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

Thu Aug 10 17:22:18 CEST 2023

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:
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> Dear Ms./Mr.,
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> If the email text and codes below are not properly displayed, you can download the attached Word file, which has exactly the same content.
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> 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.
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> 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.
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> 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.
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> I tried to use the renv package, but I could not move forward because I am not competent in R.
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> I explained the errors that I faced during the installation below.
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> I have two computers, both operating Windows 10, 64-bit.
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> I installed R 3.5. 2 on the desktop (Windows in English) and R 3.5. 0 on the laptop (Windows in Turkish).
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> 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)?
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> I guess I will need exact web page links " in an orderly manner" to download the correct versions of everything.
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> I would appreciate it if you could advise me or forward this email to one of your assistants or experts.
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> I really appreciate any help you can provide.
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> Kind Regards
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> Please find the technical details below;
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> I used the installation order listed below;
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> I downloaded R 3.5.0 and R 3.5.2 using the link and directory below.
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> Link: [ https://www.freestatistics.org/cran/ | https://www.freestatistics.org/cran/ ]
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> Directory: Download R for Windows > install R for the first time > Previous releases > R 3.5.2 (December, 2018) or R 3.5.0
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> I downloaded RStudio from the link below;
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> [ https://posit.co/download/rstudio-desktop/ | https://posit.co/download/rstudio-desktop/ ]
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> 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.
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> Rtools : [ https://cran.r-project.org/bin/windows/Rtools/ | https://cran.r-project.org/bin/windows/Rtools/ ]
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> Devtools : [ https://cran.r-project.org/web/packages/devtools/index.html | https://cran.r-project.org/web/packages/devtools/index.html ]
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> ggplot2 : [ https://cran.r-project.org/web/packages/ggplot2/index.html | https://cran.r-project.org/web/packages/ggplot2/index.html ]
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> [ https://ggplot2.tidyverse.org/ | https://ggplot2.tidyverse.org/ ]
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> [ https://cran.r-project.org/web/packages/ggplot2/ggplot2.pdf | https://cran.r-project.org/web/packages/ggplot2/ggplot2.pdf ]
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> plyr : [ https://cran.r-project.org/web/packages/plyr/index.html | https://cran.r-project.org/web/packages/plyr/index.html ]
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> shiny : [ https://cran.r-project.org/web/packages/shiny/index.html | https://cran.r-project.org/web/packages/shiny/index.html ]
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> [ https://shiny.posit.co/r/getstarted/shiny-basics/lesson1/index.html | https://shiny.posit.co/r/getstarted/shiny-basics/lesson1/index.html ]
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> [ https://github.com/rstudio/shiny | https://github.com/rstudio/shiny ]
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> cytofkit : [ https://github.com/JinmiaoChenLab/cytofkit | https://github.com/JinmiaoChenLab/cytofkit ]
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> [ https://bioconductor.riken.jp/packages/3.3/bioc/html/cytofkit.html | https://bioconductor.riken.jp/packages/3.3/bioc/html/cytofkit.html ]
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> [ https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005112&type=printable | https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1005112&type=printable ]
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> Below, I provide the errors and warnings that I faced for 2 weeks for both R versions;
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> Please find the errors and warnings below;
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> CYTOFKIT FOR R VERSION 3.5. 2
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>> library(cytofkit)
> Loading required package: ggplot2
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> Loading required package: plyr
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> Error: package or namespace load failed for ‘cytofkit’:
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> package ‘cytofkit’ was installed by an R version with different internals; it needs to be reinstalled for use with this R version
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> ERROR: this R is version 3.5.2, package 'cytofkit2' requires R >= 4.0.0
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> In R CMD INSTALL
