I'm trying to install R through brew and I get the following error. Here is the snippet
==> Pouring r--4.1.0_1.big_sur.bottle.tar.gz
Error: Couldn't find manifest matching bottle checksum.
Please report this issue:
https://docs.brew.sh/Troubleshooting
/usr/local/Homebrew/Library/Homebrew/software_spec.rb:400:in `tab_attributes'
/usr/local/Homebrew/Library/Homebrew/formula.rb:2339:in `bottle_tab_attributes'
/usr/local/Homebrew/Library/Homebrew/utils/bottles.rb:100:in `load_tab'
/usr/local/Homebrew/Library/Homebrew/formula_installer.rb:1154:in `pour'
/usr/local/Homebrew/Library/Homebrew/formula_installer.rb:394:in `install'
/usr/local/Homebrew/Library/Homebrew/install.rb:303:in `install_formula'
/usr/local/Homebrew/Library/Homebrew/cmd/install.rb:207:in `block in install'
/usr/local/Homebrew/Library/Homebrew/cmd/install.rb:205:in `each'
/usr/local/Homebrew/Library/Homebrew/cmd/install.rb:205:in `install'
/usr/local/Homebrew/Library/Homebrew/brew.rb:131:in `<main>'
I also did the following and they are all fine:
brew update
brew doctor
brew upgrade
I'm not sure how to address the error. I tried brew install checksum but there is nothing by that name.
I have r 4.1.0 on Catalina. Trying to upgrade to 4.1.0_1 end up with the same error. But it works when I try to upgrade again.
brew upgrade r
Not sure if it could work for you to try to install again?
Related
I wanted to install "DESeq2" package in R, but it was missing the xml2-config file. I found somewhere that it can be obtained by installing the libxml2 package, but when I tried it gives error that it's not available for R version 3.4.2. Anyone has idea what to do?
You can install the dev version: devtools::install_github("r-lib/xml2")
After running what #amarchin wrote it didn't work instantly but R suggested to install libxml2-dev. So I run: sudo apt-get install libxml2-dev in Terminal.
And then in R console I typed the code from #amarchin: devtools::install_github("r-lib/xml2")
And it worked :)
I am working on Ubuntu 16.04 with R-version 3.4.2.
I want to install the R-Package "protolite" (more precisely, I want to install "tmap" where protolite is a prerequisite). I have libprotocol version 2.6.1 installed:
$ protoc --version
returns libprotoc 2.6.1.
When I type install.packages "protolite" , R gives me the warning:
Package protobuf was not found in the pkg-config search path.
Perhaps you should add the directory containing 'protobuf.pc'
to the PKG_CONFIG_PATH environment variable
No package 'protobuf' found
Later the installation fails with
/usr/bin/ld: cannot find -lprotobuf
collect2: error: ld returned 1 exit status
Since libprotocoll is installed, I searched for the pc file by
apt-file search protobuf.pc
which returned
libprotobuf-dev: /usr/lib/x86_64-linux-gnu/pkgconfig/protobuf.pc
So I added
export PKG_CONFIG_PATH=/usr/lib/x86_64-linux-gnu/pkgconfig
however, this did not resolve the issue. Can somebody help me out?
Note: I spent hours trying to install "tmap" by now, at first my problem was that I had installed libprotocol 3.2, which I had to delete to install tmap/protolite because the installation required libprotocol 2.6.1. So maybe this deletion/new installation brought some things in disorder on my computer.
Using
sudo apt-get install -y libprotobuf-dev protobuf-compiler
worked for me.
For anyone having the same problem. I checked with the Synaptic Package manager and found that not all libprotobuf versions were installed. In fact, just a lite version had been installed. Installing all "libprotobuf-dev 2.6.1-1.3 made it work.
I am trying to install two packages in R (3.3.2): devtools and git2r. They are depending on the existence of zlib. This comes with macOS Sierra (10.12.3) and it's version 1.2.8 by default.
When I'm trying to install these packages I get the error below.
I've been trying a lot of things.
directly installing via CRAN in RStudio: no effect.
trying to locate zlib on macOS: can't find zlib.
installing via R CMD INSTALL git2r: no effect.
I notice someone has a similar issue posted on GitHub: https://github.com/ropensci/git2r/issues. There is no solution yet.
Does anyone here have an idea?
Thanks!
Sander
ERROR MESSAGE BELOW
configure error in "/private/tmp/RtmpP6HZFx/R.INSTALLe73412909267/git2r"
configure error
The zlib library that is required to build git2r was not found.
Please install:
zlib1g-dev (package on e.g. Debian and Ubuntu)
zlib-devel (package on e.g. Fedora, CentOS and RHEL)
and try again.
If the zlib library is installed on your system but the git2r configuration is unable to find it, you can specify the include and lib path to zlib with:
"R CMD INSTALL --configure-args='--with-zlib-include=INCLUDE_PATH --with-zlib-lib=LIB_PATH' git2r"
See "config.log" for more details
ERROR: configuration failed for package "git2r"
*removing "/usr/local/lib/R/3.3/site-library/git2r"
UPDATE: the same issue persists on macOS X 10.12.5 in combination with R 3.4.0 - the latter I need for DESeq2.
Solution...Mmm. Not really. I simply uninstalled R and all the packages, and than I reinstalled everything again. I installed R and RStudio via homebrew, following the instructions here: https://rud.is/b/2015/10/22/installing-r-on-os-x-100-homebrew-edition/.
Oddly enough: all issues disappeared.
UPDATE #1: this solution does not - obviously - work for the combination R 3.4.0 and macOS X 10.12.5. We need a solution for this issue.
