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sunduanchen / Scissor

Scissor package
GNU General Public License v3.0
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Error in normalize.quantiles(dataset0) : ERROR; return code from pthread_create() is 22 #15

Open harrywo-zz opened 2 years ago

harrywo-zz commented 2 years ago

Got a error when running your tutorial using your data: Error in normalize.quantiles(dataset0) : ERROR; return code from pthread_create() is 22 I am using R 4.1.1

Can you help to figure out what happened there?

sunduanchen commented 2 years ago

Can you try the solutions in https://github.com/Bioconductor/bioconductor_docker/issues/22?

tiandongli commented 2 years ago

Got a error when running your tutorial using your data: Error in normalize.quantiles(dataset0) : ERROR; return code from pthread_create() is 22 I am using R 4.1.1

Can you help to figure out what happened there?

I have the same error

Lycidas97 commented 2 years ago

I met same error, this solution https://support.bioconductor.org/p/122925/#124701 works for me. BiocManager::install("preprocessCore", configure.args="--disable-threading", force = TRUE)

Tianjun-Lan commented 2 years ago

I met the same error and I tried to solve it followed the above method. However, I didn't solved it. So, can you help to figure out what happened there?

yimwy commented 2 years ago

Same error, manual re-installation doesnt seems to work.

Tianjun-Lan commented 2 years ago

Thank you. I change a mechine and it solved.     ------------------ Original ------------------ From: @.>; Date:  Tue, Feb 15, 2022 10:05 PM To: @.>; Cc: @.>; @.>; Subject:  Re: [sunduanchen/Scissor] Error in normalize.quantiles(dataset0) : ERROR; return code from pthread_create() is 22 (Issue #15)

 

Same error, manual re-installation doesnt seems to work.

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GuohuaZhu commented 2 years ago

I was able to run it on the local R , but not on the R server's . There may be a problem here. But I don't know how to fix it.

qi-shen commented 2 years ago

I have the same error

sayhitoemily commented 2 years ago

I have the same error

xiaoyaohao commented 2 years ago

I meet the same problem in linux R server, maybe the issue comes from the update of preprocessCore. I change the bulk dataset to matrix and try again and again, sometimes it will work.

l13a commented 2 years ago

i have the same error

chenx9 commented 2 years ago

I tried the above solution but still got the error

Chen-Guanming commented 1 year ago

I also got the same error. After checking the raw code, I found normalize.quantiles and quantile function need a matrix. I don't know why the dataset0 is not a matrix after cbind. I guess a different package version caused the question. Therefore, I think you can change the raw code of Scissor function to deal with the question.

Here is the raw code of Scissor function: _dataset0 <- cbind(bulk_dataset[common,], scexprs[common,]) # Dataset before quantile normalization. dataset1 <- normalize.quantiles(dataset0) # Dataset after

You can amend it as: _dataset0 <- cbind(bulk_dataset[common,], scexprs[common,]) # Dataset before quantile normalization. dataset1 <- normalize.quantiles(as.matrix(dataset0)) # Dataset after

After testing, it was well done. However, I found it needs a very large memory. Therefore, you should be careful with the memory of your computer or servers.

Tang-RH commented 1 year ago

I also meet the problem in linux R server, and I solved it by followed the solution: https://github.com/Bioconductor/bioconductor_docker/issues/22 To manually installed preprocessCore package, run the following commands in terminal:

git clone https://github.com/bmbolstad/preprocessCore.git
R CMD INSTALL "preprocessCore" --configure-args="--disable-threading"
Cristinawangting commented 1 year ago

I encountered the same problem, I tried manual installation or BiocManager::install("preprocessCore", configure.args="--disable-threading",force = TRUE). BUT it didn't work.

Xiazistarry commented 5 months ago

It did not work on the server. But it worked locally.

ghost commented 4 months ago

same error happens when I tried to run the code openSesame(), I tried to solve by usng the

git clone https://github.com/bmbolstad/preprocessCore.git R CMD INSTALL "preprocessCore" --configure-args="--disable-threading"

but they are showing the error

'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for details. Replacement repositories: CRAN: https://cran.rstudio.com/ Bioconductor version 3.18 (BiocManager 1.30.23), R 4.3.3 (2024-02-29) Installing package(s) 'peprocessCore' Warning message: package ‘peprocessCore’ is not available for Bioconductor version '3.18' A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages

then I tried using clone,

again I got error, what should I do?

sidrahmaryam-cyber commented 4 months ago

Hello, I get the same error. Error in normalize.quantiles(dataset0) : Matrix expected in normalize.quantiles In addition: Warning messages: 1: In asMethod(object) : sparse->dense coercion: allocating vector of size 4.3 GiB 2: In asMethod(object) : sparse->dense coercion: allocating vector of size 3.3 GiB

I tried to run on my local machine as well as the server, also tried the aforementioned solution, but couldn't solve the issue. Can anyone please help regarding this if they have been able to solve?