I need to download packages and install from local directory. But I'm having trouble installing ggplot2. I get no warning, but it seems the library is not installed. Output is below, any suggestions? Operating system is Windows. After running, the directory C:...\R\win-library\3.1 contains subdirectory ggplot2-master.
> install.packages("C:/.../packages/ggplot2-master.zip", repos = NULL, type="source")
Installing package into ‘C:/.../R/win-library/3.1’
(as ‘lib’ is unspecified)
> library(ggplot2)
Error in library(ggplot2) : there is no package called ‘ggplot2’
The correct action was to download the binaries instead of the source.
Note, the following command prompts for the file path:
install.packages(file.choose(), repos=NULL)
The computer is behind a firewall, so the install.package command does not work. I should have downloaded the binary install, but downloaded the source by mistake. So, the corrective action is to download the binary files. I want to point out that in my notes on R, it clearly states to download the binary file. Part of the joys of getting older, not remembering why I came into this room.... Also, rambling...
Related
I already referred this post,post,
I am trying to install an R package called Aphrodite.
So, I downloaded the zip folder of R package from github and tried the below command
install.packages("C:/Users/test12/Downloads/Aphrodite.zip",repos=NULL,dependencies=TRUE,type="source")
The above command results in below message and moves the cursor to next line without any error message. Please note that all my packages goes into the below folder only.
Installing package into ‘C:/Users/test12/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
However, when I try to use the below command, I get an error as shown below
library(Aphrodite)
Error in library(Aphrodite) :
‘Aphrodite’ is not a valid installed package
I also tried the below option but it doesn't display some of the folders which are available in the master directory. The details of it can be referred in this post
install.packages("devtools")
library(devtools)
install_github("ohdsi/Aphrodite") #APHRODITE is the package name
library(Aphrodite)
How can I load the package when it is installed from a custom directory? Why the package is not being recognized even though it is in the usual libpath folder?
I'm trying to download the package "Seurat" in R, the package is installed and it's now in my list of packages.
** testing if installed package keeps a record of temporary installation path
* DONE (patchwork)
The downloaded source packages are in
‘C:\Users\parnian\AppData\Local\Temp\RtmpAVgSd8\downloaded_packages’
But when I try to call it (library(Seurat)) I get the following error:
> library(Seurat)
Error: package or namespace load failed for ‘Seurat’:
object ‘wrap_plots’ is not exported by 'namespace:patchwork'
I read the similar questions and manually installed "patchwork":
> install.packages("patchwork")
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:
https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘C:/Users/parnian/Documents/R/win-library/4.0’
(as ‘lib’ is unspecified)
R also tells me to install Rtools whhich I have, but when I follow these commands:
> writeLines('PATH="${RTOOLS40_HOME}\\usr\\bin;${PATH}"', con = "~/.Renviron")
there are no more folders in rtools40/home . I don't get the usr\bin... in the address above.
but when I want to verify that make can be found (Sys.which("make")), I get this:
> Sys.which("make")
make
""
Also the downloaded packages of Seurat are saved in a location that doesn't even exist in my computer! How is that possible?
How can I fix this?
Thank you
I was having the same problem. Turns out there are two 'patchwork' packages in R somehow. I got a hint that this was the problem from the answer provided here (https://github.com/satijalab/seurat/issues/2818)
The other patchwork has the current update of 2.4. So what you should do is uninstall the current patchwork and use
devtools::install_github("thomasp85/patchwork")
I did this and it fixed the problem!
I am on Windows 7 and I am using R Studio 0.99.902 with R3.3.1. When I am trying to install a package I get the Warnings:
Warning: unable to access index for repository http://cran.rstudio.com/src/contrib:
cannot open URL 'http://cran.rstudio.com/src/contrib/PACKAGES'
Warning: unable to access index for repository http://www.stats.ox.ac.uk/pub/RWin/src/contrib:
cannot open URL 'http://www.stats.ox.ac.uk/pub/RWin/src/contrib/PACKAGES'
It is the first time I see it and I cannot solve it. Can anyone help me ?
