search

navinlabcode / copykat

Other
213 stars 55 forks source link

no applicable method for 'dlmSmooth' applied to an object of class "c('double', 'numeric')" #71

Open 050114dragon opened 2 years ago

050114dragon commented 2 years ago

Hi, could you please help me to solve an error

the command is copykat.test <- copykat(rawmat=exp.rawdata, sam.name="test")

the log info is [1] "running copykat v1.1.0" [1] "step1: read and filter data ..." [1] "33694 genes, 302 cells in raw data" [1] "12156 genes past LOW.DR filtering" [1] "step 2: annotations gene coordinates ..." [1] "start annotation ..." [1] "step 3: smoothing data with dlm ..." Error in UseMethod("dlmSmooth", y) : no applicable method for 'dlmSmooth' applied to an object of class "c('double', 'numeric')"

050114dragon commented 2 years ago

I use docker image (mparikhbroad/copykat) to run it , success!

I think the error perhaps comes from dlm package,so I build dlm package from source code(dlm_0.7-1.tar.gz，dlm_1.0-0.tar.gz，dlm_1.1-5.tar.gz),but error also exists

AClab-sgarcia commented 2 years ago

The same thing happens to me, I have installed CopyKAT today and it gives me the same error also in step 3. I ran it on another computer where the package was already installed and I had no problem. There must be a problem with dlm package.

qiangfan2022 commented 2 years ago

The same thing happens to me, I have installed CopyKAT today and it gives me the same error also in step 3. I ran it on another computer where the package was already installed and I had no problem. There must be a problem with dlm package.

you can remove “dlm”, and reinstall "dlm". I bug at the step4 with “hclust”

AClab-sgarcia commented 2 years ago

The same thing happens to me, I have installed CopyKAT today and it gives me the same error also in step 3. I ran it on another computer where the package was already installed and I had no problem. There must be a problem with dlm package.

you can remove “dlm”, and reinstall "dlm". I bug at the step4 with “hclust”

This did not work for me, I am not able to install de 'dlm' package, how did you do this?

Lao-Tz commented 2 years ago

The same error happened to me . And when removed the 'dlm' package, I can't install it anymore. It's version R 4.2.2.

sitarapersad commented 2 years ago

I am also having this issue with R 4.2.2 on an M1 chip - just tagging along to see if there is a solution