Installation using pak::pkg_install("omnideconv/spacedeconv", dependencies=TRUE) not working

[joan-yanqiong]

Hello,

I'm trying to install the spacedeconv package and all its dependencies. However it seems that the Seurat version and R versions are clashing. I'm using a conda/mamba environment.

First I used the R-version 4.4.1 for installation, but got the following error:

r$> pak::pkg_install("omnideconv/spacedeconv", dependencies=TRUE)
✔ Updated metadata database: 3.09 MB in 7 files.                         
✔ Updating metadata database ... done                          
Error:                                                                      
! error in pak subprocess
Caused by error: 
! Could not solve package dependencies:
* omnideconv/spacedeconv: Can't install dependency Seurat (<= 4.4.0)
Type .Last.error to see the more details.

Then I used

mamba install -c conda-forge r-seurat=4.4.0

this installed the R-version 4.3.3, after which I retried the pak command:

r$> pak::pkg_install("omnideconv/spacedeconv", dependencies=TRUE)

✔ Updated metadata database: 1.46 MB in 1 file.                          
✔ Updating metadata database ... done                          
Error:                                                                      
! error in pak subprocess
Caused by error: 
! Could not solve package dependencies:
* omnideconv/spacedeconv: Can't install dependency drieslab/Giotto
* drieslab/Giotto: Needs R >= 4.4.1
Type .Last.error to see the more details.

Therefore I tried to do the following:

mamba install -c conda-forge "r-seurat<=4.4.0" r-base=4.4.1

Which led to the following log:

The following packages are incompatible
├─ r-base 4.4.1**  is requested and can be installed;
└─ r-seurat <=4.4.0  is not installable because there are no viable options
   ├─ r-seurat [3.1.0|3.1.1|...|3.1.5] would require
   │  └─ r-base >=3.5,<3.6.0a0 , which conflicts with any installable versions previously reported;
   ├─ r-seurat [4.3.0|4.3.0.1|4.4.0] would require
   │  └─ r-base >=4.3,<4.4.0a0 , which conflicts with any installable versions previously reported;
   ├─ r-seurat [3.1.0|3.1.1|...|3.2.3] would require
   │  └─ r-base >=3.6,<3.7.0a0 , which conflicts with any installable versions previously reported;
   ├─ r-seurat [3.1.5|3.2.0|...|4.1.1] would require
   │  └─ r-base >=4.0,<4.1.0a0 , which conflicts with any installable versions previously reported;
   ├─ r-seurat [4.0.2|4.0.3|...|4.3.0] would require
   │  └─ r-base >=4.1,<4.2.0a0 , which conflicts with any installable versions previously reported;
   ├─ r-seurat [4.1.1|4.2.0|...|4.4.0] would require
   │  └─ r-base >=4.2,<4.3.0a0 , which conflicts with any installable versions previously reported;
   └─ r-seurat [1.4.0.16|2.2.0|...|4.4.0] conflicts with any installable versions previously reported.

So I hope someone can help me to install pak::pkg_install("omnideconv/spacedeconv", dependencies=TRUE).