I installed the Anaconda package and then tried to install the IJulia package and I get:
As you can see Update didnt work either, which was the only possible instruction I could find upon a quick search...
Thanks.
There seems to be something wrong in your Julia installation.
The easiest thing to do (although a bit drastic) is probably to delete the .julia directory in your home directory and try again. The installed packages are stored in that directory, so deleting it will "reinitialise" the package manager.
Note also that it is no longer necessary to separately install Anaconda in order to use IJulia -- if it does not find a Jupyter installation, it will install the required packages itself.
Related
I use renv to manage R package dependencies. The global cache works great for all packages that are installed with install.packages command; however, if I install the same package with devtools::install_version command it only installs it locally. As a result, any changes in the version number require manual installations again and again.
Do you have any idea how to address this issue?
I found the problem with my approach. Instead of using install_version, I should have used renv::install(). Here is an example:
Instead of using:
devtools::install_version(package="BART", version = "2.2")
Use
renv::install("BART")
renv::install("BART#2.2")
after updating my R version to 3.6.1 version - the rGrain and rGraphviz packages do not work. First the error was suggesting that the packages are not writable. However after updating some libraries and trying to source it outside from the BiocManager right now the error appears saying that the compilation fails. Does anybody know how to fix it?
I have already tried multiple options like sourcing it outside and directly from BiocManager and other sources however with no results.
I would appreciate any type of help suggesting how to fix or just install packages gRain and Rgraphviz.
Not writable is biocmanager being poorly programmed and somehow wanting to install some secondary packages into the main R folder in program files, rather than the usual R\win-library\ in documents.
You can workaround that by launching the R console or Studio with administrator privileges when installing/updating.
new to Cygwin. I downloaded apg-cyg and have been using it to install packages.
Recently I installed R and the current version in Cygwin packages is R.3.2.4. I wanted to install the latest R package but couldn't find a way from googling on how to do it inside Cygwin.
Is this possible to do or I just have to wait for the Cygwin packages updating their packages to the latest version? It would be nice to be able to update a package using the source file inside Cygwin..
Edit:
I should mention that I tried to install ggplot2 inside R using install.packages() and there was non-zero exit status and the installation couldn't go through.
You can install the source using cygwin setup. Click on the mouse on the "Src?" column.
The source will be installed in /usr/src
PS: next R release 3.3.1 is in 11 days. It will be packed for cygwin if there are no build issue
Followup:
There were several build issues, it took longer than expected to build 3.3.1
https://www.cygwin.com/ml/cygwin-announce/2016-06/msg00056.html
I would like to install IJulia from a non-connected computer. However, the command Pkg.add("IJulia") seems to require a connection. Is there a way to download manually the package and then specify a local path for the install?
Thanks in advance,
That would be a problem for all the Julia packages you want to install, not only IJulia. Julia packages work by cloning stuff into ~/.julia/v0.4 and ~/.julia/v0.4/.caches (for julia 0.4 at least) you will need to grab all the things and put them in the right place yourself.
Something else you can do is to use the insteadOf option of git so that Pkg believe it is pulling things from github, when you actually have a local clone of the repository.
You can find some information on installing packages (and configuring insteadOf for git) in this section of the julia manual.
My Fedora system (Fedora 20, all up to date) has just had R updated to version 3.1.0. Since then, I've had issues installing multiple packages. glmnet failed previously, and now I'm having trouble with treemap. More specifically, I get an error during treemap installation that httpuv has zero exit status.
I never had issues with the previous version of R. Any reason this version should have such problems??
There could be many causes to do with your OS, version, permissions, other installed packages/software, etc, etc. Without seeing the full error message it's hard to know.
One possibility specific to httpuv is root privileges. I've noticed a few threads on various forums when searching for installation errors with this package and Linux, many of them mentioning root v. non-root issues. In another case, libuv needed to be upgraded.
I encounter package installation problems daily and I have some more general work-arounds as well. Hopefully one of these will solve your problem.
Install the package from source
download.file(url="http://cran.r-project.org/src/contrib/httpuv_1.3.0.tar.gz", destfile = "httpuv.tar.gz")
install.packages("httpuv.tar.gz", type = "source", repos = NULL)
Install using devtools via GitHub if the package supports it
Install RTools and re-try your package installation
Install an older version of the package
If those above do not work, then I dig deeper by referring to advice given to me by a VP of IT in my company. These comments were made in reference to frequent package installation problems I encountered when switching from Windows to Solaris:
There are two types of install/make problems. Missing .h files
and/or missing .so/.a libs. The reason for these are multiple:
1.- the package that delivers these is not installed. This means that those files cannot be found anywhere in the /usr tree. Solution is
install right package, make sure the files are there
2.- the includes are not found by the install configurator. This means some environment variable or install option is not properly set (this
is our case for RODBC). Figuring out which variable to set is
challenging without looking at the package documentation [fortunately, documentation is not hard to find!]
3.- the libs are not in the LD_LIBRARY_PATH, easy to fix.
4.- There is a deeper compile/link error, meaning the package is not compatible with the rest of the sw, or has not been properly ported.