-12-16)
Platform: i486-pc-linux-gnu (32-bit)
locale:
[1] LC_CTYPE=af_ZA.utf8 LC_NUMERIC=C
[3] LC_TIME=af_ZA.utf8 LC_COLLATE=af_ZA.utf8
[5] LC_MONETARY=C LC_MESSAGES=af_ZA.utf8
[7] LC_PAPER=af_ZA.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=af_ZA.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
Then run library(Cairo), if this is not installed
library(Cairo)
Error in library(Cairo) : there is no package called 'Cairo'
This means you will have to install the Cairo R package, which interfaces with the Cairo graphics system
> install.packages('Cairo')
It will download, build and install the package - you don't need root for this
If it was successful, you can run
>library(Cairo)
>sessionInfo()
R version 2.12.1 (2010-12-16)<br>
Platform: i486-pc-linux-gnu (32-bit)
locale:
[1] LC_CTYPE=af_ZA.utf8 LC_NUMERIC=C
[3] LC_TIME=af_ZA.utf8 LC_COLLATE=af_ZA.utf8
[5] LC_MONETARY=C LC_MESSAGES=af_ZA.utf8
[7] LC_PAPER=af_ZA.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=af_ZA.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] Cairo_1.4-5
HTH
This should do:
install.packages("Cairo")
library(Cairo)
Related
I am trying to run the some unconstrained optimization on a large problem on
a super computer, so I am trying to use the ucminf (although this problem
also works if I use the ucminf option in optimx). When I run any simple
optimization, I get the following message:
Error in .Call("mfopt", fnstr, grstr, rho, PACKAGE = "ucminf") :
"mfopt" not available for .Call() for package "ucminf"
For simplicity, here is a simple bit of test code that gives me the error.
library(ucminf)
test<-function(x){
(x-3)^2}
ucminf(0,test)
All of this works fine on my personal computer, but does not work on the
super computer. I have tried this on R/3.5.0 and R/3.3.0 on the super
computer and they both give me the same error.
Here is my Session info.
R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.9 (Final)
Matrix products: default
BLAS: /usr/public/R/3.5.0.gnu/lib64/R/lib/libRblas.so
LAPACK: /usr/public/R/3.5.0.gnu/lib64/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.iso885915 LC_NUMERIC=C
[3] LC_TIME=en_US.iso885915 LC_COLLATE=en_US.iso885915
[5] LC_MONETARY=en_US.iso885915 LC_MESSAGES=en_US.iso885915
[7] LC_PAPER=en_US.iso885915 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.iso885915 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] ucminf_1.0-5 numDeriv_2016.8-1
loaded via a namespace (and not attached):
[1] compiler_3.5.0
I have uninstalled and reinstalled the package using Rinstall('ucminf'). Does anyone have experience with this and how to fix it?
I recently installed rSymPy to perform some symbolic calculations in R. This step also installed some dependencies (“rJava”, “rjson” and “rJython”). After the installation was complete, I loaded the library and ran a very simple command which gave me an error:
> library("rSymPy")
Loading required package: rJython
Loading required package: rJava
Loading required package: rjson
> x <- Var("x")
Error in .jcheck() : No running JVM detected. Maybe .jinit() would help.
Here is my sessionInfo(), just in case you need it:
> sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS release 6.7 (Final)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] rSymPy_0.2-1.1 rJython_0.0-4 rjson_0.2.15 rJava_0.9-8
loaded via a namespace (and not attached):
[1] tools_3.2.2 tcltk_3.2.2
I have tried to install different versions of required packages, but I always get this error. I would really appreciate any help.
Thanks,
Aashish
Thanks to Gabor Grothendieck (developer of rSymPy) for pointing out that sometimes one needs to manually initialize JVM. One can simply use "sympyStart()" at the beginning of the code, and that fixes the error.
I am trying to read a large space-delimited file (14Gb) of 49,376 rows and 73,625 columns into R for analysis.
I have tried using fread from the data.table package, as suggested here.
I receive the error
Error: segfault from C stack overflow
Is there another approach that could be used here? Any other packages or some kind of work around for this error? My R session info is below.
