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Error in validityMethod(as(object, superClass)) : object 'CsparseMatrix_validate' not found #6746

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mianmianyin opened this issue Dec 3, 2022 · 46 comments
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Error in validityMethod(as(object, superClass)) : object 'CsparseMatrix_validate' not found #6746

mianmianyin opened this issue Dec 3, 2022 · 46 comments
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bug Something isn't working

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@mianmianyin
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hi, there is one error. how can i solve the problem?
Error in validityMethod(as(object, superClass)) :
object 'CsparseMatrix_validate' not found
@mianmianyin mianmianyin added the bug Something isn't working label Dec 3, 2022
@dhkong78
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dhkong78 commented Dec 3, 2022

Did you solve the problem? I met the same error.

@mianmianyin
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Did you solve the problem? I met the same error.

no

@ykbio
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ykbio commented Dec 4, 2022

I got the same error.
My R version is 4.2.2.
I installed Seurat today, and got the error while testing with the "2,700 PBMCs" tutorial.

@mianmianyin
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I got the same error. My R version is 4.2.2. I installed Seurat today, and got the error while testing with the "2,700 PBMCs" tutorial.

My R version is also 4.2.2. i also reinstalled Seurat

@chishiba0520
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I have the same question. You should update your 'Matrix' package to 1.5.3 version to follow up with the nearest version of Seurat.

@dhkong78
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dhkong78 commented Dec 5, 2022

Did you solve the problem? I met the same error.

no

I solved this by uninstalling the "Matrix" package and re-installing it.

@ykbio
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ykbio commented Dec 6, 2022

Thanks to all. I also solved this issue by re-installing the "Matrix" package.

@yuhanH
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yuhanH commented Dec 16, 2022

Thank you @chishiba0520 for solving this issue.

@yuhanH yuhanH closed this as completed Dec 16, 2022
@chen-peng-1874
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Hi all! I updated my Matrix, and the problem is still there.

@dhkong78
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dhkong78 commented Jan 16, 2023 via email

@chen-peng-1874
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chen-peng-1874 commented Jan 16, 2023 via email

@hua888195
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Thank you for your advice. I tried remove.packages(), and installed again. But this problem is still there. Peng
________________________________ From: dhkong78 @.> Sent: Monday, January 16, 2023 12:10 PM To: satijalab/seurat @.> Cc: Peng Chen @.>; Comment @.> Subject: Re: [satijalab/seurat] Error in validityMethod(as(object, superClass)) : object 'CsparseMatrix_validate' not found (Issue #6746) Try to uninstall and install it again. chen-peng-1874 @.> 于2023年1月16日周一 01:58写道：
Hi all! I updated my Matrix, and the problem is still there. ― Reply to this email directly, view it on GitHub <#6746 (comment)>https://urldefense.com/v3/__https://github.com/satijalab/seurat/issues/6746*issuecomment-1383621803*3E__;IyU!!LIr3w8kk_Xxm!rvXGBlhfZEjiUDmfwM_2_NaumV9P6Efti0StUwUN4MCR79o7iHo_cXBnSM4_7lh7AeVC8yLhkm2KHXm8rdb44eCKQw$, or unsubscribe <[https://github.com/notifications/unsubscribe-auth/AQXPK7XEJQOWXWH563XLHLLWST5R7ANCNFSM6AAAAAASSPHZNU>https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AQXPK7XEJQOWXWH563XLHLLWST5R7ANCNFSM6AAAAAASSPHZNU*3E__;JQ!!LIr3w8kk_Xxm!rvXGBlhfZEjiUDmfwM_2_NaumV9P6Efti0StUwUN4MCR79o7iHo_cXBnSM4_7lh7AeVC8yLhkm2KHXm8rdZ8VuwS9w$](https://github.com/notifications/unsubscribe-auth/AQXPK7XEJQOWXWH563XLHLLWST5R7ANCNFSM6AAAAAASSPHZNUhttps://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/AQXPK7XEJQOWXWH563XLHLLWST5R7ANCNFSM6AAAAAASSPHZNU*3E__;JQ!!LIr3w8kk_Xxm!rvXGBlhfZEjiUDmfwM_2_NaumV9P6Efti0StUwUN4MCR79o7iHo_cXBnSM4_7lh7AeVC8yLhkm2KHXm8rdZ8VuwS9w%24) . You are receiving this because you commented.Message ID: @.>
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hi did you solve the error?
I also tried to remove package and re-install , the error still there.

