Re: [R] Technical Help Request for "Version Differences" (i.e., CYTOFKIT package)
Dear Nader Habibzadeh, В Sat, 21 Oct 2023 15:11:23 +0330 Nader Habibzadeh пишет: > I came across the same issue you have demonstrated in "r-help" but > with the shiny package installation. Do any of the replies to Murat's question, e.g. [1], help? If you have a different problem, let us know what exactly it looks like [2] and we'll try to help. [1]: https://stat.ethz.ch/pipermail/r-help/2023-August/477830.html [2]: https://www.chiark.greenend.org.uk/~sgtatham/bugs.html -- Best regards, Ivan __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Technical Help Request for "Version Differences" (i.e., CYTOFKIT package)
GIven that Cytofkit is removed from Bioconductor, and you seem new to everything, I would suggest like others already have that you install the most recent version of R for Windows https://cran.r-project.org/bin/windows/base/ and seek a more up-to-date package. For flow cytometry, I would like to recommend the CytoExploreR package (https://dillonhammill.github.io/CytoExploreR/ which is built on top of the core flow cytometry packages produced by RGLab (https://cytoverse.org/) and available on Bioconductor https://bioconductor.org/packages/release/bioc/html/openCyto.html God luck, Rob On 8/4/2023 2:10 AM, MURAT DELMAN via R-help wrote: Dear Ms./Mr., 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/ | 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/ | https://posit.co/download/rstudio-desktop/ ] I downloaded packages via either [ https://cran.rstudio.com/bin/windows/contrib/r-devel/ | 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/ | https://cran.r-project.org/bin/windows/Rtools/ ] Devtools : [ https://cran.r-project.org/web/packages/devtools/index.html | https://cran.r-project.org/web/packages/devtools/index.html ] ggplot2 : [ https://cran.r-project.org/web/packages/ggplot2/index.html | https://cran.r-project.org/web/packages/ggplot2/index.html ] [ https://ggplot2.tidyverse.org/ | https://ggplot2.tidyverse.org/ ] [ https://cran.r-project.org/web/packages/ggplot2/ggplot2.pdf | https://cran.r-project.org/web/packages/ggplot2/ggplot2.pdf ] plyr : [ https://cran.r-project.org/web/packages/plyr/index.html | https://cran.r-project.org/web/packages/plyr/index.html ] shiny : [ https://cran.r-project.org/web/packages/shiny/index.html | https://cran.r-project.org/web/packages/shiny/index.html ] [ https://shiny.posit.co/r/getstarted/shiny-basics/lesson1/index.html | https://shiny.posit.co/r/getstarted/shiny-basics/lesson1/index.html ] [ https://github.com/rstudio/shiny | https://github.com/rstudio/shiny ] cytofkit : [ https://github.com/JinmiaoChenLab/cytofkit | https://github.com/JinmiaoChenLab/cytofkit ] [ https://bioconductor.riken.jp/packages/3.3/bioc/html/cytofkit.html | https://bioconductor.riken.jp/packages/3.3/bioc/html/cytofkit.html ] [ https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005112=printable |
Re: [R] Technical Help Request for "Version Differences" (i.e., CYTOFKIT package)
Dear Murat Delman, Both your messages came through, and I'm replying to the one that was the first chronologically. I have taken a look at the cytofkit package. It used to be a Bioconductor package, but was removed, most likely because it failed to build and pass a check: https://support.bioconductor.org/p/128865 Installing cytofkit will involve spending a lot of effort: you need an old Bioconductor release, hence an old version of R, hence likely old, archived version of the dependencies, and to build the packages from source because CRAN doesn't serve Windows binaries for old versions of R. In this light, may I suggest looking for alternative packages that currently pass their checks on CRAN or Bioconductor? That support thread above has some suggestions, though I lack the expertise to judge them. In particular, the cytofWorkflow vignette and the scDataviz package look promising. For "basic R literacy", I can recommend this free book by A. Shipunov: http://web.archive.org/web/20230501112111/http://ashipunov.info/shipunov/school/biol_240/en/visual_statistics.pdf In order to install packages from the current release of Bioconductor, follow the guide at https://bioconductor.org/install/. Good luck! -- Best regards, Ivan __ R-help@r-project.org mailing list -- To UNSUBSCRIBE and more, see https://stat.ethz.ch/mailman/listinfo/r-help PLEASE do read the posting guide http://www.R-project.org/posting-guide.html and provide commented, minimal, self-contained, reproducible code.
Re: [R] Technical Help Request for "Version Differences" (i.e., CYTOFKIT package)
Hi Murat, I am not sure why you are using R 3.5. CRAN has R 4.3.1 https://cran.r-project.org/bin/windows/base/ I suggest you start over and install R 4.3.1 and then your cytofkit install might work. Good luck, Eric On Fri, Aug 4, 2023 at 5:47 PM Murat DELMAN wrote: > > Dear Ms./Mr., > > > I sent an email to this email address from my institutional address > muratdel...@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=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,
Re: [R] Technical Help Request for "Version Differences" (i.e., CYTOFKIT package)
Dear Murat: See the "posting guide" (link below) for how and what to post on this list. I believe that in that guide it is recommended that you first update your R version and packages to the latest versions (R 3.5 is rather old now). You should probably reinstall R and all packages from the main CRAN website: https://cran.r-project.org/ Note that once you install R, you can read ?install.packages for how to install the latest versions of all the packages you need that are on CRAN. Note that R and RStudio are different software products. So once R is installed, you can download and install the packages you need from the Posit website if you prefer, again with the latest versions. If for some reason CRAN is not available to you or some of the packages you need are not on CRAN(e.g. github only packages) or won't run on your computer, then the process will be more complicated, and others will have to help you. CRAN has a rigorous process for assuring compatibility of packages and R versions, so that packages not on CRAN may not be compatible with the latest R version. All I can suggest is that you avoid such packages **if possible** (I understand that it may not be). You can search CRAN's "Task Views" (link on https://cran.r-project.org/ )for alternative CRAN packages that may have the functionality you seek. Cheers, Bert On Fri, Aug 4, 2023 at 8:40 AM MURAT DELMAN via R-help wrote: > > > > > Dear Ms./Mr., > > > > > > > > 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/ | > 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/ | > https://posit.co/download/rstudio-desktop/ ] > > > > > > > I downloaded packages via either [ > https://cran.rstudio.com/bin/windows/contrib/r-devel/ | > 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/ | > https://cran.r-project.org/bin/windows/Rtools/ ] > > > > Devtools : [ https://cran.r-project.org/web/packages/devtools/index.html | > https://cran.r-project.org/web/packages/devtools/index.html ] > > > > ggplot2 : [ https://cran.r-project.org/web/packages/ggplot2/index.html | > https://cran.r-project.org/web/packages/ggplot2/index.html ] > > > > [ https://ggplot2.tidyverse.org/ | https://ggplot2.tidyverse.org/ ]