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> Installation paths not writeable, unable to update packages
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> path: C:/Program Files/R/R-3.5.2/library
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> packages:
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> boot, class, cluster, codetools, KernSmooth, Matrix, nlme, nnet, rpart, spatial, survival
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> There were 23 warnings (use warnings() to see them)
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>> warnings()
> Warning messages:
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> 1: packages ‘caTools’, ‘umap’ are not available (for R version 3.5.2)
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> 2: In i.p(...) : installation of package ‘DEoptimR’ had non-zero exit status
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> 3: In i.p(...) : installation of package ‘mvtnorm’ had non-zero exit status
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> 4: In i.p(...) : installation of package ‘XML’ had non-zero exit status
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> 5: In i.p(...) : installation of package ‘fastmap’ had non-zero exit status
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> 6: In i.p(...) : installation of package ‘sass’ had non-zero exit status
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> 7: In i.p(...) : installation of package ‘jquerylib’ had non-zero exit status
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> 8: In i.p(...) : installation of package ‘later’ had non-zero exit status
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> 9: In i.p(...) : installation of package ‘fontawesome’ had non-zero exit status
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> 10: In i.p(...) : installation of package ‘miniUI’ had non-zero exit status
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> 11: In i.p(...) : installation of package ‘RcppTOML’ had non-zero exit status
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> 12: In i.p(...) : installation of package ‘pcaPP’ had non-zero exit status
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> 13: In i.p(...) : installation of package ‘robustbase’ had non-zero exit status
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> 14: In i.p(...) : installation of package ‘cachem’ had non-zero exit status
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> 15: In i.p(...) : installation of package ‘promises’ had non-zero exit status
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> 16: In i.p(...) : installation of package ‘reticulate’ had non-zero exit status
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> 17: In i.p(...) : installation of package ‘rrcov’ had non-zero exit status
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> 18: In i.p(...) : installation of package ‘memoise’ had non-zero exit status
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> 19: In i.p(...) : installation of package ‘httpuv’ had non-zero exit status
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> 20: In i.p(...) : installation of package ‘bslib’ had non-zero exit status
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> 21: In i.p(...) : installation of package ‘rmarkdown’ had non-zero exit status
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> 22: In i.p(...) : installation of package ‘htmlwidgets’ had non-zero exit status
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> 23: In i.p(...) :
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> installation of package ‘C:/Users/murat-delman/AppData/Local/Temp/Rtmp8GGq71/file4d0c54c135b4/cytofkit2_0.99.80.tar.gz’ had non-zero exit status
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>> devtools::install_github("JinmiaoChenLab/cytofkit")
> Error in rbind(info, getNamespaceInfo(env, "S3methods")) :
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> number of columns of matrices must match (see arg 2)
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> INSTALLING GGPLOT2 FOR R VERSION 3.5. 0
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>> library(cytofkit)
> Loading required package: ggplot2
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> Warning: namespace ‘cli’ is not available and has been replaced
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> by .GlobalEnv when processing object ‘.Random.seed’
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> Error: package or namespace load failed for ‘ggplot2’ in rbind(info, getNamespaceInfo(env, "S3methods")):
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> number of columns of matrices must match (see arg 2)
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> Error: package ‘ggplot2’ could not be loaded
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> In addition: Warning message:
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> package ‘ggplot2’ was built under R version 4.2.3
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>> library(cytofkit)
> Error: package ‘ggplot2’ required by ‘cytofkit’ could not be found
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>> install.packages("D:/Programlar/ggplotgui_1.0.0.zip", repos = NULL, type = "win.binary")
> Installing package into ‘C:/Users/murat/Documents/R/win-library/3.5’
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> (as ‘lib’ is unspecified)
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> package ‘ggplotgui’ successfully unpacked and MD5 sums checked
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>> install.packages("D:/Programlar/ggplot2/ggplot2_3.0.0.tar.gz", repos = NULL, type = "source")
> Installing package into ‘C:/Users/murat/Documents/R/win-library/3.5’
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> (as ‘lib’ is unspecified)
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> * installing *source* package 'ggplot2' ...
