the similar error occurs every time for packages like dplyr,data.table.
If you can't or don't want to make the default folder writeable (often we don't want that, depending on where it is), then choose a great spot on your computer where you want the libraries you install and then place this in your .Rprofile file (often in your My Documents folder
.libPaths("full path to your personal library folder")
This will not overwrite the default .libPaths; it will just append your personal folder to the folders that R knows about already (so it can still find the system installed libraries)
Related
I am working under linux/unix (ubuntu centos darwin)
I often build from source and install my biotools folders in a non-canonical place in order to have full write access to that place for all users and also to avoid overwriting/conflicting with important files placed by the OS in /usr/... and /usr/local/...
I put the tool build folders in /opt/biotools and alias all exe files in /opt/biotools/bin (which is in my PATH)
Now some apps need to access dependencies or libraries usually written in /usr/local/share or /usr/local/lib, ...
Is it possible to add such folders like /opt/biotools/share, /opt/biotools/lib, ... and have the system find them?
Should I add these folders to the PATH?
Thanks for your help
I have a "copy deployed" installation of R with no R-specific environment variables set.
I want to source a file from within Rprofile.site:
source("how/to/find/this/file/my_settings.R")
Where could I place my my_settings.R file so that it can be found from within Rprofile.site no matter in which path Rprofile.site is installed?
BTW: I want to avoid an absolute path to my_settings.R this would work indeed. I'd prefer to use the same folder as Rprofile.site or a path relative to it to support copy deployment of R.
Edit 1: The problem is that getwd is always different depending on the current folder from which you start R
If you can't use absolute paths and that your working directory is not stable, one way is to use .libPaths or .Library.
By default your Rprofile should be in directory paste0(.Library,"/../etc/") or paste0(.libPaths()[2],"/etc/") so you can put your file there and source it with :
source(paste0(.Library,"/../etc/my_settings.R"))
source(paste0(.libPaths()[2],"/etc/my_settings.R"))
As far as I understand the first option is stable (I don't think one can change the value of .Library).
If you use the second option just make sure that if in the future you alter your .libPaths() you do it after sourcing your file.
See ?.libPaths for more info on default folders.
I want to remove the meteor installation from my meteor project directory while keeping my source code intact, so that I can archive the project without the installed packages. I also want the package configuration to be retained in the archive so that I can re-install the project without having to re-add and re-remove the packages again.
How do I do this?
Meteor already creates a .gitignore file for you. That file tells you everything that should be archived. So you can simple look at that file and only archive that (either by deleting everything else, or just writing a script that reads the .gitignore file and interprets it). Alternatively, of course, you could just add everything to git (in which case git will interpret the .gitignore file for you), and then create an archive from the git repo.
Of course, that .gitignore file only excludes .meteor/local, so as Kyll already said, you could just delete that folder.
I am working with a "factory fresh" version of RStudio on Windows 7. R is installed under C:/Program Files which means the default libraries are stored here, and the two locations contained in .libPaths() on startup are both within this folder.
I want to work with another R library (igraph). Since the C:\Program Files folder is write-protected, I have set up another area to work in: C:\Users\nick\R and installed the igraph library in C:\Users\nick\R\library. I can manually add this location to the .libPaths() variable and use the library with no problems.
However, my problem is getting RStudio to automatically add this location to the .libPaths() variable on startup. I read that I could add the relevant command to my .Rprofile file - but I couldn't find any such file (presumably they are not automatically created when RStudio is installed). I then created a file called .Rprofile containing only this command. This only seemed to work when the .Rprofile file was saved in C:\Users\nick\Documents (which is the path stored in both the R_USER and HOME environmental variables). What I would like is to have the .Rprofile file stored in C:\Users\nick\R.
I have read all the information in ?Startup and it talks about where to store commands that run on startup. But I just can't make this work. For example there seems to be no way to change the location of the home directory without reading a file stored in the home directory. I don't seem to have any .Renviron files and creating these myself doesn't seem to work either.
I would really appreciate an answer in simple terms that explains how I could go about changing where the .Rprofile file is read from.
In Windows, you set the R_USER profile by opening up a command line and running:
SETX R_PROFILE_USER "C:/.../.Rprofile"
Where (obviously) the path is the path to your desired .Rpofile. In R, you can check that it worked:
Sys.getenv("R_PROFILE_USER")
Should return the path you specified. Note that you likely need to have all R sessions closed before setting the R_USER variable.
Just assume we are installing some libraries from its source distributed by the way GNU promoted. When using "./configure --prefix" to specify where to install.
(1) does Make generate the binaries under the current directory? Does Make install then copies them from the current directory (which is from where Make is run) to $prefix? If the answers are yes, I have two questions, each for different cases.
(2) when the current directory and $prefix are not the same, can I remove all the files generated by Make under current directories to save some space?
(3) when the current directory and $prefix are the same, will make install do nothing or copy the files to themselves? Can I just skip the make install step?
The answer to your first question is probably yes.
As for the rest, you may find a make clean which will tidy up the files created by the initial make.
I think the makefile will be able to handle the situation where current directory and $prefix are not the same, and do the right thing.
The current directory would not usually be the destination of files created by makefiles.
(of course it depends on how the makefile is written, so I can't give definite answers, but I've generally been impressed with the makefiles I've used)
You are absolutely right: make just creates files in current directory and make install copies it to the destination directories, based on $prefix and other variables maintained by configure script.
You can wipe out the whole directory you've ran the build at. It will not be used, because, well, that's what "install" means: you build in one directory and the the files are placed in the proper places of your system.
Usually install destination and the directory you build in differ. The hierarchy of the files being installed usually do not relate to directory hierarchy of the build system. Just install to the other dir: it's cheap to create just yet another directory.