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

Fri Aug 4 18:15:40 CEST 2023

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
<r-help using r-project.org> 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)
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> 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()
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> 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")
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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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> >
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> INSTALLING GGPLOT2 FOR R VERSION 3.5. 0
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> > library(cytofkit)
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> 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)
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> 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")
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> 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")
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> 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 ] "
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> > install.packages(packageurl, repos=NULL, type="source")
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> 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")
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> 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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>
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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
>
> ** byte-compile and prepare package for lazy loading
>
> 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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>
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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 ] "
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> > install.packages(packageurl, repos=NULL, type="source")
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> 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 ] "
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> > install.packages(packageurl, repos=NULL, type="source")
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> 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 ] '
>
> Content type 'application/x-gzip' length 3031461 bytes (2.9 MB)
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> downloaded 2.9 MB
>
>
>
> * installing *source* package 'ggplot2' ...
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> ** package 'ggplot2' successfully unpacked and MD5 sums checked
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> ** R
>
> ** data
>
> *** moving datasets to lazyload DB
>
> ** inst
>
> ** byte-compile and prepare package for lazy loading
>
> Warning: namespace 'cli' is not available and has been replaced
>
> by .GlobalEnv when processing object 'txhousing'
>
> Error in rbind(info, getNamespaceInfo(env, "S3methods")) :
>
> number of columns of matrices must match (see arg 2)
>
> ERROR: lazy loading failed for package 'ggplot2'
>
> * removing 'C:/Users/murat/Documents/R/win-library/3.5/ggplot2'
>
> In R CMD INSTALL
>
> Warning in install.packages :
>
> installation of package ‘C:/Users/murat/AppData/Local/Temp/Rtmp8sLmoj/downloaded_packages/ggplot2_3.3.0.tar.gz’ had non-zero exit status
>
>
>
> > pak::pkg_install("tibble")
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> 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")
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> Error in load_private_package("cli") :
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> Cannot load cli from the private library
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>
>
> > pkg_install("tibble")
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> 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")
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> Installing package into ‘C:/Users/murat/Documents/R/win-library/3.5’
>
> (as ‘lib’ is unspecified)
>
> package ‘ggplot2’ successfully unpacked and MD5 sums checked
>
>
>
> Kind Regards
>
>
> Murat Delman, Ph.D.
> Izmir Institute of Technology
> Integrated Research Centers
>
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