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> ** package 'ggplot2' successfully unpacked and MD5 sums checked
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> ** R
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> ** data
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> *** moving datasets to lazyload DB
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> ** inst
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> ** byte-compile and prepare package for lazy loading
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> Warning: namespace 'cli' is not available and has been replaced
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> by .GlobalEnv when processing object 'txhousing'
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> Error in rbind(info, getNamespaceInfo(env, "S3methods")) :
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> number of columns of matrices must match (see arg 2)
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> ERROR: lazy loading failed for package 'ggplot2'
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> * removing 'C:/Users/murat/Documents/R/win-library/3.5/ggplot2'
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> In R CMD INSTALL
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> Warning in install.packages :
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> installation of package ‘D:/Programlar/ggplot2/ggplot2_3.0.0.tar.gz’ had non-zero exit status
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>> packageurl <- " [ https://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_3.3.0.tar.gz | https://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_3.3.0.tar.gz ] "
>> install.packages(packageurl, repos=NULL, type="source")
> Installing package into ‘C:/Users/murat/Documents/R/win-library/3.5’
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> (as ‘lib’ is unspecified)
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> trying URL ' [ https://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_3.3.0.tar.gz | https://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_3.3.0.tar.gz ] '
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> Content type 'application/x-gzip' length 3031461 bytes (2.9 MB)
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> downloaded 2.9 MB
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> * installing *source* package 'ggplot2' ...
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> ** package 'ggplot2' successfully unpacked and MD5 sums checked
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> ** R
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> ** data
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> *** moving datasets to lazyload DB
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> ** inst
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> ** byte-compile and prepare package for lazy loading
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> Warning: namespace 'cli' is not available and has been replaced
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> by .GlobalEnv when processing object 'txhousing'
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> Error in rbind(info, getNamespaceInfo(env, "S3methods")) :
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> number of columns of matrices must match (see arg 2)
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> ERROR: lazy loading failed for package 'ggplot2'
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> * removing 'C:/Users/murat/Documents/R/win-library/3.5/ggplot2'
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> In R CMD INSTALL
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> Warning in install.packages :
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> installation of package ‘C:/Users/murat/AppData/Local/Temp/RtmpI776iL/downloaded_packages/ggplot2_3.3.0.tar.gz’ had non-zero exit status
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>> install.packages("ggplot2")
> Installing package into ‘C:/Users/murat/Documents/R/win-library/3.5’
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> (as ‘lib’ is unspecified)
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> Warning in install.packages :
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> unable to access index for repository [ https://cran.rstudio.com/bin/windows/contrib/3.5 | https://cran.rstudio.com/bin/windows/contrib/3.5 ] :
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> cannot open URL ' [ https://cran.rstudio.com/bin/windows/contrib/3.5/PACKAGES | https://cran.rstudio.com/bin/windows/contrib/3.5/PACKAGES ] '
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> installing the source package ‘ggplot2’
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> trying URL ' [ https://cran.rstudio.com/src/contrib/ggplot2_3.4.2.tar.gz | https://cran.rstudio.com/src/contrib/ggplot2_3.4.2.tar.gz ] '
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> Content type 'application/x-gzip' length 3153811 bytes (3.0 MB)
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> downloaded 3.0 MB
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> * installing *source* package 'ggplot2' ...