This issue is likely caused by the package being too old or too new for your R version. For example, if a package is released during R-3.4.1, it will not be available for R-3.3.1. Packages which are removed from CRAN before your R version are also not available. The package DESCRIPTION file shows if there is a hard restriction on which R versions the package will run.
Search for the package's CRAN page and see its status. You may still be able to install the package by downloading the package source (the tar.gz file) and in RStudio selecting Install from: Package Archive File in the Tools/Install Packages... menu (or using install.packages with repos = NULL). Beware that the package is not available from CRAN for a reason; you may need to make some changes to the package for it to work correctly.
Running options(download.file.method="libcurl") then installing packages did the trick for me. You may find an answer here.
Please note that compiling from source for Windows requires the appropriate version of Rtools that is compatible with the R version you are working with. This list is available at the Rtools site:
https://cran.r-project.org/src/contrib/Archive/
If compilation from source is complicated, it is also possible to find the Windows-compiled binaries (.zip files) for older versions of R at:
https://cran-archive.r-project.org/bin/windows/contrib
This link is referenced by the ReadMe file available at the "regular" repository for Windows binaries for different versions of R, namely at:
https://cran.r-project.org/bin/windows/contrib
Once the zip file is downloaded, you can run the following R code line to install the package:
# Use repos=NULL so that the first argument is a path to the local zip file
# containing the binary package to install
# (as opposed to just the name of the package to install from the web)
install.packages("<local-path-to-downloaded-zip-file>", repos=NULL)
I'm trying to install the 'yaml' and 'stringi' packages in R-Studio, and it keeps giving me these errors:
> install.packages("stringi")
Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘stringi’
These will not be installed
or
> install.packages('yaml')
Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘yaml’
These will not be installed
How can I get these to install properly?
The error is due to R being unable to find a binary version of the package on CRAN, instead only finding a source version of the package and your Windows installation being unable to compile it. Usually this doesn't occur, but in this case was caused by the (temporary) outage of some of the mirrors at CRAN. If you type:
> getOption('repos')
CRAN CRANextra
"http://cran.rstudio.com" "http://www.stats.ox.ac.uk/pub/RWin"
attr(,"RStudio")
[1] TRUE
You will see that R uses "http://cran.rstudio.com" by default to look for a package to download. If you see the cran mirrors web page you can see at the top that "http://cran.rstudio.com" actually redirects you to different servers world wide (I assume according to the geo location).
When I had the above issue, I solved it by manually changing the repo to one of the urls in the link provided. I suggest you use a different country (or even continent) in case you receive the above error.
I provide below some of the urls in case the link above changes:
Brazil http://nbcgib.uesc.br/mirrors/cran/
Italy http://cran.mirror.garr.it/mirrors/CRAN/
Japan http://cran.ism.ac.jp/
South Africa http://r.adu.org.za/
USA https://cran.cnr.Berkeley.edu/
You need to run the function install.packages as follows:
install.packages('<package_name>', repo='http://nbcgib.uesc.br/mirrors/cran/')
#or any other url from the list or link
One of them should then work to install a binary from an alternative mirror.
You need to install RTools to build packages like this (i.e., a source package rather than a binary). After you install Rtools, then try again to install.packages("ggplot2") and R will prompt you with:
Do you want to attempt to install these from source?
y/n:
(see the picture below)
You need to answer y and it will try to compile the package so it can be installed.
Struggled with this issue today, solved it for now by first downloading the windows binary and then installing e.g.
install.packages("https://cran.r-project.org/bin/windows/contrib/3.3/stringi_1.1.1.zip", repos =NULL)
Just go to https://cran.r-project.org/ and then R Binaries/Windows/contrib and copy the url as argument to install.packages()
Install the package from a zip file - downloadable from the r-project website.
