Comments (18)
Hi @Dahlia90
Are you sure you ran this command to install nichenetr?
devtools::install_github("saeyslab/nichenetr")
This should work for R 4.0.2 (I tested it on Windows 10 and Ubuntu 20.04). If not, please give your R ``sessionInfo()` details.
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Hi @Dahlia90
Can you tell me whether you are able to install other packages from github via devtools::install_github to check whether it is a devtools/github or nichenetr problem?
Recently, another Mac user had problems installing nichenetr as well (#42)
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Hi @Dahlia90
Could you maybe try to install nichenetr from an older R version (3.6.X or 4.0.0? - I know from a colleague that it gets installed when having R 4.0.0) to check whether this is an R version problem?
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OK, then it seems it has more likely something to do with your pc settings. I would suggest comparing them to your colleague's and trying to find the issue by doing that. I am sorry that I cannot give any further recommendations to try out to. If you would be able to solve the issue, it would be nice that you let us know here how you did it, because probably some other people might get stuck with the same problem.
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And can you give the exact error message?
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Hi @Dahlia90
(1): nichenetr is not on CRAN, so this will never work
(2): did you install limma via BiocManager::install("limma")
? and can you afterwords load the package library(limma)
? If both answers are yes, maybe it could be useful to check out this issue hunzikp/velox#30. If those tips would still not work, you could clone the nichenetr directory so you get the repo locally and then install it locally from within R studio.
(3): running a devtools command in bash will not work, so you would need to run R first, and then fix the typos in “sayeyslab/nitchnetr” to "saeyslab/nichenetr”
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Hi @Dahlia90
Thank you for pointing this out, but this is just a warning and not an error, and not a reason why this failed.
But here you again installed from github. I would try to install it locally as follows: clone the directory from github --> go to the nichenetr directory --> open the nichenetr R project in Rstudio --> go to 'Build' in Rstudio --> 'Install'
and see whether this gives the same error message.
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Hi @Dahlia90
Sorry it did not work. Unfortunately for you and me, this error message is not really helpful. I have no idea what is going on. By looking around the web for possible solutions, I did not come across any directly but I can give some suggestions to try out:
*The error 1900 Killed: 9 points to a non-nichenetr problem, but probably to an error in the combination Mac-Rstudio-nichenetr (it seems that issues with Rstudio, Rstudio Cloud/Server, Docker, Conda, ... could be occuring).
If you were installing nichenetr from RStudio, I would
- first try to install nichenetr from a clean R session on the command line (so: open terminal --> launch R 4.0.2 --> devtools::install_github("saeyslab/nichenetr").
- If that fails, and you have a form of Conda (e.g. Miniconda) installed on your computer, maybe remove it and then try to install nichenetr again
- if that still fails: try reinstalling R and RStudio (downloading R from CRAN, and RStudio from rstudio.com), then install nichenetr (try Rstudio and R via terminal).
- if that still fails: check the DESCRIPTION page of nichenetr and install each of the dependencies separately and then try to install nichenetr again.
If all these steps still failed:
you can check following sites for more information and see whether they might be useful for you:
- https://github.com/jacobxk/setup_macOS_for_R
- https://stackoverflow.com/questions/19533220/cannot-install-r-package-from-source-in-mac-osx-maverick
- https://community.rstudio.com/t/killed-error-during-installation-for-many-packages/24239/8
- https://stackoverflow.com/questions/58473798/macos-rstudio-accessing-wrong-clang-after-upgrade-to-catalina
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Related Issues (20)
- Inquiry about Signaling and Gene Regulatory Networks Data in Omnipath and NicheNet HOT 1
- Query: AUPR HOT 1
- Error while plotting a ligand-receptor interaction network
- Error running nichenet_seuratobj_aggregate on v5 Seurat obj HOT 7
- Assistance Needed: nichenetr Package Installation Error in R
- Zenodo Data Inquiry HOT 1
- Identifying bonafide ligand-receptor pairs in the updated ligand-receptor database (V2)
- SeuratV5 HOT 4
- Error finding log fold change information of ligands from sender cells (Seurat V5 object) HOT 6
- How exactly the ligand activity were calculate? HOT 1
- I cannot run the "get_weighted_ligand_receptor_links" and "prepare_ligand_receptor_visualization" while I have nichnetr installed HOT 2
- Preferable metric to infer cell-to-cell communication HOT 1
- what is ligand_tf_matrix for?? HOT 1
- `get_exprs_avg` changes underscore to hyphen in cell type names
- How to choose the best ligand to continue analysis with the potential ligand?
- How should I assign a pathway/pathways to the target genes when running nichenetr? HOT 3
- cannot complete assign_ligands_to_celltype HOT 2
- missing function for circos plot visualization HOT 2
- I can't install nichenet HOT 1
- Condition_colname is not used for subsetting in nichenet_seuratobj_aggregate HOT 2
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