When I try to install xml2 on an RStudio server I get the following error:
xml2_url.cpp: In function ‘Rcpp::List url_parse(Rcpp::CharacterVector)’:
xml2_url.cpp:85: error: ‘struct _xmlURI’ has no member named ‘query_raw’
xml2_url.cpp:85: error: ‘struct _xmlURI’ has no member named ‘query_raw’
make: *** [xml2_url.o] Error 1
ERROR: compilation failed for package ‘xml2’
My session info is
> sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-unknown-linux-gnu (64-bit)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C 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
loaded via a namespace (and not attached):
[1] devtools_1.8.0 digest_0.6.8 git2r_0.10.1 grid_3.1.1 httr_0.6.1 memoise_0.2.1 RCurl_1.95-4.3 rversions_1.0.0 stringr_0.6.2
[10] tools_3.1.1 XML_3.98-1.1
The xml2 R-package perfectly installs on my macbook air...
Related
I have installed a package in our server already and was working properly.
After a few hourse, once I wanted to load it again, I'm getting the following error:
library("SPONGE")
Error: package or namespace load failed for ‘SPONGE’ in dyn.load(file, DLLpath = DLLpath, ...):
unable to load shared object '/home/adinfo/R/x86_64-pc-linux-gnu-library/3.4/gRbase/libs/gRbase.so':
/usr/lib/x86_64-linux-gnu/libstdc++.so.6: version `CXXABI_1.3.9' not found (required by /home/adinfo/R/x86_64-pc-linux-gnu-library/3.4/gRbase/libs/gRbase.so)
I've also tried to install it again using
source("https://bioconductor.org/biocLite.R")
biocLite("SPONGE")
But I've got again the error that "Installation has zero exit"
Can someone help me with that?
> sessionInfo()
R version 3.4.0 (2017-04-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)
Matrix products: default
BLAS: /TL/opt/R-3.4.0/lib/libRblas.so
LAPACK: /TL/opt/R-3.4.0/lib/libRlapack.so
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
loaded via a namespace (and not attached):
[1] compiler_3.4.0 tools_3.4.0
>
I have a downloadHandler() in Shiny that generates an html document using R markdown. This document generates rgl plots, which are added to the document using hook_webgl. The application is running on a Shiny server. Everything works fine the first time the download button is used, but on the following occasions I get the error "You must enable Javascript to view this page properly". I am using rglwidgets, but I get the same issues using shinyRGL.
> sessionInfo()
R version 3.2.4 Revised (2016-03-16 r70336)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS
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] shiny_0.13.2 rmarkdown_0.9.5 knitr_1.12.3 rglwidget_0.1.1434
[5] rgl_0.95.1441
loaded via a namespace (and not attached):
[1] htmlwidgets_0.6 magrittr_1.5 R6_2.1.2 tools_3.2.4
[5] htmltools_0.3.5 Rcpp_0.12.4 jsonlite_0.9.19 digest_0.6.9
[9] xtable_1.8-2 httpuv_1.3.3 mime_0.4
I am using default command to install multicore package
install.packages('multicore','http://www.rforge.net/')
as written here http://www.rforge.net/multicore/files/ but I recieve warning:
install.packages('multicore','http://www.rforge.net/')
Warning in install.packages :
'lib = "http://www.rforge.net/"' is not writable
Would you like to use a personal library instead? (y/n) y
Warning in install.packages :
package ‘multicore’ is not available (for R version 3.1.2)
Does anybody know any solution to this? I can not use previous versions of R.
I would like to use mclapply function from that package.
Thanks for help.
My session info is:
> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-redhat-linux-gnu (64-bit)
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] stringi_0.4-1 ggplot2_1.0.0
loaded via a namespace (and not attached):
[1] colorspace_1.2-4 digest_0.6.8 grid_3.1.2 gtable_0.1.2
[5] MASS_7.3-35 munsell_0.4.2 plyr_1.8.1 proto_0.3-10
[9] Rcpp_0.11.3 reshape2_1.4.1 scales_0.2.4 stringr_0.6.2
[13] tools_3.1.2
Why do you need it?
