I am trying to install the packages on R v3.2.4 from GitHub, and even after installing Rcpp I keep getting an error:
install_github("marmap","ericpante")
Skipping install of 'marmap' from a github remote, the SHA1 (3e62fc8d) has not changed since last install.
Use 'force = TRUE' to force installation
Warning message:
Username parameter is deprecated. Please use ericpante/marmap
Any idea of what the possible problem might be? Should I downgrade R to run it or there is a better option?
PS. running on OSX 10.12.1 (Sierra)
library(marmap)
Attaching package: 'marmap'
The following object is masked from 'package:grDevices':
as.raster
Related
I had a script working with tabulizer, but had to clean my hard drive and reinstall R, and now I cant seem to even download and access the tabulizer library. I am now using R version 4.1.2 64 bit, and am thinking maybe I need to use an earlier version of R??? Here is the error message I get when I try and install tabulizer.
install.packages("tabulizer")
Installing package into ‘C:/Users/cdonner/Documents/R/win-library/4.1’
(as ‘lib’ is unspecified)
Warning in install.packages :
package ‘tabulizer’ is not available for this version of R
A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
I have tried to go to go to Cran (https://cran.r-project.org/src/contrib/Archive/tabulizer/) and download and unzip the libraries to my directory, but then I get an errors again. Any ideas? Thanks.
Enter this into the command window!
remotes::install_github(c("ropensci/tabulizerjars", "ropensci/tabulizer"), INSTALL_opts = "--no-multiarch")
It is not on CRAN.
You have to install using
ghit::install_github("ropensci/tabulizer")
or
devtools::install_github("ropensci/tabulizer")
github
I have just come to dealing with the same problem, but I got to solve it through the following steps:
the tabulizer package requires a Java environment. You need to download Java 64-bit or Java 32-bit through.
Make sure before that your windows/ mac is 32 bit or 64 bit by using the function sessionInfo().
Install the rJava package in R.
Create the Java environment through the command: Sys.setenv(JAVA_HOME="C:/Program Files/Java/jdk-18/")
Attention: the path of the file in step 3 is for java 64. the path for java 32 would be Sys.setenv(JAVA_HOME="C:/Program Files (x86)/Java/jdk-18/").
The other thing is that jdk-18 changes depending on everylaptop, in my case it is jdk-18, in your case it could jdk-17 for example.
Finally activate the library: library(rJava)
Voila. rJava and tabulizer work smoothly and nicely.
Got the same problem. (A lot) Packages were missing
I had to update R
Install java for R
Install Rtools42 from CRan
Install remotes
before running the command of #Dunbar111
remotes::install_github(c("ropensci/tabulizerjars", "ropensci/tabulizer"), INSTALL_opts = "--no-multiarch")
Following this question, I am trying to install the package (running R64 as admin on Windows):
devtools::install_github("markhwhiteii/processr")
or
devtools::install_github("cardiomoon/processR")
However, I get the error message:
Error: Failed to install 'processr' from GitHub:
(converted from warning) cannot remove prior installation of package 'digest'
no matter which update option I select. Running the command .libPaths() I found the packages installation folder C:/Program Files/R/R-3.6.2/library and manually deleted the digest package and reinstalled it with package.install("digest"). But I still get the same error! I would appreciate it if you could help me understand what is the problem and how I can resolve it.
The simplest solution is to say no when install_github asks if it should replace digest.
If it still fails for some reason (and I can't see why; neither package requires a specific version of digest and you've reinstalled it in any case), then the problem is that devtools itself uses digest, so it can't be removed as long as devtools is loaded. So you can't use install_github.
You have a couple of options:
Clone the repo, then from the command line, run R CMD INSTALL . in that directory. Note that you'll need to insert the path to your R executable.
