I was trying to use rpy2 to interoperate R and python in jupyter. It was just a curiosity experiment. It is not working due to package imports.
But what is not an experiment is to be able to install packages in R . I can no longer do so after installing rpy2. The following is happening in R:
> install.packages('ggplot2')
.. various errors including
In file included from /Users/steve/miniconda3/lib/R/include/R.h:50:
/Users/steve/miniconda3/bin/../include/c++/v1/cmath:317:9: error: no member named 'signbit' in the global namespace
Why is miniconda3 in the picture at all here?
Later we see:
ERROR: compilation failed for package ‘isoband’
* removing ‘/Users/steve/miniconda3/lib/R/library/isoband’
ERROR: dependency ‘isoband’ is not available for package ‘
Why is the R library directory now pointed to miniconda3 ? How do I get back to the normal R libraries location?
Related
I am trying to install an R package along with its dependencies. But it is throwing error.
$ install.packages(rvest_0.3.5.tar.gz, dependencies=True)
-bash: syntax error near unexpected token `rvest_0.3.5.tar.gz,'
I am new to R please help me how can I download this along with it dependencies.
Before this, I tried following
$ R CMD INSTALL rvest_0.3.5.tar.gz
* installing to library ‘/Library/Frameworks/R.framework/Versions/4.0/Resources/library’
ERROR: dependencies ‘httr’, ‘magrittr’, ‘selectr’ are not available for package ‘rvest’
But it failed with dependent packages are missing error. And obviously it is cumbersome to install the dependent packages manually. Hence I tried package.install
You need to run it with quotes and capital TRUE:
install.packages("rvest_0.3.5.tar.gz", dependencies = TRUE)
Note this will only work if you have unix-like system and the file is located in your current working directory (check with running getwd() from your R session). Otherwise you need to provide full path to the file (like "~/somefolder/mydata/rvest_0.3.5.tar.gz").
If you run Windows, then you need .zip file instead of .tar.gz.
If you are connected to internet, just run:
install.packages("rvest")
I want to install a package named "locClass" in R but always failed and kept getting the following warning:
install.packages("locClass", repos="http://download.r-forge.r-project.org/")
Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘locClass’
These will not be installed
The install command is referred to: https://r-forge.r-project.org/R/?group_id=1187
Also, I downloaded the package source from the above website. But R returned the following:
library(locClass)
Error in library(locClass) : ‘locClass’ is not a valid installed package
My R version is 3.3.3. I tried the 3.4.0 but failed the same way.
This is not exactly a solution but an alternative to utilize functionality of package locClass. Download the package file of locClass from here and source(functions.R) present here. This way you can use all functions available in package.
Note : function.R means FLXMCL.R, FLXMCLconstant.R etc.
I'm still looking for a better solution but this is a temporary alternative.
I am running OSX 10.10, R-Studio Version 0.99.484, and R version 3.2.2.
I just made a fresh install of R and R-Studio using the installers from their respective websites. I use install.packages to install "mosaic" and then I try loading it using library, but it gives me the following error:
library("mosaic", lib.loc="/Library/Frameworks/R.framework/Versions/3.2/Resources/library")
Error : object ‘dendro_data.hclust’ is not exported by 'namespace:ggdendro'
Error: package or namespace load failed for ‘mosaic’
I tried reinstalling ggdendro but nothing. Does anyone have any advice on how to deal with this issue?
I encountered this same error and seem to have somewhere along the way resolved it. Steps taken include:
cleaned out my libraries (local and System)
used Disk Utility to repair any odd permissions
reinstalled R
opened RStudio and imported package with dependencies from the repository:
> install.packages("mosaic", lib="/Library/Frameworks/R.framework/Versions/3.2/Resources/library")
console prompted me to choose the older precompiled package or the newer, I chose older
Do you want to install from sources the package which needs compilation?
y/n: n
mosaic loaded happily
> library("mosaic", lib.loc="/Library/Frameworks/R.framework/Versions/3.2/Resources/library")
I tryed to install from file an old version of RgoogleMaps package with this command
install.packages("F://RgoogleMaps_1.1.9.15.tar.gz", repos = NULL, type="source")
but i found this error message:
* installing *source* package 'RgoogleMaps' ...
