I am facing a problem with an R package that I am writing and trying to build with a pre-compiled shared library. Let me try to briefly describe the problem:
this package (let's call it mypack) relies on a shared library mylib.dll that is already compiled and that I cannot compile on the fly while building the R package.
the library mylib.dll has been compiled on a x64 machine under Windows and can be loaded in R with dyn.load.
the package contains the required file NAMESPACE, where useDynLib(mylib.dll) is specified. The function .onLoad containing the instruction library.dynam('mylib.dll', pkg, lib) is also specified in a file zzz.R.
the R package mypack is built with Rtools using the usual command Rcmd INSTALL, and I then add a directory libs where I save mylib.dll.
when I try to load the package in R with library(mypack), I get the following error message:
Error: package 'mypack' is not installed for 'arch=x64'
This is puzzling me. Why can the shared library be loaded smoothly in R, but when I build a package using it I am getting this weird error message?
Thank you very much in advance for your help!
That error message comes from this code in library:
if (nzchar(r_arch) && file.exists(file.path(pkgpath,
"libs")) && !file.exists(file.path(pkgpath, "libs",
r_arch)))
stop(gettextf("package %s is not installed for 'arch=%s'",
sQuote(pkgname), r_arch), call. = FALSE, domain = NA)
which is telling me you need a {package}/libs/{arch} folder in your built package (ie the installed directory) with an {arch} that matches your system's arch, as given by r_arch <- .Platform$r_arch
I'm guessing your build has failed to make this correctly. Is there any C code in your source?
Related
I am trying to build an R package (DESeq2) from source so that I can debug it. I've installed all the dependencies required and I'm following Hillary Parker's instructions for creating R packages. I'm running this on CentOS 6.6 using R-3.4.2.
I run :
library("devtools")
install("DESeq2", keep_source=TRUE)
It installs it in the directory with all my other R libraries. When I look at the installed DESeq2 library it is missing all the DESeq2/R/*.R and DESeq2/src/*.cpp files.
QUESTION : Where are these files and why didn't they get installed? This does not seem like the expected behavior.
R uses binary database format for installed packages to pack the objects into a database-alike file format for efficiency reasons (lazy loading). These database files (*.rdb and *.rdx) are stored in the R sub folder of the package installation path (see ?lazyLoad).
Even if
you are looking at the right place to find the installed package (use .libPaths() in R to find the installation folder)
and you have installed the package with the source code (like you did or
via install.packages("a_CRAN_package", INSTALL_opts = "--with-keep.source"))
you will not find R files in R folder there.
You can verify that the source code is available by picking one function name from the package and print it on the console. If you can see the source code (with comments) the package sources (R files) are available:
print(DeSeq2::any_function)
To make the source code available for debugging and stack traces you can set the option keep.source.pkgs = TRUE (see ?options) in your .Rprofile file or via an environment variable:
keep.source.pkgs:
As for keep.source, used only when packages are
installed. Defaults to FALSE unless the environment variable
R_KEEP_PKG_SOURCE is set to yes.
Note: The source code is available then only for newly installed and updated packages (not for already installed packages!).
For more details see: https://yetanothermathprogrammingconsultant.blogspot.de/2016/02/r-lazy-load-db-files.html
I was trying to install the package RINDSEL but I am unable to install it and I keep getting the following error:
Error in install.packages : cannot open the connection
I downloaded the package from:
rindsel_1.0_2.zip | Integrated Breeding Platform
and loaded it from the directory. Other packages from the directory can be installed but just not this one.
Is the package corrupt or could there be any other error?
I would really be grateful for any help. Thanks in advance
Rename the zip file RinSel Software into Rindsel. That's the name specified in the discription file.
Then, you can install the package in R with the command
install.packages("C:/path/to/Rindsel.zip",repos=NULL,type="win.binary")
That works fine... at first (!!!).
Problem with the Rindsel package is. It is quite old. It was build with R 2.13.1. Therefore, if you want to load the library which would be the next step to use the package in R you will get the error:
Problems building package (Error: "package has been build before R-3.0.0")
My suggestion: Contact the authors of the package and ask them if they can either provide the source file that you can build the package by yourself or if they can bundle the Rindsel package with a newer R version.
(Or you could try to hunt down an old R version and see if you can get the thing running with an old R... However, I would not seriously suggest to do that. It would probably result in conflicting dependencies with the other required packages...)
EDIT 15-02-2018: OP asked if one can build an R package with sources that are presumeably the Rindsel source files.
Yes, basically, you could do that. You would have to make a your own description and namespace file and put the source file in the R folder than invoke the command in R to build it....
But it's not neccessary with the script files provided by the link the OP posted.
OP, just run the scripts in R! It's quite easy.
Download the zip-file and extract it on your machine.
Go to that directory. The R command would be
setwd('path/to/your/directory')
Than run the R script, e.g, the KNIndex.r. It's simple:
source('KNIndex.r')
Then the script will run and produce some output / prompts.
