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xlucpu / MOVICS

Multi-Omics integration and VIsualization in Cancer Subtyping
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Package won't install #5

Closed prvst closed 3 years ago

prvst commented 3 years ago

Hi, I tried to install MOVICS but could not do it because one of the dependencies is now deprecated and not available for R's latest version.

Error: Failed to install 'MOVICS' from GitHub: (converted from warning) package ‘SNFtool’ is not available for this version of R

The package SNFtool was removed from CRAN.

xlucpu commented 3 years ago

Hi, Sorry I just noticed your message. Currently, please install SNFtool independently from installing MOVICS. You can download the compressed file and install SNFtool locally (https://cran.r-project.org/src/contrib/Archive/SNFtool/), or use the following commond to install SNFtool in your R platform.

if (packageVersion("devtools") < 1.6) {
  install.packages("devtools")
}
devtools::install_github("maxconway/SNFtool")

I will update MOVICS to solve this issue ASAP.

Thank you for this.

xlucpu commented 3 years ago

I have updated the MOVICS (0.99.14) and please check if it can be installed.

prvst commented 3 years ago

Hi. Thanks for replying. I tried installing SNFTool manually as you said, but unfortunately, that also fails, see below:

ERROR: dependency ‘heatmap.plus’ is not available for package ‘SNFtool’

Apparently, heatmap.plus is also deprecated and removed from CRAN.

xlucpu commented 3 years ago

Dependencies must by installed when you have to install a package manually which means you have to install "heatmap.plus" first. If this package has other dependencies, you have to install them one by one manually.

Anyway. I have updated MOVICS and please check if it can be installed now.

prvst commented 3 years ago

Sorry, still not able to install it. ERROR: dependencies ‘SNFtool’, ‘ridge’ are not available for package ‘MOVICS

Also, the heatmap.plus package is not available anymore, not even in GitHub, so SNFTool cannot be installed.

xlucpu commented 3 years ago

I understand this situation.

In this manner MOVICS can be only installed given that you have heatmap.plus installed already. Therefore, please refer to https://cran.r-project.org/src/contrib/Archive/heatmap.plus/ and install heatmap.plus from local.

As for ridge package, please refer to ToubleShooting at the MOVICS main page. I summaried the solusion if you are using MacOS system.

Since MOVICS depends on a lot of external R package, I cannot make sure all these dependencies are constantly in maintain. Thus, the bottom line to get MOVICS installed is to make sure that you have all the dependencies installed.

prvst commented 3 years ago

Thanks. I had to go through a few other dependencies that are missing or not available, but after a couple of hours, I installed them.