** package 'RgoogleMaps' successfully unpacked and MD5 sums checked
ERROR: a 'NAMESPACE' file is required
* removing 'C:/Users/Famiglia Mazza/Documents/R/win-library/3.1/RgoogleMaps'
* restoring previous 'C:/Users/Famiglia Mazza/Documents/R/win-library/3.1/RgoogleMaps'
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-31~1.2/bin/x64/R" CMD INSTALL -l "C:\Users\Famiglia Mazza\Documents\R\win-library\3.1" "F://RgoogleMaps_1.1.9.15.tar.gz"' had status 1
Warning in install.packages :
installation of package ‘F://RgoogleMaps_1.1.9.15.tar.gz’ had non-zero exit status
what can I do? I'm using R on Windows
In R 2.14.0 a requirement was made that all packages had namespaces, but as a transitional arrangement those that didn't would have one automatically generated at install time.
A package R code but without a ‘NAMESPACE’ file will have a default
one created at R CMD build or R CMD INSTALL time, so all packages will
be installed with namespaces. A consequence of this is that
.First.lib() functions need to be copied to .onLoad() (usually) or
.onAttach(). For the time being, if there is an auto-generated
‘NAMESPACE’ file and no .onLoad() nor .onAttach() function is found
but .First.lib() is, it will be run as the attach hook (unless the
package is one of a list of known exceptions, when it will be run as
the load hook).
However, by R 3.0.0 this transitional arrangement was ended:
The transitional support for installing packages without namespaces
(required since R 2.14.0) has been removed. R CMD build will still add
a namespace, but a .First.lib() function will need to be converted.
R CMD INSTALL no longer adds a namespace (so installation will fail),
and a .First.lib() function in a package will be ignored (with an
installation warning for now).
As an exception, packages without a ‘R’ directory and no ‘NAMESPACE’
file can still be installed.
Therefore, I suggest you use an older version of R to run this package. One prior to R 3.0.0 should suffice, and the latest one prior to that is R 2.15.3.
I was trying to install RTextTools package for R, but failed. Here is the output from the screen
> > install.packages("RTextTools")
Warning in install.packages("RTextTools") :
argument 'lib' is missing: using 'C:\Users\datamining\Documents/R/win-library/2.10'
--- Please select a CRAN mirror for use in this session ---
Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/2.10
Warning message:
In getDependencies(pkgs, dependencies, available, lib) :
package ‘RTextTools’ is not available
What's the reason for this problem, and how to fix it? Thanks.
There are two distinct, but related, issues:
You are running version 2.10 of R which is two years old. CRAN supports only the current version with pre-built binaries. You could try installing from source.
RTextTools, as can be seen on its CRAN page also requires at least R version 2.13.
So in short: you should upgrade.
I have resolved the issue. I have Download RTextTools From Given Link.
https://cran.r-project.org/src/contrib/Archive/RTextTools/
and copy RTextTools_1.4.2.tar.gz file in project root folder then run this command in project folder in terminal
"R CMD INSTALL RTextTools_1.4.2.tar.gz"
After running this command I receive below error
"ERROR: dependencies ‘SparseM’, ‘randomForest’, ‘tree’, ‘e1071’, ‘ipred’, ‘caTools’, ‘maxent’, ‘glmnet’, ‘tau’ are not available for package ‘RTextTools’".
Now install each dependencies from RStudio or RConsole (Any Editor used by you) by simply running this code.
install.packages("caTools").
Install all 9 required packages One By One (In My Case it was 9 Packages Dependencies required by RTextTools) all packages will be installed except 'maxent'.
Now download maxent from the given link.
https://cran.r-project.org/src/contrib/Archive/maxent/.
and copy maxent_1.3.3.1.tar file in project folder then run this command in project folder in terminal.
"R CMD INSTALL maxent_1.3.3.1.tar"
Now For RTextTools Run this command again in Terminal.
"R CMD INSTALL RTextTools_1.4.2.tar.gz"
All is done Now..
But the Last Step is
Load the RTextTools using.
library(RTextTools)
You will see one more Error: Load SparseM Now Loading SparseM use code below.
library(SparseM)
and in the last Load RTextTools
library(RTextTools)
RTextTools is dependent on a number of packages, most of which require R 2.13+. You should always keep R updated to the latest version, since each update contains numerous bug fixes and performance enhancements.
If you can't install packages from repository or the packages are not available anymore, just follow this steps:
Install.packages("devtools")
check -- library("devtools")
install_github("cran/maxent")
install_github("cran/RTextTools")