Most of its functionality has been integrated into the parallel package which already comes with R. Have a look at its vignette, eg from within R via vignette() or else from here.
And the reason you cannot install 'multicore' is because it has been withdrawn by R Core, given how its functionality is (essentially entirely) in 'parallel' now.
I'd like to install this Package from bitbucket: https://bitbucket.org/mkuhn/parallelrandomforest/
But this is what happends if i run install_bitbucket
> devtools::install_bitbucket("mkuhn/parallelrandomforest")
Downloading bitbucket repo mkuhn/parallelrandomforest#master
Error in download(dest, src, auth) : client error: (404) Not Found
If i run the command from ?install_bitbucket namely install_bitbucket("dannavarro/lsr-package") it works perfectly.
Any ideas
R version 3.1.2 (2014-10-31)
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 LC_MESSAGES=C
[7] LC_PAPER=C LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=C LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] RCurl_1.95-4.5 bitops_1.0-6 devtools_1.7.0 httr_0.6.1 stringr_0.6.2 tools_3.1.2
Usually the master branch should be called master, but they managed to call it default.
devtools::install_bitbucket("mkuhn/parallelrandomforest#default")
Exporting an Rcpp function with a different name succeeds on one machine but fails on the other. The R environments are very similar. What am I doing wrong?
Details
I have an R package with an Rcpp function that is exported with the following signature (in sample_int_crank.cpp):
// [[Rcpp::export(sample.int.crank)]]
IntegerVector sample_int_crank(int n, int size, NumericVector prob) {
...
This function is declared empty in a corresponding R file (sample_int_crank.R):
sample.int.crank <- function(n, size, prob) {
}
EDIT: When I remove this R file, the function is available. But where do I place roxygen2 comments for this function?
Now, when I install the package from GitHub,
library(devtools)
install_github('wrswoR', 'muelleki', '0.0.6')
on machine A it says:
> sample.int.crank
internal C++ function <0x29ddc40>
signature : Rcpp::IntegerVector sample.int.crank(int, int, Rcpp::NumericVector)
and on machine B:
> sample.int.crank
function(n, size, prob) {
}
<environment: namespace:wrswoR>
EDIT: If sample_int_crank.R is removed from the package, the output looks different, but identical on A and B. What is going on here?
library(devtools)
install_github('wrswoR', 'muelleki')
> sample.int.crank
function (n, size, prob)
{
.Call("wrswoR_sample_int_crank", PACKAGE = "wrswoR", n, size,
prob)
}
<environment: namespace:wrswoR>
The sessionInfo() seems to be more or less identical, at least for R and Rcpp -- A:
> sessionInfo()
R version 2.15.3 (2013-03-01)
Platform: x86_64-pc-linux-gnu (64-bit)
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=C 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] wrswoR_0.0.6 logging_0.7-102 Rcpp_0.10.3 devtools_0.8
loaded via a namespace (and not attached):
[1] digest_0.5.2 evaluate_0.4.2 httr_0.1.1 memoise_0.1
[5] parallel_2.15.3 plyr_1.7.1.99.2 RCurl_1.95-0 stringr_0.6.1
[9] tools_2.15.3 whisker_0.1
B:
> sessionInfo()
R version 2.15.3 (2013-03-01)
Platform: x86_64-pc-linux-gnu (64-bit)
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=C 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] wrswoR_0.0.6 logging_0.6-92 Rcpp_0.10.3 devtools_1.1
loaded via a namespace (and not attached):
[1] digest_0.6.3 evaluate_0.4.3 httr_0.2 memoise_0.1
[5] parallel_2.15.3 RCurl_1.95-4.1 stringr_0.6.2 tools_2.15.3
[9] whisker_0.1
Any idea?
Concerning your question
But where do I place roxygen2 comments for this function?
I have to disappoint you that here simply is no support for roxygen(2) in Rcpp Attributes. Maybe you want to contribute that?
On the other hand, writing normal C++ functions in src/ and calling them from normal R functions is of course supported, and can be used by roxygen2 just fine.
As to what devtools does to your package: Also no idea. Neither Romain nor myself uses devtools, so you are in undocumented and undefined territory.