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> ** package 'ggplot2' successfully unpacked and MD5 sums checked
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> ** R
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> ** data
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> *** moving datasets to lazyload DB
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> ** inst
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> ** byte-compile and prepare package for lazy loading
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> Warning: namespace 'cli' is not available and has been replaced
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> by .GlobalEnv when processing object 'txhousing'
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> Error in rbind(info, getNamespaceInfo(env, "S3methods")) :
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> number of columns of matrices must match (see arg 2)
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> ERROR: lazy loading failed for package 'ggplot2'
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> * removing 'C:/Users/murat/Documents/R/win-library/3.5/ggplot2'
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> In R CMD INSTALL
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> Warning in install.packages :
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> installation of package ‘ggplot2’ had non-zero exit status
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> The downloaded source packages are in
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> ‘C:\Users\murat\AppData\Local\Temp\RtmpI776iL\downloaded_packages’
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>> packageurl <- " [ https://cran.r-project.org/web/packages/ggplot2/index.html | https://cran.r-project.org/web/packages/ggplot2/index.html ] "
>> install.packages(packageurl, repos=NULL, type="source")
> Installing package into ‘C:/Users/murat/Documents/R/win-library/3.5’
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> (as ‘lib’ is unspecified)
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> trying URL ' [ https://cran.r-project.org/web/packages/ggplot2/index.html | https://cran.r-project.org/web/packages/ggplot2/index.html ] '
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> Content type 'text/html' length 468435 bytes (457 KB)
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> downloaded 457 KB
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> Error in getOctD(x, offset, len) : invalid octal digit
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> In R CMD INSTALL
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> Warning in install.packages :
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> installation of package ‘C:/Users/murat/AppData/Local/Temp/RtmpI776iL/downloaded_packages/index.html’ had non-zero exit status
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>> packageurl <- " [ https://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_3.3.0.tar.gz | https://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_3.3.0.tar.gz ] "
>> install.packages(packageurl, repos=NULL, type="source")
> Installing package into ‘C:/Users/murat/Documents/R/win-library/3.5’
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> (as ‘lib’ is unspecified)
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> trying URL ' [ https://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_3.3.0.tar.gz | https://cran.r-project.org/src/contrib/Archive/ggplot2/ggplot2_3.3.0.tar.gz ] '
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> Content type 'application/x-gzip' length 3031461 bytes (2.9 MB)
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> downloaded 2.9 MB
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> * installing *source* package 'ggplot2' ...
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> ** package 'ggplot2' successfully unpacked and MD5 sums checked
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> ** R
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> ** data
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> *** moving datasets to lazyload DB
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> ** inst
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> ** byte-compile and prepare package for lazy loading
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> Warning: namespace 'cli' is not available and has been replaced
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> by .GlobalEnv when processing object 'txhousing'
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> Error in rbind(info, getNamespaceInfo(env, "S3methods")) :
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> number of columns of matrices must match (see arg 2)
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> ERROR: lazy loading failed for package 'ggplot2'
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> * removing 'C:/Users/murat/Documents/R/win-library/3.5/ggplot2'
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> In R CMD INSTALL
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> Warning in install.packages :
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> installation of package ‘C:/Users/murat/AppData/Local/Temp/Rtmp8sLmoj/downloaded_packages/ggplot2_3.3.0.tar.gz’ had non-zero exit status
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>
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>> pak::pkg_install("tibble")
> Error in load_private_package("cli") :
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> Cannot load cli from the private library
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>> pak::pkg_install("tidyverse/tibble")
> Error in load_private_package("cli") :
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> Cannot load cli from the private library
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>> pkg_install("tibble")
> Error in pkg_install("tibble") : could not find function "pkg_install"
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>> install.packages("D:/Programlar/ggplot2/ggplot2_3.4.2.zip", repos = NULL, type = "win.binary")
> Installing package into ‘C:/Users/murat/Documents/R/win-library/3.5’
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> (as ‘lib’ is unspecified)
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> package ‘ggplot2’ successfully unpacked and MD5 sums checked
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>
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> Kind Regards
>
>
> Murat Delman, Ph.D.
> Izmir Institute of Technology
> Integrated Research Centers
>
> ______________________________________________
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-- 
__________________________________________________
Robert W. Baer, Ph.D.
Professor of Physiolgy
Kirksville College of Osteopathic Medicine
A.T. Still University of Heallth Sciences
800 W. Jefferson St.
Kirksville, MO 63501
P: 660-626-2322

The ATSU Mission
A.T. Still University of Health Sciences serves as a learning-centered university dedicated to preparing highly competent professionals through innovative academic programs with a commitment to continue its osteopathic heritage and focus on whole person healthcare, scholarship, community health, interprofessional education, diversity, and underserved populations.

Proud recipient of INSIGHT Into Diversity’s 2017-19 Higher Education Excellence in Diversity Awards.