Is there a way to use cytofkit on R version 3.6.3?
Entering edit mode
Mari ▴ 10
Last seen 3.6 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]: 

  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 ''
Content type 'application/zip' length 982859 bytes (959 KB)
downloaded 959 KB

trying URL ''
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
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 • 1.4k views
Entering edit mode
Last seen 2 days ago
United States

cytofkit was removed from Bioconductor in version 3.9 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 ; because the package has C code, you would need to install the Windows compiler tool chain, 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.

Entering edit mode

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.

Entering edit mode

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

Entering edit mode

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:

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:

Entering edit mode

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


Login before adding your answer.

Traffic: 362 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6