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Surprising behavior and bugs in R 4.0.4

4 messages · Miso Na, Duncan Murdoch, Jiefei Wang +1 more

Original
Miso Na
# 
Dear helpers,

Although I uninstalled and reinstalled R more than 3 times to delete the error in api_create, it did not work. The error is representing on the very first page on R consol.
Error: could not find function "api_create"

I guess this error makes impossible to install library 'SCMAP', 'SingleCellExperiment' or 'Seurat'.
For example, I got this error when I tried to install those libraries.
Installing package into 'C:/Users/user/Documents/R/win-library/4.0'
(as 'lib' is unspecified)
Error: could not find function "api_create"
Execution halted
Error: Failed to install 'Seurat' from GitHub:
  (converted from warning) installation of package 'C:/Users/user/AppData/Local/Temp/RtmpKYL3Pe/file2c2c6cb0766e/Seurat_4.0.1.tar.gz' had non-zero exit status


My sessionInfo is here!
R version 4.0.4 (2021-02-15)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 19041)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252
[2] LC_CTYPE=English_United States.1252
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
system code page: 949

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

loaded via a namespace (and not attached):
[1] compiler_4.0.4

Thanks for your help!
Duncan Murdoch
#
On 20/03/2021 1:04 a.m., Miso Na wrote:
Why would you think this is a bug in R, rather than in whatever 
unreleased package(s) you were trying to install?

Duncan Murdoch
Jiefei Wang
# 
Hi Miso,

Have you tried to install Seurat from CRAN? What you were using is the
GitHub version of the package and has been actively updating, so the
problem might be from the package.

Best,
Jiefei
On Sat, Mar 20, 2021 at 10:32 PM Miso Na <mna3 at jhu.edu> wrote:

            

      
      
      
    

        

      
      
    

        

  
  


  


      

    

    

      
      

        


  

        

      Eric Berger
    

    

      
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I have no familiarity with these packages but I did a search in CRAN on
api_create and found it is defined in the plotly package. I then confirmed
that the seurat package does reference plotly.

You might try installing the plotly package before trying to install seurat.

HTH,
Eric

        
On Sat, Mar 20, 2021 at 6:05 PM Jiefei Wang <szwjf08 at gmail.com> wrote: