Is there a way to use cytofkit on R version 3.6.3?
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Mari ▴ 10
@mari-23053
Last seen 4.1 years ago

I keep on getting this warning message when I try to install cytofkit in R version 3.6.3.

    > BiocManager::install("cytofkit")
Bioconductor version 3.9 (BiocManager 1.30.10), R 3.6.3 (2020-02-29)
Installing package(s) 'cytofkit'
Installation path not writeable, unable to update packages: foreign, lattice, nlme, nnet
Old packages: 'fs', 'plyr'
Update all/some/none? [a/s/n]: 
a

  There are binary versions available but the source versions are later:
     binary source needs_compilation
fs    1.3.1  1.3.2              TRUE
plyr  1.8.5  1.8.6              TRUE

  Binaries will be installed
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/fs_1.3.1.zip'
Content type 'application/zip' length 982859 bytes (959 KB)
downloaded 959 KB

trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/plyr_1.8.5.zip'
Content type 'application/zip' length 1304574 bytes (1.2 MB)
downloaded 1.2 MB

package ‘fs’ successfully unpacked and MD5 sums checked
package ‘plyr’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
    C:\Users\AppData\Local\Temp\RtmpUBAsIj\downloaded_packages
Warning message:
package ‘cytofkit’ is not available (for R version 3.6.3)

I have tried to use R version 3.5, but when I do this I get an error for caTools, saying that it requires a version of R (≥ 3.6.0). Is there any solution to this problem? I am new to R, so I am not aware of other methods. Thank you in advance.

cytofkit • 1.7k views
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@martin-morgan-1513
Last seen 6 weeks ago
United States

cytofkit was removed from Bioconductor in version 3.9 http://bioconductor.org/about/removed-packages/ so yes you must use R 3.5.

cytofkit was removed for a reason (because it failed to pass build & check) so it is at some level known to be 'broken' and therefore not a good choice. If you still want to use it, you could try installing an earlier version of caTools from https://cran.r-project.org/src/contrib/Archive/caTools/ ; because the package has C code, you would need to install the Windows compiler tool chain https://cran.r-project.org/bin/windows/Rtools/, download the archived version, then install from 'source' with install.packages("caTools_1.17.1.tar.gz") (I'm not certain of the version number), and then install cytofkit using BiocManager::install(). This would definitely be a hard-core but not impossible exercise.

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Thank you so much for your reply! I really appreciate it! What would you recommend to use in place of cytofkit? I have tried to just use FlowSOM, as that is the clustering algorithm I would like to use, but I don't know how to incorporate this into tsne or umap for visualisation.

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Sorry, it's not really my area of expertise; perhaps someone else will chime in with suggestions.

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Mari, my 4th package, scDataviz, is currently passing through submission to Bioconductor. There is still a bit of work to get it 'just right', though. You can take a look at the GitHub vignette to see if it could be of use: https://github.com/kevinblighe/scDataviz

I am pretty sure that there is a way to take FlowSOM output and use it for UMAP or tSNE. I have not incorporated FlowSOM into my package, though.

You should take a look here, too, where I believe they have done what you want to do:

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Thank you very much! I really appreciate the help!! I will have a look at what you linked!

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