@MartaSanchezCarbonell
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Hello! Same error here, has anyone find the solution? I've also tryed to install matrix again but it isn't working.

@yuhanH yuhanH reopened this Jan 24, 2023
@hua888195
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hua888195 commented Jan 24, 2023 •
edited
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I tried this solution again and again from 3 days ago.
The error is still there.

I tried uninstalled and install "Matrix" many times. And FindNeighbors could not work.

This is my code.
library(dplyr)
library(Seurat)
library(patchwork)
pbmc <- FindNeighbors(pbmc, dims = 1:10)
Computing nearest neighbor graph
Computing SNN
Error in validityMethod(as(object, superClass)) :
object 'CsparseMatrix_validate' not found

@surinderchd
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Same Here,
I have been working on this error for 4 days but have not solved it. All packages update or other suggestions are tried, there is no success.

merged_seurat_filtered <- FindNeighbors(object = merged_seurat_filtered, dims = 1:20)
Computing nearest neighbor graph
Computing SNN
Error in validityMethod(as(object, superClass)) :
object 'CsparseMatrix_validate' not found

@MartaSanchezCarbonell
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Hello! I could solve the problem! In my case I needed to update the version of Rtools to get the real last update from the package Matrix. Otherwise, even if I was uninstalling and reinstalling again the Matrix package, it was not functioning well.

So I did:
install.packages('installr')
library(installr)
install.Rtools()
install.packages('Matrix')
library(Matrix)

And then it worked fine! I hope I can help any of you with this info :)

@hua888195
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Hello! I could solve the problem! In my case I needed to update the version of Rtools to get the real last update from the package Matrix. Otherwise, even if I was uninstalling and reinstalling again the Matrix package, it was not functioning well.

So I did: install.packages('installr') library(installr) install.Rtools() install.packages('Matrix') library(Matrix)

And then it worked fine! I hope I can help any of you with this info :)

Thank you so much.
I’ll try that.

Have a good day.

@surinderchd
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Hello! I could solve the problem! In my case I needed to update the version of Rtools to get the real last update from the package Matrix. Otherwise, even if I was uninstalling and reinstalling again the Matrix package, it was not functioning well.

So I did: install.packages('installr') library(installr) install.Rtools() install.packages('Matrix') library(Matrix)

And then it worked fine! I hope I can help any of you with this info :)

Thank You for help.
Now it shows Warning message:
cannot allocate vector of size 1.1 Gb

@MartaSanchezCarbonell
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Hello! I could solve the problem! In my case I needed to update the version of Rtools to get the real last update from the package Matrix. Otherwise, even if I was uninstalling and reinstalling again the Matrix package, it was not functioning well.
So I did: install.packages('installr') library(installr) install.Rtools() install.packages('Matrix') library(Matrix)
And then it worked fine! I hope I can help any of you with this info :)

Thank You for help. Now it shows Warning message: cannot allocate vector of size 1.1 Gb

You can try what they suggest here: https://stackoverflow.com/questions/5171593/r-memory-management-cannot-allocate-vector-of-size-n-mb

@chen-peng-1874
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chen-peng-1874 commented Jan 24, 2023 via email

@surinderchd
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Hello! I could solve the problem! In my case I needed to update the version of Rtools to get the real last update from the package Matrix. Otherwise, even if I was uninstalling and reinstalling again the Matrix package, it was not functioning well.

So I did: install.packages('installr') library(installr) install.Rtools() install.packages('Matrix') library(Matrix)

And then it worked fine! I hope I can help any of you with this info :)

yes i have tried it, but bad luck, an error is still there. :(

@TarikExner TarikExner mentioned this issue Feb 2, 2023
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@JamieLord25
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So I have been wrestling with this issue for a couple days and I think I figured out a fix. Many in this thread have said to update the Matrix package. However, I tried this by doing update.package() and that didn't work. I eventually found a thread where someone mentioned that they should be in 1.5.3 version of Matrix and even after I updated in R. So i just deleted the Matrix package and then downloaded the latest version through CRAN and i finally got it to work.

@satkinson0115
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For those finding that removing and reinstalling via remove.packages() and install.packages() wasn't working to fix this problem (i.e. it wouldn't update the version) I had to go to the library location and manually delete the Matrix folder in order to remove the old version. Then install.packages("Matrix") correctly installed version 1.5-3.

