There is an issue regarding installation of COMUNET on up to date distribution, namely with the dependencies on ComplexHeatmap and SDMTools.
Environment
I tested installation on R versions 4.1.1, 4.2.0 and 4.2.1, but I expect similar problems occuring on all versions >3.6.2
Expected behaviour
When using the command given in the installation section
devtools::install_github("ScialdoneLab/COMUNET/COMUNET")
COMUNET and its dependencies should be installed.
Actual behaviour
R tries to install COMUNET but fails to install the above mentioned dependencies.
Suggestion
Adding the used functions from the two packages directly into COMUNET would solve the issue. Another option would be to get it working and find a way to add COMUNET to CRAN to also avoid similar issues occuring in the future.
Workaround
It is possible to just download the R files from the Github and manually inserting them into the used R files using source(). When using functions depending on ComplexHeatmap and SDMTools, these can also be downloaded and included (here and here.
Another way without manually including all files is installing the dependencies directly and afterwards installing COMUNET:
-
It is possible to install ComplexHeatmap manually using
``if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ComplexHeatmap")``
as given here
-
SDMTools gives more trouble, as it doesn't exist on CRAN anymore. There are three possible ways to install it:
-
One can try the method mentioned here: install.packages("remotes") remotes::install_version("SDMTools", "1.1-221")
This didn't work for me.
-
If Rtools is installed it may be possible to directly download and build the .tar.gz files. This also didn't work for me.
-
Lastly one can try to install SDMTools using the Github mirror:: devtools::install_github("cran/SDMTools)")
After one verified that these two are installed it is possible to use the command from the installation section and install COMUNET.
There is an issue regarding installation of COMUNET on up to date distribution, namely with the dependencies on ComplexHeatmap and SDMTools.
Environment
I tested installation on R versions 4.1.1, 4.2.0 and 4.2.1, but I expect similar problems occuring on all versions >3.6.2
Expected behaviour
When using the command given in the installation section
devtools::install_github("ScialdoneLab/COMUNET/COMUNET")COMUNET and its dependencies should be installed.
Actual behaviour
R tries to install COMUNET but fails to install the above mentioned dependencies.
Suggestion
Adding the used functions from the two packages directly into COMUNET would solve the issue. Another option would be to get it working and find a way to add COMUNET to CRAN to also avoid similar issues occuring in the future.
Workaround
It is possible to just download the R files from the Github and manually inserting them into the used R files using
source(). When using functions depending on ComplexHeatmap and SDMTools, these can also be downloaded and included (here and here.Another way without manually including all files is installing the dependencies directly and afterwards installing COMUNET:
It is possible to install ComplexHeatmap manually using
``if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("ComplexHeatmap")``
as given here
SDMTools gives more trouble, as it doesn't exist on CRAN anymore. There are three possible ways to install it:
One can try the method mentioned here:
install.packages("remotes") remotes::install_version("SDMTools", "1.1-221")This didn't work for me.
If Rtools is installed it may be possible to directly download and build the .tar.gz files. This also didn't work for me.
Lastly one can try to install SDMTools using the Github mirror::
devtools::install_github("cran/SDMTools)")After one verified that these two are installed it is possible to use the command from the installation section and install COMUNET.