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Grand master

Posts: 169

Joined: Thu Mar 13, 2014 5:58 pm

Location: NYC

Post Fri Nov 17, 2017 2:33 pm


Dear CyTOFers,

I'm please to announce cytutils, a set of utilities that we're developing focused on cytometry data processing and evaluating quality control and reproducibility. The current methods include a utility for channel renaming, calculating JS divergence to compare the similarity of 2D maps, and calculating AOF (Average Overlap Frequency) to evaluate staining quality. Props to El-ad Amir and Melanie Davila for leading the development and testing of these tools.

I hope you find them useful.


Adeeb Rahman
Icahn School of Medicine at Mount Sinai, NYC



Posts: 129

Joined: Mon Oct 31, 2016 6:26 pm

Post Fri Nov 17, 2017 2:42 pm

Re: Cytutils

And thanks Adeeb for leading the charge :-) I'm repeatedly impressed by the Mount Sinai HIMC's ability to design and acquire data sets that are conductive for computational development.

By the way, the channel renaming feature was inspired by Mike Leipold's thread -- I hope the community finds it useful.



Posts: 2

Joined: Fri Aug 04, 2017 3:59 pm

Post Thu Jun 06, 2019 12:52 pm

Re: Cytutils

Dear all,

I've previously used Cytutils without any issues.
Unfortunately, I was forced to re-install R on my computer (I know, horrible decision) and ever since I can't seem to get Cytutils going anymore.
Google did not seem to have any information on this particular issue..

Hopefully there's someone here who can help out.
I copy-pasted the installation commands as stated on github: the Devtools part runs without issues, it's the cytutils that appears to be the problem

This is the output I got when trying to install the package:

> install_github("ismmshimc/cytutils")
Downloading GitHub repo ismmshimc/cytutils@master
checking for file 'C:\Users\hjkoppejan\AppData\Local\Temp\Rtmp6NJuul\remotes21e78c15f7b\ismms-himc-cytutils-6813c28/DESCRIPTION' (830ms)
- preparing 'cytutils':
checking DESCRIPTION meta-information ...
- checking for LF line-endings in source and make files and shell scripts
- checking for empty or unneeded directories
- building 'cytutils_0.1.0.tar.gz'

Installing package into ‘\\vf-d2-home/d2home$/hjkoppejan/MyDocs/R/win-library/3.6’
(as ‘lib’ is unspecified)

CMD.EXE was started with the above path as the current directory.
UNC paths are not supported. Defaulting to Windows directory.
* installing *source* package 'cytutils' ...
** using staged installation
** R
** inst
Error in file.create(to[okay]) :
(converted from warning) cannot create file '\vf-d2-home/d2home$/hjkoppejan/MyDocs/R/win-library/3.6/00LOCK-cytutils/00new/cytutils/CITATION', reason 'No such file or directory'
* removing '\\vf-d2-home/d2home$/hjkoppejan/MyDocs/R/win-library/3.6/cytutils'

Error in i.p(...) :
(converted from warning) installation of package ‘C:/Users/HJKOPP~1/AppData/Local/Temp/Rtmp6NJuul/file21e7853793683/cytutils_0.1.0.tar.gz’ had non-zero exit status
In addition: Warning messages:
1: In untar2(tarfile, files, list, exdir) :
skipping pax global extended headers
2: In untar2(tarfile, files, list, exdir) :
skipping pax global extended headers

Any suggestions as to what could be wrong and how to fix it?


LUMC - Leiden



Posts: 125

Joined: Wed Dec 21, 2016 9:22 pm

Location: Marseille, France

Post Thu Jun 06, 2019 1:37 pm

Re: Cytutils

Dear Hester,

i think the main problem is due to the fact that your home directory is not in your computer but on a shared folder in the network. In the error messages, there is one saying "UNC paths are not supported." (UNC meaning shared network folders on a local area network). R does not support such folder and it's better that the packages are in the disk of the computer you are using.

I think the best is to contact the local computer administrator in order to fulfill the policies of your institute.

Alternatively, you can try to define the R library folder and tell it to R. See https://stackoverflow.com/questions/151 ... ls-to-work


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