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

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1

Dear Ms./Mr.,

If the text and codes below are not properly displayed, you can download the Word file, which has exactly the same content in the link that is at the end of this message.

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 in the link 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 in the link below;

OR

Download the image and zoom it by right-clicking and "save image as"

R-programming_-Technical-Help-docx-Google-Docs
R-programming_-Technical-Help-docx-Google-Docs1921×13605 2.91 MB

Kind Regards

System Information:

  • RStudio Edition: Desktop Latest
  • RStudio Version: Desktop Latest
  • OS Version: Windows 10
  • R Version: 5.3.0 and 5.3.2
  • sessionInfo():

Referred here from support.rstudio.com

2

Can you clarify what you wish to learn ?

3

Dear Ms./Mr.,

If the text and codes below are not properly displayed, you can download the Word file, which has exactly the same content in the link that is at the end of this message.

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 in the link 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 in the below;

Kind Regards

4

R 3.5.0 is now 5 years old; Did you have a positive reason to this choice of R version ?
I think you will have an easier time installing a modern R. While I'm still happily using R4.2, R4.3.1 is available :
https://cran.r-project.org/bin/windows/base/
There shouldnt be any particular issue using a modern version of R studio IDE with this
Get an appropriate RTools for the version you chose : RTools: Toolchains for building R and R packages from source on Windows
Then probably the other sticking point for you is that cytofkit is a bioconductor package so you likely need to install bioconductor.

5

The package named cytofkit works in R 3.5.2. This is why I have to use this version of R. But when I install other dependencies of cytofkit, they are not accepted to R 3.5.2 :frowning:

I used the links you provided.

Is there a way or a guide that shows the consistent versions of packages to be installed and their proper order of installations?

I guess I need step by step guide to install Rtools, devtools, ggplot2, shiny, cytofkit, etc.

6

You can view the errors and warnings in the link below;

8

I'm afraid I wont open a docx file from google.
If you have text, it can be reproduced in the forum.

9

R-programming_-Technical-Help-docx-Google-Docs
R-programming_-Technical-Help-docx-Google-Docs1921×13605 2.91 MB

I am sending you its image to make it easier to review. I think you can download the image and zoom it. Right click and "save image as"

10

This is an image of text; please provide as text; screenshots are generally unhelpful.

I understand now your issue, relates to bioconductor having removed support for this package.
https://bioconductor.org/about/removed-packages/
and the earliest version of bioconductor that supports it does seem to require exactly R version 3.5
so now I understand why that is your goal.

11

Because I am a new user, the system does not allow me to upload attachments. I will try to copy paste the errors in my next reply.

12

I cannot send more than 2 links yet :frowning:

That's why I cannot send you text file :frowning:

13

I downloaded my package from the link below. But the problems continued. You can see my package on the website. I think I have done everything correctly but it still doesn't work.

Bioconductor-Removed-Packages
Bioconductor-Removed-Packages742×212 31.8 KB

14

Bioconductor-Bioconductor-3-9-Released
Bioconductor-Bioconductor-3-9-Released734×141 18.2 KB

15

I also get the error below when I try to install cytofkit:

if (!requireNamespace("BiocManager", quietly = TRUE))

  • install.packages("BiocManager")

BiocManager::install("cytofkit")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories",
package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.8 (BiocManager 1.30.21.1), R 3.5.2 (2018-12-20)
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
Warning message:
package(s) not installed when version(s) same as or greater than current; use force = TRUE to
re-install: 'cytofkit'

16

The other error when I try to install bioconductor 3.8

Do you know how to install bioconductor 3.8 into R 3.5.2 or R 3.5.0 ?

if (!require("BiocManager", quietly = TRUE))

  • install.packages("BiocManager")

Bioconductor version 3.8 (BiocManager 1.30.21.1), R 3.5.2 (2018-12-20)
Bioconductor version '3.8' is out-of-date; the current release version '3.17' is available with R
version '4.3'; see Bioconductor - Install

BiocManager::install(version = "3.8")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories",
package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.8 (BiocManager 1.30.21.1), R 3.5.2 (2018-12-20)
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

the other error is

library(cytofkit)
Loading required package: ggplot2
Loading required package: plyr
Error: package or namespace load failed for ‘cytofkit’ in rbind(info, getNamespaceInfo(env, "S3methods")):
number of columns of matrices must match (see arg 2)

17

I am not sure why we are talking about R 3.5.0 and ancient bioconductor versions here - The cytofkit package in its devel version works quite well with a recent R version as well

devtools::install_github("JinmiaoChenLab/cytofkit")

installs successfully with R 4.3.1 !

See GitHub - JinmiaoChenLab/cytofkit: cytofkit: an integrated flow/mass cytometry data analysis pipeline