Can Jupyterlab extensions be downloaded and installed later on offline?
If so, how?
In the documentation it says:
You can also install an extension that is not uploaded to npm, i.e., my-extension can be a local directory containing the extension, a gzipped tarball, or a URL to a gzipped tarball.
However, I can't seem to figure out how to do this.
How?
This github issue details the following solution. I tried it and it worked on the Bokeh jupyter lab extension.
outside, do a jupyter lab install of all extensions of interest
copy $PREFIX/share/jupyter/lab/static from the outside machine onto a shared/thumb drive
inside, overwrite/create that same folder
Make sure jupyterlab isn't running when you replace the static folder.
This is a temporary solution, and a more active discussion of the plans to make this process easier can be found here
Related
I wish to use the NASAaccess tool in R. I have installed the curl software in my system, and also have created the _netrc file in the home directory as instructed (including teh _netrc, .netrc, .urscookie). However when I try to run the code it asks to create the netrc files in the home directory which I have already done. What should be the problem here?
I re-installed the curl software, re-wrote the files in the home directory, praded the R version. It should have worked by now providing the rainfall data output.
I have had to install Ubuntu command line on windows10 in order to install R and download a package that is not supported on R for windows. This has worked fine, however, I need to set the working directory in R to the folder containing the files the package needs to work with. I have looked at lots of forums about changing directory and I have no luck!
My default working directory is a hidden folder created by windows when I installed ubuntu command line. I can access this, but I dont need this folder...I need to change the working directory in R to a folder on the D drive on my computer. I have tried to no avail!!
I have tried the normal setwd() command with the following combinations, all of which return the error 'cannot change working directory'
setwd("D:/RNA-seq data/")
setwd("d:/RNA-seq)
setwd("~D:/RNA-seq)
I am really frustrated that I cannot carry out this simple command (maybeI am doing something fundamentally wrong) or maybe this is a limitation because of the hidden default home folder set by windows? Please not I cannot transfer the necessary files in to the default folder created by windows for 'home/R' as it is on the C drive and there isnt enough space on disk. I need to navigate to the folder on d drive in order to carry out my code!!
Any help would be really really appreciated! Many thanks!
I have developed a solution using R and want to transfer it to the production server (CentOS 7) which has no Internet connection to install packages. To facilitate installation of packages, I used packrat to bundle the packages I used in my R script to the project.
Using packrat::bundle(), I have created a tar file of the project and moved the file to the server and untar the zip file.
According to a post in Blogger, once I open the project, When R is started from that directory, Packrat will do its magic and make sure the software environment is the same as on the source machine.
However, when I open the project in Server (using R-Studio Server 0.99), nothing happens and it throws error of unknown packages.
When manually execute the "packarat/init.R" file below error is thrown
Error in ensurePackageSymlink(source, target) :
Target '/home/R_Projects/prjName/packrat/lib-R/base' already exists and is not a symlink
Well, I found the problem and solve it. The symlink error is related to centOS (it is not related to R). I just simply removed all the folders inside the
/home/R_Projects/prjName/packrat/lib-R
Because these folder exist, the packrat is unable to create symlink with the same name inside the lib-R folder. If I remove them, it will create a link (shortcut) to the actual folder where the r package is located.
Hope it helps future readers.
I have a computer behind a very restrictive proxy server it only allows me to surf the web and download programs it does not allow programs like the Atom text editor to download it's packages.
My question is how do I install them using only browser based downloads?
It is certainly possible:
Find the package you want to install, for example the activate-power-mode package.
Click on the Repo button to go to the GitHub repository.
Click Releases towards the top of the UI, then click on the most recent release, 0.4.1 in this case.
Download the source code release in either Zip or GZip depending on your platform.
Extract the content of the archive to a known permanent location, I have chosen:
C:\Source\Atom
Run the following command from your terminal / command prompt (make sure to include quotes around the path):
apm link "C:\Source\Atom\activate-power-mode-0.4.1"
Restart or Reload Ctrl-Alt-R Atom and the package will now be installed.
You can alternatively extract the package directly to your ~/.atom/packages folder however you will have to rename the folder to exactly match the name of the package, additionally uninstalling the package from Atom will delete the files which could be annoying if it is an accidental deletion.
Because of package dependencies a safest bet is this:
Install package normally on connected computer
Copy contents from your ~/.atom/packages
Paste contents to ~/.atom/packages on offline computer
Restart Atom
At least this worked for me like a charm.
The answer of Richard Slater is informative and the answer of Andriy Buday could look less professional. But, in my case, the answer of Andriy Buday was also very important.
I tried to install two packages atom-beautify and prettier-atom by following the answer of Richard Slater and had some problems of not being able to find some modules. It was not only me who had these problems. Consider checking the following links.
The issue of "cannot find module event-kit"
https://github.com/Glavin001/atom-beautify/issues/1734
https://github.com/Glavin001/atom-beautify/issues/1366#issuecomment-269716306
When I decompressed a file (atom-beautify-0.30.3.tar.gz) I received from GitHub respository, I could find out directories like appveyor, docs, and examples. But I could not find out a directory named node_modules which was present when I installed this package atom-beautify using Atom Editor online.
To check if the absence of directory node_modules is the only problem, I went through the following steps.
Start Atom Editor.
Install atom-beautify using Atom Editor online like the answer of Andriy Buday suggests.
Close Atom Editor.
Move atom-beautify directory from ~/.atom/packages (that was %HOMEDIRECTORY%%HOMEPATH%.atom\packages in my case because I used cmd on Windows 10) to somewhere else.