Install from the GitHub archive of the master branch: install.packages("https://github.com/markhwhiteii/processr/archive/master.tar.gz")
The steps to install the markhwhiteii/processr package:
install.packages("devtools")
library(devtools)
install.packages("https://github.com/markhwhiteii/processr/archive/master.tar.gz")
for testing the instalation:
library(processr)
processr::model1
Sent a PR on the GitHub repo.
and if you want to run R in the Jupyter environment just follow the instructions to install and regsiter the kernel:
install.packages('IRkernel')
IRkernel::installspec()
I am writing an R package that depends on Stan and Rstan. I run the installation on an Azure machine Standard_D64_v3 and install r-base and r-cran-stan with sudo apt-get and rstan and Rcpp with R's install.packages()(among others, see shell setup script and R setup script).
This process worked OK last month. Today I was able to install the package (as evidenced by the welcome message) and then have a runtime error from incompatible versions.
...
* DONE (PosteriorBootstrap)
Reloading attached PosteriorBootstrap
Welcome to PosteriorBootstrap, a parallel approach for adaptive non-parametric learning
Error: package ‘StanHeaders’ 2.18.1 was found, but > 2.18.1 is required by ‘rstan’
In addition: Warning message:
version 2.18.1.10 of ‘StanHeaders’ masked by 2.18.1 in /usr/lib/R/site-library
Execution halted
I do not have StanHeaders anywhere in my code so I suspect the problem is between different packages. How can I solve this problem with versions?
As #nicola wrote in the comments, the fix is to reinstall StanHeaders with:
install.packages("StanHeaders")
The previous code may have stopped working because of a new version of R, but I could not determine the cause.
I updated R 3.4.4 to R 3.5.0 today. And my package cannot pass R CMD check anymore. It fails at checking whether package can be installed ... ERROR.
In another hand my package works, I can install it and use it as long as I don't check it.
The error is the following:
Error: package or namespace load failed for ‘sp’:
package ‘lattice’ was installed by an R version with different internals; it needs to be reinstalled for use with this R version
Error : package ‘sp’ could not be loaded
I tried to reinstall lattice these ways:
sudo apt-get --reinstall install r-cran-lattice
or
remove.packages("lattice", lib="~/R/x86_64-pc-linux-gnu-library/3.5")
install.package("lattice")
The package lattice is installed correctly in both cases. But it does not solve my problem. Also I ensured to have a single version of lattice removing either the r-cran one or the self compiled version. Nothing works.
Edit By the way I can do library(sp) or library(lattice) it works. But not with R CMD check
The error message tells you that the binary you are attempting to install comes from an insufficient / incompatible R version.
Two fixes:
Install from source as you did. After that check with AP <- available.packages() that you really only have one.
Use the correct binarie: read this README at CRAN and switch to Michael's 'R 3.5' repos. Many of us have been doing that for weeks.
Lastly, the r-sig-debian list is a friendly place for these questions and more. Subscribe first so that you can post.
I am fairly new to R. I have tried to google my question, and tried a few things, to no avail.
I am working on a MAC * High Sierra version 10.13.5
I am working with R * R version 3.5.0 (2018-04-23) -- "Joy in Playing"
I am unable to install the package "gtools", and I don't know what to do to make it work??
install.packages("gtools", type="source")
Warning: unable to access index for repository https://mirrors.sorengard.com/cran/src/contrib:
cannot open URL 'https://mirrors.sorengard.com/cran/src/contrib/PACKAGES'
Warning message:
package ‘gtools’ is not available (for R version 3.5.0)
I have also tried to install from a file saved on my computer, but this did not work either
library(gtools)
Error: package or namespace load failed for ‘gtools’:
package ‘gtools’ was installed by an R version with different internals; it needs to be reinstalled for use with this R version
You could try specifying a specific repository, for example:
install.packages("gtools", repos="https://cran.rstudio.com/")
Why are you using install from source? typically to install a package u only need to use the command
install.packages("gtools")
Then it will automatically ask u for a mirror to download from. It seems like "gtools" is available for R 3.5, so try to download it from another mirror and it should work.