R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US LC_NUMERIC=C LC_TIME=en_US
[4] LC_COLLATE=en_US LC_MONETARY=en_US LC_MESSAGES=en_US
[7] LC_PAPER=en_US LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_US LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] data.table_1.9.4
loaded via a namespace (and not attached):
[1] chron_2.3-45 tools_3.0.2
The error was occurring due to insufficient memory. Once I increased the memory limit, fread worked as expected.
I have a case where foreach using doMC as a backend produces different behaviors on different machines.
On a linux server running Ubuntu 12.04.4 LTS the following code (adapted from the foreach vingette) runs 5 jobs simultaneously on a single core, which is not the desired behavior.
library(foreach)
library(doMC)
registerDoMC(cores=5)
getDoParWorkers()
x <- iris[which(iris[,5] != "setosa"), c(1,5)]
trials <- 10000
r <- foreach(icount(trials), .combine=cbind) %dopar% {
ind <- sample(100, 100, replace=TRUE)
result1 <- glm(x[ind,2]~x[ind,1], family=binomial(logit))
coefficients(result1)
}
Session info:
> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-pc-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=C LC_COLLATE=C LC_MONETARY=C
[6] LC_MESSAGES=C LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=C LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] doMC_1.3.3 iterators_1.0.7 foreach_1.4.2
loaded via a namespace (and not attached):
[1] codetools_0.2-8 compiler_3.1.0 tools_3.1.0
The same code run on a Mac running OSX 10.7.5 produces the desired and expected behavior of running 5 jobs on 5 different cores.
Session info:
> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-apple-darwin10.8.0 (64-bit)
locale:
[1] C
attached base packages:
[1] parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] doMC_1.3.2 iterators_1.0.6 foreach_1.4.1
loaded via a namespace (and not attached):
[1] codetools_0.2-8 compiler_3.0.1 tools_3.0.1
I have also observed the same behavior using other parallel backends. Both machines have 20+ cores. Any ideas on what's going on?
The issue was caused by OpenBLAS. Switching to ATLAS solved the problem. The recipe for switching between BLAS libraries in Linux is on Nathan VanHoudnos's blog:
Switching between BLAS libraries
Now we can switch between the different BLAS options that are installed:
sudo update-alternatives --config libblas.so.3gf
There are 3 choices for the alternative libblas.so.3gf (providing /usr/lib/libblas.so.3gf).
Selection Path Priority Status
------------------------------------------------------------
* 0 /usr/lib/openblas-base/libopenblas.so.0 40 auto mode
1 /usr/lib/atlas-base/atlas/libblas.so.3gf 35 manual mode
2 /usr/lib/libblas/libblas.so.3gf 10 manual mode
3 /usr/lib/openblas-base/libopenblas.so.0 40 manual mode
Press enter to keep the current choice[*], or type selection number:
Side note: If the above returned:
update-alternatives: error: no alternatives for libblas.so.3gf
Try
sudo update-alternatives --config libblas.so.3
I've just found out that I can get antialiased R graphics on Windows via Cairo so I've installed the package right away. Unfortunately, though, I'm stuck trying to save the output.
I can't seem to copy it and right click doesn't do anything.
Ideas?
This should work (it does for me using R 2.14 under linux):
cairo_pdf("spam.pdf")
plot(1:10)
dev.off()
and the resulting pdf is in the current work directory. Alternatively, when having the cairo package installed, you can use:
CairoPDF("spam.pdf")
plot(1:10)
dev.off()
to get the same effect.
Information on my system:
> sessionInfo()
R version 2.14.1 (2011-12-22)
Platform: i686-pc-linux-gnu (32-bit)
locale:
[1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
[3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
[5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8
[7] LC_PAPER=C LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] fortunes_1.4-2
loaded via a namespace (and not attached):
[1] tools_2.14.1
The Cairo functions are now included in most R distributions. All you need to do is just specify type="cairo":
png(filename="fn.png",
type="cairo",
units="in",
width=5,
height=4,
pointsize=12,
res=96)
...
dev.off()
I wrote a blog-post about the Cairo packages and found out about the new feature through a comment :-)