UPDATE #2: I have discovered what I believe was the issue: a wrong path to the xcode command line tools.
sudo xcode-select --reset did the trick and now xcode-select -p points to /Library/Developer/CommandLineTools. And which xcode-select points to /usr/bin/xcode-select. Googling I discovered that it is not needed to install Xcode through the App Store as it states on http://railsapps.github.io/xcode-command-line-tools.html:
"On earlier versions of macOS, it was more difficult to install Xcode Command Line Tools. It required a huge download of the full Xcode package from the Mac App Store or registration as an Apple developer for a smaller Command Line Tools package. Mac OS X Mavericks made installation of Xcode Command Line Tools much simpler.".
i was having the same problem. i have a note 8(samsung). just go to GitHub and install zlib from there.
When I go File-New File-R Notebook, it tells me to install some packages, but then it fails giving me this message:
Notebook Creation Failed:
"One of more packages required for R Notebook creation were not installed"
I'm trying to install those packages manually, but the package installation window disappears so quickly that I can't even see which ones I should install.
I googled it around, but couldn't fine any resource.
Can anyone help me with this?
Maybe at least provide a list of packages required to run R Notebook?
R notebooks are actually not created with a package named either RNotebook or notebook or anything similar but rather with the rmarkdown package, and it needs to be a current version. So the command would be:
install.packages("rmarkdown", dependencies=TRUE) # needs to be >= version 1.3
Then your pulldown menu selections should succeed in a current version of RStudio. .... at least that is if you have the system requirements listed in the CRAN webpage:
SystemRequirements: pandoc (>= 1.12.3) - http://pandoc.org
This worked for me:
Install latest version of R from cran website
Start RStudio pointing to this version of R.
On Mac set env variable as show below and start RStudio from terminal
Then "Install Package" in RStudio for "markdown" and other ppackages will work properly installing latest required packages to open notebook
➜ export RSTUDIO_WHICH_R=/usr/local/bin/R
Don't press the error message, and read whatever you can from the installation popup under it. In my case the last message was that it has problems compiling "digest". I installed "digest" manually (install.packages("digest",type = "binary")). Then it all worked.
Mac, R version 3.6, Rstudio desktop 1.2.
I had exactly the same problem. By reading the error logs, I found g++ command not found. So just installed it and it worked fine next time I've tried.
I faced the same problem. I am using the latest version of R and RStudio and all of the installed packages are up-to-date.
Now, talking about the error in installation of packages. Follow the steps below and you will have R Notebook up and running:
Run the command
install.packages("rmarkdown", dependencies=TRUE)
You will observe several messages on the console during installation. Browse through them and jot the ones where there is ERROR in installation of some other dependent package. In my case, it was 'backports'. The error message will be like this:
ERROR: compilation failed for package 'backports'
It can be different in your case but the point is to note down the name of the package that is facing compilation issues. Use an editor(npp) to save the name of the package.
Once you get the name of the package, execute the following command:
install.packages("backports", type="binary")
After successful execution of the above command, go to File drop down and select R Markdown. Go with auto installation of the rmarkdown and rprojroot packages. They will be successfully installed and you can now use R Notebook
Let us know if this solution worked for you.
I just found the answer myself so I'm posting.
I guess there was something wrong with the server.
I went into tools-global options-packages and chose different CRAN mirror, then it worked.
UPDATE YOUR VERSION OF R - that was my solution, I had the same problem.
( First two commands ensure you get the MOST RECENT version of R which I found on a Digital Ocean page)
$ sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
$ sudo add-apt-repository 'deb [arch=amd64,i386] https://cran.rstudio.com/bin/linux/ubuntu xenial/'
$ sudo apt-get update
$ sudo apt-get install r-base
WITHOUT the first two lines I ended up with R version 3.2.3 (2015-12-10) -- "Wooden Christmas-Tree"
WITH the first two lines I got R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
After reinstalling R Studio, the Files -> RMarkdown was able to install all those subpackages and WORK. Hurray!
I'm running R 3.0.2 on OS X Mavericks.
I was able to install rattle (Rattle 2.6.27 r148) and gtk+ in R and run rattle. The screen shows up, but I cannot load any files in rattle. Here is the error message:
(R:18008): Gtk-WARNING **: Attempting to store changes into `/Users/amir/.local/share/recently-used.xbel', but failed: Failed to create file '/Users/amir/.local/share/recently-used.xbel.0HMGBX': No such file or directory
(R:18008): Gtk-WARNING **: Attempting to set the permissions of `/Users/amir/.local/share/recently-used.xbel', but failed: No such file or directory
Error in resetRattle() : attempt to apply non-function
It keep giving the last error every time I try to load a csv file into it.
Thanks
Here is the details of what worked for me:
First install XCode and command line tools:
sudo xcode-select --install
Then install XQuartz from http://xquartz.macosforge.org/landing/
Then install brew from http://brew.sh
and then brew some Gtk stuff:
brew install gtk+ cairo
Then set the compiling folder to right place:
export PKG_CONFIG_PATH=/opt/X11/lib/pkgconfig:/Library/Frameworks/GTK+.framework/Versions/Current/Resources/lib/pkgconfig:$PKG_CONFIG_PATH
Then run r in command line and install these packages using source:
install.packages(“RGtk2”,type=”source”)
install.packages(“Cairo”,type=”source”)
install.packages(“cairoDevice”,type=”source”)
install.packages("rattle", repos="http://rattle.togaware.com", type="source")
then everything should be ready for working with rattle in OSX
I had the same problem with rattle on Mac. However, it is now fixed in a recent update. I came across the fix here:
https://groups.google.com/forum/#!forum/rattle-users
Worth keeping an eye on, Graham Williams is very active on the thread.
Run this line to install the latest Rattle that fixes the most commonly reported issues on Mac OSX
install.packages("rattle", repos="http://rattle.togaware.com", type="source")