Please, how can I get "GraphClusterAnalysis" package installed? I am trying to use the "Highly connected sub graphs" (HCS) clustering algorithm for my data. I have tried to use install.packages() for the installation but I keep getting: package ‘GraphClusterAnalysis’ is not available (for R version 3.0.3).
I was able to use a method called "highlyConnSG()" for the HCS clustering algorithm which I retrieved after installing "RGBL" and "graph" packages from source "https://biconductor.org/bioLite.R". So to install those packages, type in the R environment command line:
source("https://biconductor.org/biocLite.R")
biocLite("RBGL")
biocLite("graph")
As far as I can see, this is a library, written by the authors of the book ( https://www.csc2.ncsu.edu/faculty/nfsamato/practical-graph-mining-with-R/PracticalGraphMiningWithR.html ).
Also on this page is provided the link to the archive with this library itself (here is the link: https://www.csc2.ncsu.edu/faculty/nfsamato/practical-graph-mining-with-R/R-code/GraphClusterAnalysis.zip ).
So you can load this library and after that you can try to install the library from source. Here is the stackoverflow question about how to do it:
How do I install an R package from source?
Nevertheless, as for me I wasn't successful in installing it from source.
Related
Downloaded package from below URL.
Attempted to install using below command; response shown.
library(dalton.rqi,lib.loc='/home/X/Desktop/')
Error: package ‘dalton.rqi’ was built before R 3.0.0: please re-install it
https://my.clevelandclinic.org/departments/anesthesiology/depts/outcomes-research/risk-quantification
It appears this is a compiled package that maybe I don't have the source for? Is there a way to force install of the package? I'm unable to install using Rstudio GUI in its current form as a zip. Tried repackaging to tar.gz has Rstudio was looking for and also had a non-zero exit status error.
Any ideas?
I'm afraid this can't be achieved directly. The error message says it well: to use a package in R it needs to be built on an R version matching yours.
I can suggest two ways to move forward:
Contact the authors, ask for the R sources (it is somewhat surprising they did not make them available in the first place), and build the package yourself.
Downgrade your R version as far back as needed to match the one this pre-built package used.
I want to install a package named "locClass" in R but always failed and kept getting the following warning:
install.packages("locClass", repos="http://download.r-forge.r-project.org/")
Package which is only available in source form, and may need compilation of C/C++/Fortran: ‘locClass’
These will not be installed
The install command is referred to: https://r-forge.r-project.org/R/?group_id=1187
Also, I downloaded the package source from the above website. But R returned the following:
library(locClass)
Error in library(locClass) : ‘locClass’ is not a valid installed package
My R version is 3.3.3. I tried the 3.4.0 but failed the same way.
This is not exactly a solution but an alternative to utilize functionality of package locClass. Download the package file of locClass from here and source(functions.R) present here. This way you can use all functions available in package.
Note : function.R means FLXMCL.R, FLXMCLconstant.R etc.
I'm still looking for a better solution but this is a temporary alternative.
My R package vignette uses tikz/pgf graphics. The R CMD check command throws an error message on operating systems where the LaTeX package tikz/pgf is not installed. On a vanilla Ubuntu system, for example, the Ubuntu package 'pgf' must be installed for R CMD check to complete without an error message. The CRAN servers seem to have tikz/pgf installed, but I cannot make sure this is always and everywhere the case. Is there any way I can add a dependency on pgf to the DESCRIPTION file of my R package? Can I just add it to the 'Depends' field (even though it is not an R package)? I would not like to trash the diagram because the package vignette is an article that was published in the Journal of Statistical Software, and I would like to use it as a vignette without any modification.
From http://cran.r-project.org/doc/manuals/R-exts.html#The-DESCRIPTION-file :
Other dependencies (external to the R system) should be listed in the ‘SystemRequirements’ field, possibly amplified in a separate README file.
There won't be any automatic check or informative error message generated by the R installation process, but at least the information will be stored in a consistent place ...
I installed BQuant package in my windows system.When I loaded the package it showed the following error Error: package ‘BQuant’ is not installed for 'arch=i386' . Can anyone please sort it out.If not is there any other packages for NMR analysis in R.
Since according to your recent other question you are only interested in a good peak detection algorithm, you could get the code of the relevant functions directly from the package source (look in folder R inside the zip).
I installed a R package as suggested by How do I install an R package from source?, using R CMD INSTALL [my_pkg_path.tgz]. Package sources are downloaded from r-project.org, e.g., http://cran.r-project.org/web/packages/fields/index.html
However, when I try to load the package using say library(fields), I got the error that complains the package are built for universal-apple-darwin:
Error: package ‘fields’ was built for universal-apple-darwin9.8.0
Guess it's something to do with architecture, but no idea how to resolve it. Any idea? Thanks.
It looks like you downloaded the package's Mac OSX binary file, which usually ends in .tgz - try downloading the package source (usually something ending in .tar.gz) and installing the package again.
Depending on what your operating system is, you may need an additional set of software before you can install packages from source. If the above suggestion doesn't work, would you provide some information about the OS, for example from sessionInfo()?