Decompress atom-beautify-0.30.3.tar.gz and move or copy atom-beautify-0.30.3 directory from this decompressed result into %HOMEDIRECTORY%%HOMEPATH%.atom\packages as the answer of Andriy Buday suggests.
Rename directory %HOMEDIRECTORY%%HOMEPATH%.atom\packages\atom-beautify-0.30.3 to %HOMEDIRECTORY%%HOMEPATH%.atom\packages\atom-beautify as the answer of Richard Slater suggests.
Move or copy node_modules directory from the directory moved at step 4 into %HOMEDIRECTORY%%HOMEPATH%.atom\packages\atom-beautify.
Start Atom Editor.
I found that no error message appeared and that package atom-beautify worked properly, thus I am thinking that absence of node_modules directory was the only problem of the file atom-beautify-0.30.3.tar.gz I received from GitHub repository.
I am afraid if it is normal that directory node_modules is not contained in the file atom-beautify-0.30.3.tar.gz downloaded from GitHub repository because of any rules I do not know yet, like placing directories like node_modules somewhere else. If there really are such rules and somebody tells me about such rules by adding an answer or a comment here, I will appreciate it a lot.
I am not sure if it is same with all other packages, but I found that it was same at least with package prettier-atom.
I wish it helps somebody.
+++++++++++++++++++++++++++
I found why the directory node_modules was not contained in atom-beautify-0.30.3.tar.gz.
I checked answers of the following link.
How can I manually download packages for atom editor and install them (manually)?
Answer by D3181 included a link to a page of http://discuss.atom.io/ (I could get a helpful answer by Alchiadus from the link) and suggested running apm install in the package's directory. If it is necessary to use a file downloaded from GitHub repository like atom-beautify-0.30.3.tar.gz, it is necessary to run apm install in the package's directory before copying or moving into %HOMEDIRECTORY%%HOMEPATH%\.atom\package (~/.atom/package in case of *nix) of the offline computer.
Decompress the file downloaded from GitHub repository like atom-beautify-0.30.3.tar.gz.
Go into the directory like atom-beautify-0.30.3 of the decompressed result.
Run apm install on an online computer. (If the directory of apm.cmd is not in PATH, run {directory of apm.cmd}\apm.cmd install.)
Rename directory like atom-beautify-0.30.3 to the correct name of the package like atom-beautify.
Move directory with the correct name of the package like atom-beautify into %HOMEDIRECTORY%%HOMEPATH%\.atom\packages of the offline computer.
Run Atom Editor on the offline computer and check if the package works properly.
It seems normal that the directory node_modules is not included the the compressed file downloaded from GitHub repository.
I am working on a remote server using RStudio. This server has no access to the Internet. I would like to install the package "stringi." I have looked at this stackoverflow article, but whenever I use the command
install.packages("stringi_0.5-5.tar.gz",
configure.vars="ICUDT_DIR=/my/directory/for/icudt.zip")
It simply tries to access the Internet, which it cannot do. Up until now I have been using Tools -> Install Packages -> Install from Packaged Archive File. However, due to this error, I can no longer use this method.
How can I install this package?
If you have no internet access on local machines, you can build a distributable source package that includes all the required
ICU data files (for off-line use) by omitting some relevant lines in
the .Rbuildignore file. The following command sequence should do the trick:
wget https://github.com/gagolews/stringi/archive/master.zip -O stringi.zip
unzip stringi.zip
sed -i '/\/icu..\/data/d' stringi-master/.Rbuildignore
R CMD build stringi-master
Assuming the most recent development version is 1.3.1,
a file named stringi_1.3.1.tar.gz is created in the current working directory.
The package can now be installed (the source bundle may be propagated via
scp etc.) by executing:
R CMD INSTALL stringi_1.3.1.tar.gz
or by calling install.packages("stringi_1.3.1.tar.gz", repos=NULL),
from within an R session.
For a Linux machine the easiest way is from my point of view:
Download the release you need from Rexamine in tar.gz format to your local pc. In opposition to the version on CRAN it already contains the icu55\data\ folder.
Move the archive to your target linux machine without internet access
run R CMD INSTALL stringi-1.0-1.tar.gz (in case of release 1.0-1)
You provided the wrong value of configure.vars.
It indicates that you have to give the directory's name, not a final file name.
Correct your code to the following:
install.packages("stringi_0.5-5.tar.gz",
configure.vars="ICUDT_DIR=/my/directory/for/")
Regards,
Sean
Follow the steps below
Download icudt55l.zip seperately from server where you have internet access with
wget http://www.mini.pw.edu.pl/~gagolews/stringi/icudt55l.zip
Copy the downloaded packages to the server where you want to install stringi
Execute the following command
R CMD INSTALL --configure-vars='ICUDT_DIR=/tmp/ALL' stringi_1.1.6.tar.gz
icudt55l.zip is copied to /tmp/ALL
The suggestion from #gagolews almost worked for me. Here's what actually did the trick with RStudio.
Download the master.zip file that will save as stringi-master.zip.
Unzip the file onto your desktop. The unzipped folder should be stringi-master.
Edit the .Rbuildignore file by removing ^src/icu55/data and ^src/icu61/data or similar lines.
Move the folder from your desktop to the home directory of your server.
Create a New Project in RStudio with ~/stringi-master as the Existing Directory
From RStudio's menu, select Build and Build Source Package. (You may need to first select Configure Build Tools. For Project build tools choose Package then select OK.)
It should create a tar.gz file, in the following format: stringi_x.x.(x+1).tar.gz. For example, if the current version of stringi is 1.5.3, it will create version 1.5.4. (I received a few warnings that didn't seem to affect the outcome.)
Move the newly created package to your local repository. Update the repository index. And install the package.