In basic R
go to Packages
Install packages from local files.
In RStudio
go to Packages
Install packages
Install from Package Archive File.
I had this issue when using an out-of-date version of R, so no binaries were available. The simple solution was to update my version of R.
Anything worked for me, until I found out my computer had an old version of R installed. Uninstalling everything and installing the newest R version worked!
I had to download the latest version of Rtools:
Go into the downloads folder and double click it to install it.
Close and reopen any R session.
Now packages should install like normal.
However, if you still have trouble, try installing the package from source (using type="source")
Like this:
install.packages("dplyr", type="source")
It took a good amount of time to install RMySQL on my Linux machine but I was able to install it after changing environment variables and copy and paste lib.dll file.
However, I'm now trying to install RMySQL on my 64bit window machine, but so far there's no progress yet for two days. It broke down after "running command sh ./configure.win had status 127 error, and I cannot find what this means.
Can anyone shed some lights on this?
install.packages('RMySQL',type='source')
Installing package into ‘C:/Users/chu/Documents/R/win-library/3.1’
(as ‘lib’ is unspecified)
trying URL 'http://cran.rstudio.com/src/contrib/RMySQL_0.9-3.tar.gz'
Content type 'application/x-gzip' length 165363 bytes (161 Kb)
opened URL
downloaded 161 Kb
* installing *source* package 'RMySQL' ...
** package 'RMySQL' successfully unpacked and MD5 sums checked
Warning: running command 'sh ./configure.win' had status 127
ERROR: configuration failed for package 'RMySQL'
* removing 'C:/Users/chu/Documents/R/win-library/3.1/RMySQL'
Warning in install.packages :
running command '"C:/PROGRA~1/R/R-31~1.0/bin/x64/R" CMD INSTALL -l "C:\Users\chu\Documents\R\win-library\3.1" C:\Users\chu\AppData\Local\Temp\RtmpKA9e7I/downloaded_packages/RMySQL_0.9-3.tar.gz' had status 1
Warning in install.packages :
installation of package ‘RMySQL’ had non-zero exit status
The downloaded source packages are in
‘C:\Users\chu\AppData\Local\Temp\RtmpKA9e7I\downloaded_packages’
for linux users..
install- libmysql first
sudo apt-get install libmysql++-dev
then try.
I was facing the same error. Given below is the link to a way around that worked for me.
http://www.ahschulz.de/2013/07/23/installing-rmysql-under-windows/
In short, the location of library libmysqll.dll required for compilation, had to be changed from lib folder to bin folder of the home directory set for MySQL in environment variables.
By default, R uses the /tmp directory to install packages. On security conscious machines, the /tmp directory is often marked as “noexec” in the /etc/fstab file. This means that no file under /tmp can ever be executed. Packages that require compilation or that have self-inflating data will fail with the error mentioned.
The solution is to set the TMPDIR environment variable outside R (in your shell), which R will use as the compilation directory. How to do this depends on the shell. bash:
mkdir ~/tmp
export TMPDIR=~/tmp
Then R can compile and install the package.
I ran into the same problem while updating packages on Windows server for latest version of R. I solved it by installing from a .zip file vs .tar.gz.
I actually had to go through the process of first downloading the package, and then installing from it (not from mirror) for other reasons.
Here is what it looked like:
pk <- 'caTools'
download.packages(pk, "R-3.2-packages/" ,type = "win.binary")
install.packages(
dir("R-3.2-packages/",pattern=pk,full.names = TRUE),
repos = NULL,
type = "source")
Hope this helps.
Solution if anyone faced the same problem on windows:
Make sure your MYSQL_HOME environment variable is set correctly and libmysql.dll is copied to bin folder!!!
Run install.packages('RMySQL') then when the "Do you want to install from sources..." window pops up select No.
Then copy the downloaded binary packages location from console.
Go to Packages -> Install, paste the location into Package archive and click Install.