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bzhanglab / WebGestaltR

R package for WebGestalt
https://bzhanglab.github.io/WebGestaltR/
34 stars 14 forks source link

The html looks completely different #42

Closed njbowen closed 5 months ago

njbowen commented 5 months ago

I couldn't verify above as no "link" existed.

Description of the result that you previously got in the original version, and the new result that you got.

The html looks completely different and can't get to the Enrichment Results with the html file. See attached image of WebGestaltR on the left and WebGestaltR-rust on the right. WebGestaltR_vs_WebGestaltR-rust

iblacksand commented 5 months ago

Thank you for reporting the issue with the HTML and the GitHub template.

This is most likely caused by an issue on our end where the necessary JavaScript files were not at the right location. This should be fixed, and you can try reloading the HTML file.

You may need to reset your browser cache with Ctrl+Shift+R (⌘+Shift+R for Mac).

If this does not solve your issue, please let me know.

njbowen commented 5 months ago

this version? devtools::install_github("bzhanglab/WebGestaltR") the installation info has been removed from the github page. the cran version was still the non rust version as of a couple of days ago.

iblacksand commented 5 months ago

That is the right version. You shouldn't have to change anything about the HTML file that you had the issue with in the initial post. If you refresh that HTML file it should load correctly. If that does not fix the error, please let me know.

njbowen commented 5 months ago

i believe the html is fixed as you suggest, as i still see the "new" "We use cookies" alert (in image pasted below, that I hadn't seen until the rust-version, correct?) and suspect that the Project_XXX that I opened was generated with the -rust version. However, I am not sure, as I have many project results folders in the current working dir.

I had removed the rust version, as I was teaching a course and needed it to work with the students' R scripts last week, so we used the previous version of WebGestaltR from CRAN, at the time, the non-rust version, i believe.

Today, I was trying to reinstall the Rust version in it's own micromamba env on mac os Mac info: iMac Retina 4K, 21.5-inch, 2019 Processor 3.2 GHz 6-Core Intel Core Graphics Radeon Pro 555X 2 GB Memory 16 GB 2667 MHz DDR4 Startup disk Macintosh HD macOS 14.4.1 (23E224) with this command in R: R version 4.3.3 (2024-02-29)

devtools::install_github("bzhanglab/WebGestaltR")

and have this error now: ERROR: dependency 'readr' is not available for package 'WebGestaltR'

I had this error last week and not sure how I got around it and actually tested WebGestaltR - rust version....

image

iblacksand commented 5 months ago

This seems like the readr package did not install in your environment. What happens if you install readr independently?

install.packages("readr")

Also, do you have a Mac ARM chip (M1, M2, etc)? If so, do you have the ARM version of R installed? I am not sure of the underlying code in the readr package, but if you have the Intel version of R and an ARM chip in your computer, this could cause an installation issue.

iblacksand commented 5 months ago

Also the HTML file is generated with the Rust version, which is good news. The cookie notification will only appear in the new Rust-based package.

njbowen commented 5 months ago

It's a intel iMac and R gets installed automatically in the micromamba env, but I'll check to see if that's an issue. No ARM stuff yet. These errors are only showing up for R inside of conda/mamba/micromamba envs, so maybe it is a compatibility thing with R and the packages, or something similar as you suggest.
even with installing just readr, I get the same tzdb, vroom and readr errors: Warning messages: 1: In install.packages("readr") : installation of package 'tzdb' had non-zero exit status 2: In install.packages("readr") : installation of package 'vroom' had non-zero exit status 3: In install.packages("readr") : installation of package 'readr' had non-zero exit status

last question(s), will the default, CRAN, version eventually change to the rust version? or will there always be the pre-Rust and post-rust options for webgestaltR? i noticed the name is the same now both versions as WebGestaltR . also saw the alternate/diff web url beginning with 2024., how will that work? thanks and all the best, -

iblacksand commented 5 months ago

It is interesting that readr is not installing correctly. The readr github page suggests installing tidyverse, which will install readr along with it.

# The easiest way to get readr is to install the whole tidyverse:
install.packages("tidyverse")

Perhaps that can fix the installation problem. I am not familiar with mamba, but there appears to be a package that you can use from conda-forge/r-readr-feedstock.

conda config --add channels conda-forge
conda config --set channel_priority strict

mamba install r-readr

For the last question, we aim to upload the new R Package to CRAN, but it will require some configuration changes on our end, as CRAN has different policies for packages using Rust.

2024.webgestalt.org is the new version of webgestalt that uses the new Rust package in the backend, along with new features, such as the ability to run analysis with multiple lists at a time.

The gene set data has also been updated. We are keeping 2024.webgestalt.org on the separate URL for the time being, as the new data will change the results of the analysis, and we want to give users time to transition to the new version. Over time, 2024.webgestalt.org will become www.webgestalt.org, and the current website will move to 2019.webgestalt.org.

If you want to use the new data, you can add hostName = "https://2024.webgestalt.org" as a parameter to the WebGestaltR function. I'll add this to the documentation as well.