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drieslab / Giotto

Spatial omics analysis toolbox
https://drieslab.github.io/Giotto_website/
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Giotto installation Error: object 'get_dimReduction' is not exported #941

Closed jiangzh-coder closed 1 month ago

jiangzh-coder commented 2 months ago

Hi

i used newest installation steps from "https://drieslab.github.io/Giotto_website/articles/ecosystem.html", then i tried to install "SgsAnnDataV2" from "https://github.com/bio-xtt/SgsAnnDataV2".

Necessary for installation from R

if(!"pak" %in% installed.packages()) { install.packages("pak") } pak::pkg_install("drieslab/Giotto") pak::pkg_install('drieslab/GiottoClass') pak::pkg_install('drieslab/GiottoUtils') pak::pkg_install('drieslab/GiottoVisuals') pak::pkg_install('drieslab/GiottoData')

Ensure Giotto Suite is installed

if(!"Giotto" %in% installed.packages()) { pak::pkg_install("drieslab/Giotto") } library(Giotto)

Ensure Giotto Data is installed

if(!"GiottoData" %in% installed.packages()) { pak::pkg_install("drieslab/GiottoData") } library(GiottoData)

Ensure the Python environment for Giotto has been installed

genv_exists = checkGiottoEnvironment() if(!genv_exists){

The following command need only be run once to install the Giotto environment

installGiottoEnvironment() } library(Giotto)

devtools::install_github("bio-xtt/SgsAnnDataV2") ############However, i met following errors: Error: object 'get_dimReduction' is not exported by 'namespace:Giotto' Execution halted ERROR: lazy loading failed for package 'SgsAnndata2023'

########the 2nd error is: when i tried to load " Failed with error: ‘lazy-load database 'C:/Users/zhou_/AppData/Local/R/win-library/4.3/Giotto/R/Giotto.rdb' is corrupt’

Thank you and Best wishes Jiang

josschavezf commented 1 month ago

Hi @jiangzh-coder we have made several recent updates to the package, are you still facing this issue?

jiajic commented 1 month ago

get_dimReduction() is a deprecated function that has since been made internal. The new exported function that replaces it is getDimReduction(). From the discussion on SgsAnnDataV2, it looks like this should be resolved with their newest version.