For future readers,
I was able to fix the error by running RStudio with administrative privileges to get the command to work.
If that does not fix it, you might wish to try
Installing "r tools" if that is not installed already. That can be downloaded from
https://cran.r-project.org/bin/windows/Rtools/
Download a relevant package that you are trying to install (e.g., tidyverse_1.3.0.zip) from https://cran.rstudio.com/
and install that from local path
It can also be installed directly from the web using install.packages("https://cran.rstudio.com/bin/windows/contrib/4.0/tidyverse_1.3.0.zip")
I had the same problem. R was not able to extract and compile the package files to the default installation directory for some system-specific reasons (not R related).
I was able to fix this by specifying the installation directory of the package lib using:
install.packages("your package", lib = 'path/to your/required/installation/directory')
You can then load the package by specifying the lib.loc option while loading it:
library('your package', lib.loc='path/to your/required/installation/directory')
A better solution:
Create a new environment variable (if you are using windows) R_LIBS_USER with the following directory path/to your/required/installation/directory.
This will change the default installation directory of the packages and make it easier to load and install them without specifying the location everytime.
I'm currently running R version 3.4.2 on Windows and have ggplot2 (via tidyverse) and sf package versions 3.4.2. I'm attempting to map spatial data using the ggplot2 sf kit.
When trying to run geom_sf, I receive an error: could not find function "geom_sf".
When I search the ggplot2 package using ls("package:ggplot2"), geom_sf is not listed in the library files.
I installed devtools and ran devtools::install_github("tidyverse/ggplot2"). However, I receive an error: Installation failed: Failed to connect to raw.githubusercontent.come port 443: Timed out. I assume the firewall at work is halting this connection.
To get around this, I tried downloading the zip manually from https://github.com/tidyverse/ggplot2 and running install.packages('ggplot2-master.zip', lib = 'C:/filepath') and receive the error: package 'ggplot2-master.zip' is not available (for R version 3.4.2). I was getting the same error before I updated from 3.4.1.
TLDR: I'm having the same issue as this user: Error when plotting sf object --- Error: could not find function "geom_sf"
but the solution does not work for me.
Does anyone see where I may be missing something? Or how to access this highly referenced (more streamlined) package?
If you downloaded from the URL you cited then the appropriate next step would be to execute this at the R session command line assuming your package is in the working directory:
install.packages('ggplot2', repo=NULL, lib = 'C:/filepath')
The .zip extension is implicit in trying to install from a binary windows file and you need to tell it NOT to attempt downloading from CRAN.
A colleague ported more than a thousand S functions and Fortran subroutines to R. The native R functions are contained in 5 .RData files and the Fortran subroutines are contained in 2 .dll files.
I can load these files into the R workspace using
for (i in 1:5){ load(list.files()[grep("RData",strsplit(list.files(),"\\W+"))][i]) }
for (i in 1:2){dyn.load(list.files()[grep("dll" ,strsplit(list.files(),"\\W+"))][i]) }
After some troubleshooting I know that the relationships between R code and the Fortran subroutines were already well established by the original author.
Now I want to create a package from these files because I'm unable to deploy my ioslides_presentations with these dll files since shinyapps.io is built with Linux. This is my first attempt at creating an R package, I don't intend to publish it to the CRAN, I'm only interested in generating a local zip file that I and my students can load.
MY PROCESS
After loading the functions in the workspace using the above code, I ran package.skeleton and system("R CMD build package") which successfully created "package_1.0.tar.gz". After completing the DESCRIPTION file, I put the .dll files I the src sub-directory and included useDynLib(DLL1), useDynLib(DLL2) in the NAMESPACE file.
However, when I run system("R CMD INSTALL build package_1.0.tar.gz") I get the following error:
Error in library.dynam(lib, package, package.lib) :
DLL 'package.dll' not found: maybe not installed for this architecture?
Error: loading failed
Execution halted
I've spent a great deal of time reading through "Writing R Extensions", "Advanced R" by Hadley Wickham, and the devtools documentation. Even so, I'm having difficulty deciphering useDynLib, .onLoad, Export, Call, and Makevars and which should be used for pre-compiled Fortran code.
I really don't want to parse through all of these functions to find which require export rules if I don't have to. I'd appreciate any help getting these .dll files loaded so I can finish creating this package
Thanks in advance,
Jason
I developed an application whose main graphical outputs relie on R through the very useful RInside. I would like to "deploy" my application under linux systems without having to systematically install R and the needed packages. For that purpose I simply copied all the R directory /usr/lib/R, all the needed .so library and set R_HOME variables to the correct path.
However, I get when executing:
Error in loadNamespace(name) : there is no package called ‘Rcpp’
Execution halted
While RInside is in the directory $R_HOME/site-library/RInside. I guess that I have more to do (and that my approach was quite naive). Does anyone already tries such a task and can help on what to do ?
Yes you need to install the other dependencies as well -- and Rcpp is needed to convert data seamlessly between R and C++.