Stereo-seq tutorial: Error in Giotto::anndataToGiotto(anndata_file) : object 'sc' not found

[MatteoRiva95]

Describe the Error

I would like to run the Giotto tutorial for Stereo-seq spatial analysis (https://giottosuite.readthedocs.io/en/latest/subsections/datasets/SSeq-E12-5_E1S3-Tutorial.html). Maybe I am just missing something. I tried with another Stereo-seq .h5ad file, but the same error is still present.

Error Message

I am just running the first lines of the tutorial:

if(!"Giotto" %in% installed.packages()) { devtools::install_github("drieslab/Giotto@suite") }

library(Giotto) genv_exists = checkGiottoEnvironment() if(!genv_exists){ installGiottoEnvironment() }

anndata_download = "https://zenodo.org/record/7323947/files/E12.5_E1S3_bin200.h5ad?download=1" anndata_file = "E12.5_E1S3_bin_200.h5ad" download.file(anndata_download, anndata_file)

stereo_go <- Giotto::anndataToGiotto(anndata_file)

But I get this error:

Error in Giotto::anndataToGiotto(anndata_file) : object 'sc' not found

System Information

Platform: x86_64-pc-linux-gnu Rversion: 4.4.0 Giotto version: 1.1.2

[josschavezf]

Hi @MatteoRiva95 I see you are using an old version of Giotto, could you please update to the most recent version (4.0.8) and let us know if you still have this error?

[MatteoRiva95]

Update, after updating to Giotto 4.0.8 and forcing the use of python under the giotto conda env with: Sys.setenv(RETICULATE_PYTHON="~/.local/share/r-miniconda/envs/giotto_env/bin/python") now I get this error instead: Error in py_call_impl(callable, call_args$unnamed, call_args$named) : UnboundLocalError: local variable 'adata' referenced before assignment Of note, after reinstalling the giotto env from scratch I received the following error: Warning in .py_install_prompt(package = package, env = env) : Python packagescanpyis required and not installed. fixed by activating the env and manually installing scanpy.

[MatteoRiva95]

Hi @josschavezf do you have any news or solution about this error? Thank you in advance

[josschavezf]

hi @MatteoRiva95, It seems like the issue is solved in the development version (4.0.9), you can install it using remotes::install_github("drieslab/Giotto@suite_dev") if it asks for the development version of the other modules, you can install them with remotes:: install_github("drieslab/GiottoUtils@dev") install_github("drieslab/GiottoClass@dev") install_github("drieslab/GiottoVisuals@dev") We will release the new version in the main branch of the repositories in a few days.

[MatteoRiva95]

@josschavezf Thank you for your reply. I tried to run your command as you suggested. Unfortunately, it returns: Error: C stack usage 7975364 is too close to the limit Execution halted I tried to change with ulimit -f unlimited and I tried to change the /etc/security/limits.conf with:

• soft stack 65535
• hard stack 65535

but it keeps returning the same error. Do you know how to solve it, please? Otherwise, I will wait for the 4.0.9 version. Thank you again

[josschavezf]

@MatteoRiva95 It seems to be related to a recursive calling of functions. Try installing first the individual modules and the main Giotto at the end. GiottoUtils -> GiottoClass -> GiottoVisuals -> Giotto.

[MatteoRiva95]

@josschavezf I tried to run remotes:: install_github("drieslab/GiottoUtils@dev") --> remotes::install_github("drieslab/GiottoClass@dev") --> remotes::install_github("drieslab/GiottoVisuals@dev") --> remotes::install_github("drieslab/Giotto@suite_dev"), but unfortunately every one of these commands still returns the same error:

Error: C stack usage 7971252 is too close to the limit Execution halted

[josschavezf]

@MatteoRiva95 try using the pak package instead of remotes

install.packages("pak")

pak::pkg_install("drieslab/GiottoUtils@dev") pak::pkg_install("drieslab/GiottoClass@dev") pak::pkg_install("drieslab/GiottoVisuals@dev") pak::pkg_install("drieslab/Giotto@suite_dev")

If this option doesn't work, an alternative is downloading the repositories and installing them from the local directory.

[MatteoRiva95]

@josschavezf I tried what you suggested, but unfortunately it returns this error:

pak::pkg_install("drieslab/GiottoUtils@dev") Error in pak::pkg_install("drieslab/GiottoUtils@dev") : lazy-load database '/mnt/HDD1/R/x86_64-pc-linux-gnu-library/4.1/pak/R/pak.rdb' is corrupt In addition: Warning messages: 1: In pak::pkg_install("drieslab/GiottoUtils@dev") : restarting interrupted promise evaluation 2: In pak::pkg_install("drieslab/GiottoUtils@dev") : internal error 1 in R_decompress1 with libdeflate

Anyway, I followed your previous suggestions for Giotto installation with my boss and on his ws it works! We do not understand why it doesn't with me. So probably is a my setting problem. Thank you so much for your support @josschavezf , really appreciated!!