@chen-peng-1874
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chen-peng-1874 commented Feb 23, 2023 via email

@ziyulizy
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Using command to reinstall the Matrix doesn't work for me. So I tried to delete and install it from the packages pane, and I succeeded. Hope it could be helpful for you!

@yuhanH
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yuhanH commented Feb 27, 2023

It seems that this issue is solved by the community contribution. Thank you very much for all of you!

@yuhanH yuhanH closed this as completed Feb 27, 2023
@brunicardoso
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I had the same issue. I could only reinstall Matrix before loading Seurat. I used install.packages("Matrix", repos = "http://cran.r-project.org")

@JoyceHuangzy
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my Matrix version is 1.5-3, seurat version is 4.3.0, seuratobject version is 4.1.3 and i still had this problem. I followed the instruction to reinstall Matrix,seurat and also seuratobject, but still didn't work out. Then I restart the Rstudio, and it finally succeeded!!
If you still had this problem, you could try to reinstall the package and restart the Rstudio, probably it will work out.

@xingling666
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Because your matrix package is old version, remove it and then install new version.
remove.packages('Matrix')
install.packages("Matrix", repos="http://R-Forge.R-project.org")

@jnrmro
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jnrmro commented Jun 2, 2023 •
edited
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To anyone that is still having issues, I was able to resolve this issue by first updating to the latest version of Matrix (1.5-4.1 at time of writing), AND loading Matrix before loading any other package. I tried loading Matrix after loading other packages, and got the error.

Only after loading Matrix first, then loading other packages, including Seurat, did the issue resolve.

Hope someone finds this helpful.

r/4.2.2

@prodriguezsosa prodriguezsosa mentioned this issue Jun 13, 2023
Closed
@multimeric multimeric mentioned this issue Jul 11, 2023
Merged
@mhkowalski mhkowalski mentioned this issue Jul 21, 2023
Closed
@Harmony714
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I encountered the same issue as well. I tried to uninstall and reinstall the 'Matrix' package, but the error still persists. My R version is 4.3.1.
sc.combined <- FindNeighbors( sc.combined,reduction = "pca", dims = 1:20)
Computing nearest neighbor graph
Computing SNN
Error in validityMethod(as(object, superClass)) :
object 'Csparse_validate' not found

@mariakondili
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Hello! I could solve the problem! In my case I needed to update the version of Rtools to get the real last update from the package Matrix. Otherwise, even if I was uninstalling and reinstalling again the Matrix package, it was not functioning well.

So I did: install.packages('installr') library(installr) install.Rtools() install.packages('Matrix') library(Matrix)

And then it worked fine! I hope I can help any of you with this info :)

There must be an error in install.Rtools() right ? did you mean install.packages("Rools") ?

@Harmony714
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I solve this problem. The version of matrix should be "1.5-4.1", and the 1.6 is not suitable.

@rsggsr
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rsggsr commented Aug 1, 2023

Just curious about when we could use Matrix 1.6 in Seurat (I tried but still I have to go back to version 1.5-4.1 to access dgcMatrix in Seurat). Since I need to use other package which needs the latest version of Matrix, is there any way to upgrade Seurat to use the version 1.6?

@ayushbharati
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Hi everyone,
What happens if the error is Csparse_validate is not found instead of CsparseMatrix_validate?
I get that error when using FindNeighbors as well as when finding integration anchors?
This is the error:

Scaling features for provided objects
|++++++++++++++++++++++++++++++++++++++++++++++++++| 100% elapsed=00s
Finding all pairwise anchors
| | 0 % ~calculating Running CCA
Merging objects
Error in validityMethod(as(object, superClass)) :
object 'Csparse_validate' not found

@coleruoff
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I'm having this same error. Csparse_validate instead of CsparseMatrix_validate......

@SONGDONGYUAN1994
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I have the same error, too. I think it just occurs in the recent few days.

@yichunher
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it works! thanks!

@stemangiola
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This helped me

install.packages(c("Seurat", "SeuratObject"), type="source")

stemangiola/CuratedAtlasQueryR#116 (comment)

@flpsw
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flpsw commented Aug 22, 2023

For those having problems with Csparse_validate instead of CsparseMatrix_validate, try to create a var before calling the function with the problem like this:
Csparse_validate = "CsparseMatrix_validate"

@Milad-Razavi Milad-Razavi mentioned this issue Sep 25, 2023
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@shaniAmare
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For me even manually deleting and reinstalling of Matrix 1.6 or particularly Matrix 1.5-3 did NOT work. What actually worked was to generate Csparse_validate as mentioned by @flpsw !

