[R] Technical Help Request for "Version Differences" (i.e., CYTOFKIT package)

Fri Aug 4 09:13:55 CEST 2023

Dear Ms./Mr.,

I sent an email to this email address from my institutional address
muratdelman using iyte.edu.tr, but could not make sure if my email reached you
because sometimes emails are not delivered to the target due to
server issues and country-related limitations. I wanted to send you the
same email via my Gmail account.

If the email text and codes below are not properly displayed, you can
download the attached Word file, which has exactly the same content.

I am a cytometrist and microscopist at Izmir Institute of Technology,
Integrated Research Center. I operate a cytometer and fluorescence
microscope to acquire data from our researchers’ samples and then give them
analyzed data. I need to dive into bulk data to present all of the
information in the sample. To do this, I have recently been trying to
develop my skills in R, RStudio, and Cytofkit package for cytometry (flow,
spectral, mass, imaging mass cytometry) data analysis. I am new in this
area and must learn R for data analysis.

May I request help from you or one of your assistants who is competent in
R, RStudio, and R packages with the installation issues caused by “*version
differences*” between R itself, R packages, and their dependencies? I
really had to send this email to you anymore, because I could not run the
package “Cytofkit” and find a solution on the internet.

It has been nearly 2 weeks since I have been trying to solve the errors and
warnings. I am in a vicious circle and cannot move forward anymore. This is
why I needed help from an expert competent in R programming.

I tried to use the renv package, but I could not move forward because I am
not competent in R.

I explained the errors that I faced during the installation below.

I have two computers, both operating Windows 10, 64-bit.

I installed R 3.5.*2* on the desktop (Windows in English) and R 3.5.*0* on
the laptop (Windows in Turkish).

I know that you are very busy with your work, but may you (or your
assistant) help me by informing me *how to install consistent versions of
R, RStudio, and packages/dependencies* (for example, Cytofkit, ggplot2,
Rtools, devtools, plyr, shiny, GUI)?

I guess I will need exact web page links "*in* *an orderly manner" to
download* the correct versions of everything.

I would appreciate it if you could advise me or forward this email to one
of your assistants or experts.

I really appreciate any help you can provide.

Kind Regards

*Please find the technical details below;*

I used the installation order listed below;

I downloaded R 3.5.0 and R 3.5.2 using the link and directory below.

Link: https://www.freestatistics.org/cran/

Directory: Download R for Windows > install R for the first time > Previous
releases > R 3.5.2 (December, 2018) or R 3.5.0

I downloaded RStudio from the link below;

https://posit.co/download/rstudio-desktop/

I downloaded packages via either
https://cran.rstudio.com/bin/windows/contrib/r-devel/ or the “install
function” tab in RStudio.

Rtools : https://cran.r-project.org/bin/windows/Rtools/

Devtools : https://cran.r-project.org/web/packages/devtools/index.html

ggplot2 : https://cran.r-project.org/web/packages/ggplot2/index.html

                 https://ggplot2.tidyverse.org/

                 https://cran.r-project.org/web/packages/ggplot2/ggplot2.pdf

plyr : https://cran.r-project.org/web/packages/plyr/index.html

shiny : https://cran.r-project.org/web/packages/shiny/index.html

https://shiny.posit.co/r/getstarted/shiny-basics/lesson1/index.html

            https://github.com/rstudio/shiny

cytofkit : https://github.com/JinmiaoChenLab/cytofkit

https://bioconductor.riken.jp/packages/3.3/bioc/html/cytofkit.html

https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005112&type=printable

Below, I provide the errors and warnings that I faced for 2 weeks for both
R versions;

*Please find the errors and warnings below;*

*CYTOFKIT FOR R VERSION 3.5.**2*

> library(cytofkit)

Loading required package: ggplot2

Loading required package: plyr

Error: package or namespace load failed for ‘cytofkit’:

package ‘cytofkit’ was installed by an R version with different internals;
it needs to be reinstalled for use with this R version

ERROR: this R is version 3.5.2, package 'cytofkit2' requires R >= 4.0.0

In R CMD INSTALL

Installation paths not writeable, unable to update packages

  path: C:/Program Files/R/R-3.5.2/library

  packages:

    boot, class, cluster, codetools, KernSmooth, Matrix, nlme, nnet, rpart,
spatial, survival

There were 23 warnings (use warnings() to see them)

> warnings()

Warning messages:

1: packages ‘caTools’, ‘umap’ are not available (for R version 3.5.2)

2: In i.p(...) : installation of package ‘DEoptimR’ had non-zero exit status

3: In i.p(...) : installation of package ‘mvtnorm’ had non-zero exit status

4: In i.p(...) : installation of package ‘XML’ had non-zero exit status

5: In i.p(...) : installation of package ‘fastmap’ had non-zero exit status

6: In i.p(...) : installation of package ‘sass’ had non-zero exit status

7: In i.p(...) : installation of package ‘jquerylib’ had non-zero exit
status

8: In i.p(...) : installation of package ‘later’ had non-zero exit status

9: In i.p(...) : installation of package ‘fontawesome’ had non-zero exit
status

10: In i.p(...) : installation of package ‘miniUI’ had non-zero exit status

11: In i.p(...) : installation of package ‘RcppTOML’ had non-zero exit
status

12: In i.p(...) : installation of package ‘pcaPP’ had non-zero exit status

13: In i.p(...) : installation of package ‘robustbase’ had non-zero exit
status

14: In i.p(...) : installation of package ‘cachem’ had non-zero exit status

15: In i.p(...) : installation of package ‘promises’ had non-zero exit
status

16: In i.p(...) : installation of package ‘reticulate’ had non-zero exit
status

17: In i.p(...) : installation of package ‘rrcov’ had non-zero exit status

18: In i.p(...) : installation of package ‘memoise’ had non-zero exit status

19: In i.p(...) : installation of package ‘httpuv’ had non-zero exit status

20: In i.p(...) : installation of package ‘bslib’ had non-zero exit status

21: In i.p(...) : installation of package ‘rmarkdown’ had non-zero exit
status

22: In i.p(...) : installation of package ‘htmlwidgets’ had non-zero exit
status

23: In i.p(...) :

  installation of package
‘C:/Users/murat-delman/AppData/Local/Temp/Rtmp8GGq71/file4d0c54c135b4/cytofkit2_0.99.80.tar.gz’
had non-zero exit status

> devtools::install_github("JinmiaoChenLab/cytofkit")