CreateSeuratObject

[Dalhte]

Hello there
I have a problem with CreateSeuratObject (it was functioning just fine up until some massive librairies update)

Here is the code :
###Download RNA data

Load data PG2

filt.matrixPG2 <- Read10X_h5("/media/david/F/RN7.2/PG2RN7/outs/filtered_feature_bc_matrix.h5",use.names = T)
raw.matrixPG2 <- Read10X_h5("/media/david/F/RN7.2/PG2RN7/outs/raw_feature_bc_matrix.h5",use.names = T)
cts.raw.matrixPG2 <- raw.matrixPG2$Gene Expression
cts.filt.matrixPG2 <- filt.matrixPG2$Gene Expression

#Soupx
#quick clustering

sratPG2 <- CreateSeuratObject(counts = cts.filt.matrixPG2)

And the error :

sratPG2 <- CreateSeuratObject(counts = cts.filt.matrixPG2)
Avis : Feature names cannot have underscores ('_'), replacing with dashes ('-')
Erreur dans .Call("CRsparse_colSums", x, na.rm, FALSE, sparseResult) :
"CRsparse_colSums" not resolved from current namespace (Matrix)

I tried to reupload the Matrix package but it's not doing anything.
Can you help ?
Best David

[Dalhte]

I found the problem but still don't know the reason 👍 As I do multiomic analysis I also use the

library(TFBSTools)
And that is the only line when activated creating the problem. When I deactivate it, everything is running just fine!

[mhkowalski]

Hi,

This is a known issue with TFBS tools package (which we've reported here) Not loading the TFBStools package will fix it in the mean time.

[Gesmira]

Hi,
It seems that this issue is a result of incompatible updates of CRAN and Bioconductor packages. Although we haven't precisely diagnosed it, we have been able to fix this issue with the following steps:

• Ensure you have R version 4.3 or update to it.
• In a fresh R session, update Bioconductor with the following call:

BiocManager::install(version = "3.18")

• When prompted if you would like to update all packages, say yes. This will then update a series of Bioconductor packages which may take up to an hour.

At this point, the issue should be fixed. Let us know if you continue to encounter problems.

[Kamilloo1234]

Hi, It seems that this issue is a result of incompatible updates of CRAN and Bioconductor packages. Although we haven't precisely diagnosed it, we have been able to fix this issue with the following steps:

* Ensure you have R version 4.3 or update to it.

* In a fresh R session, update Bioconductor with the following call:

BiocManager::install(version = "3.18")

* When prompted if you would like to update all packages, say yes. This will then update a series of Bioconductor packages which may take up to an hour.

At this point, the issue should be fixed. Let us know if you continue to encounter problems.

Hi, I also have the same problem even if I do:
BiocManager::install(version = "3.18") and I updated all needed packages, too.

When I run
FindMarkers(sample.combined, ident.1 = 'Microglia_A', ident.2 = 'Microglia_B')
I am getting the error

Error in .local(x, na.rm, dims, ...) :
Object 'CRsparse_rowSums' not found

A month ago, everything worked perfect, when I loaded my saved workspace and did "FindMarkers" :-(

What else can we do?

[sgolomb]

Hello, I am also still having this problem when trying to execute RunUMAP after trying BiocManager::install(version = "3.18"), updating packages and uninstalling the Azimuth package.

I am experiencing this problem on both non-integrated and integrated reductions in my Seurat object.

Same error as reported above:
Error in .local(x, na.rm, dims, ...) :
object 'CRsparse_colSums' not found

[dcollins15]

An updated solution is available here.

Upgrading Bioconductor to v3.18 may have resolved this issue if in the process TFBSTools was rebuilt using the latest Matrix. The linked solution should hopefully work for folks who are still struggling.

[Plasmiddddd]

Hey! I tried all above include update Bioconductor, reinstall TFBSTools, and update all packages; Unfortunately, None of them work. The only way I found is not to load the Azimuth package.