Thanks so much!

@AndreaYCT
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Hi,

I have the same problem. And I removed and reinstalled package "Matrix". But I still have the same error:
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'plot': object 'Csparse_validate' not found

Any other suggestion?

Many thanks

To anyone that is still having issues, I was able to resolve this issue by first updating to the latest version of Matrix (1.5-4.1 at time of writing), AND loading Matrix before loading any other package. I tried loading Matrix after loading other packages, and got the error.

Only after loading Matrix first, then loading other packages, including Seurat, did the issue resolve.

Hope someone finds this helpful.

r/4.2.2

@shaniAmare
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Hello @AndreaYCT

Hi,

I have the same problem. And I removed and reinstalled package "Matrix". But I still have the same error: Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'plot': object 'Csparse_validate' not found

Any other suggestion?

Many thanks

To anyone that is still having issues, I was able to resolve this issue by first updating to the latest version of Matrix (1.5-4.1 at time of writing), AND loading Matrix before loading any other package. I tried loading Matrix after loading other packages, and got the error.
Only after loading Matrix first, then loading other packages, including Seurat, did the issue resolve.
Hope someone finds this helpful.
r/4.2.2

Copy-paste below code line before you do integration step:
Csparse_validate = "CsparseMatrix_validate"

HTH,
Shani

@AndreaYCT
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hi, @shaniAmare,

Thanks! But that means i have to redo all the integration and slingshot T_T

Hello @AndreaYCT

Hi,
I have the same problem. And I removed and reinstalled package "Matrix". But I still have the same error: Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'plot': object 'Csparse_validate' not found
Any other suggestion?
Many thanks

To anyone that is still having issues, I was able to resolve this issue by first updating to the latest version of Matrix (1.5-4.1 at time of writing), AND loading Matrix before loading any other package. I tried loading Matrix after loading other packages, and got the error.
Only after loading Matrix first, then loading other packages, including Seurat, did the issue resolve.
Hope someone finds this helpful.
r/4.2.2

Copy-paste below code line before you do integration step: Csparse_validate = "CsparseMatrix_validate"

HTH, Shani

@shaniAmare
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hi, @shaniAmare,

Thanks! But that means i have to redo all the integration and slingshot T_T

Hello @AndreaYCT

Hi,
I have the same problem. And I removed and reinstalled package "Matrix". But I still have the same error: Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'plot': object 'Csparse_validate' not found
Any other suggestion?
Many thanks

To anyone that is still having issues, I was able to resolve this issue by first updating to the latest version of Matrix (1.5-4.1 at time of writing), AND loading Matrix before loading any other package. I tried loading Matrix after loading other packages, and got the error.
Only after loading Matrix first, then loading other packages, including Seurat, did the issue resolve.
Hope someone finds this helpful.
r/4.2.2

Copy-paste below code line before you do integration step: Csparse_validate = "CsparseMatrix_validate"
HTH, Shani

Wherever you come this error at, run that one liner just above it. It will hopefully solve it then :)

@AndreaYCT
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hi, @shaniAmare,

It worked!!!!!!! Many thanks!!!!!

Andrea

hi, @shaniAmare,
Thanks! But that means i have to redo all the integration and slingshot T_T

Hello @AndreaYCT

Hi,
I have the same problem. And I removed and reinstalled package "Matrix". But I still have the same error: Error in h(simpleError(msg, call)) : error in evaluating the argument 'x' in selecting a method for function 'plot': object 'Csparse_validate' not found
Any other suggestion?
Many thanks

To anyone that is still having issues, I was able to resolve this issue by first updating to the latest version of Matrix (1.5-4.1 at time of writing), AND loading Matrix before loading any other package. I tried loading Matrix after loading other packages, and got the error.
Only after loading Matrix first, then loading other packages, including Seurat, did the issue resolve.
Hope someone finds this helpful.
r/4.2.2

Copy-paste below code line before you do integration step: Csparse_validate = "CsparseMatrix_validate"
HTH, Shani

Wherever you come this error at, run that one liner just above it. It will hopefully solve it then :)

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