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 <murat.del...@gmail.com> 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&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") > > Error in rbind(info, getNamespaceInfo(env, "S3methods")) : > > number of columns of matrices must match (see arg 2) > > > > > > > > > > > *INSTALLING GGPLOT2 FOR R VERSION 3.5.**0* > > > > > library(cytofkit) > > Loading required package: ggplot2 > > Warning: namespace ‘cli’ is not available and has been replaced > > by .GlobalEnv when processing object ‘.Random.seed’ > > Error: package or namespace load failed for ‘ggplot2’ in rbind(info, > getNamespaceInfo(env, "S3methods")): > > number of columns of matrices must match (see arg 2) > > Error: package ‘ggplot2’ could not be loaded > > In addition: Warning message: > > package ‘ggplot2’ was built under R version 4.2.3 > > > > > library(cytofkit) > > Error: package ‘ggplot2’ required by ‘cytofkit’ could not be found > > > > > 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’ > > (as ‘lib’ is unspecified) > > package ‘ggplotgui’ successfully unpacked and MD5 sums checked > > > > > 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’ > > (as ‘lib’ is unspecified) > > * installing *source* package 'ggplot2' ... > > ** package 'ggplot2' successfully unpacked and MD5 sums checked > > ** 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 ‘D:/Programlar/ggplot2/ggplot2_3.0.0.tar.gz’ had > non-zero exit status > > > > > packageurl <- " > 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’ > > (as ‘lib’ is unspecified) > > trying URL ' > 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) > > downloaded 2.9 MB > > > > * installing *source* package 'ggplot2' ... > > ** package 'ggplot2' successfully unpacked and MD5 sums checked > > ** 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/RtmpI776iL/downloaded_packages/ggplot2_3.3.0.tar.gz’ > had non-zero exit status > > > > > install.packages("ggplot2") > > Installing package into ‘C:/Users/murat/Documents/R/win-library/3.5’ > > (as ‘lib’ is unspecified) > > Warning in install.packages : > > unable to access index for repository > https://cran.rstudio.com/bin/windows/contrib/3.5: > > cannot open URL 'https://cran.rstudio.com/bin/windows/contrib/3.5/PACKAGES > ' > > installing the source package ‘ggplot2’ > > > > trying URL 'https://cran.rstudio.com/src/contrib/ggplot2_3.4.2.tar.gz' > > Content type 'application/x-gzip' length 3153811 bytes (3.0 MB) > > downloaded 3.0 MB > > > > * installing *source* package 'ggplot2' ... > > ** package 'ggplot2' successfully unpacked and MD5 sums checked > > ** 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 ‘ggplot2’ had non-zero exit status > > > > The downloaded source packages are in > > ‘C:\Users\murat\AppData\Local\Temp\RtmpI776iL\downloaded_packages’ > > > > > packageurl <- "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’ > > (as ‘lib’ is unspecified) > > trying URL 'https://cran.r-project.org/web/packages/ggplot2/index.html' > > Content type 'text/html' length 468435 bytes (457 KB) > > downloaded 457 KB > > > > Error in getOctD(x, offset, len) : invalid octal digit > > In R CMD INSTALL > > Warning in install.packages : > > installation of package > ‘C:/Users/murat/AppData/Local/Temp/RtmpI776iL/downloaded_packages/index.html’ > had non-zero exit status > > > > > packageurl <- " > 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’ > > (as ‘lib’ is unspecified) > > trying URL ' > 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) > > downloaded 2.9 MB > > > > * installing *source* package 'ggplot2' ... > > ** package 'ggplot2' successfully unpacked and MD5 sums checked > > ** 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") > > Error in load_private_package("cli") : > > Cannot load cli from the private library > > > > > pak::pkg_install("tidyverse/tibble") > > Error in load_private_package("cli") : > > Cannot load cli from the private library > > > > > pkg_install("tibble") > > Error in pkg_install("tibble") : could not find function "pkg_install" > > > > > 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’ > > (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 > > [image: Mailtrack] > <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> > Sender > notified by > Mailtrack > <https://mailtrack.io?utm_source=gmail&utm_medium=signature&utm_campaign=signaturevirality11&> > 08/04/23, > 10:12:50 AM > ______________________________________________ > 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. ______________________________________________ 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.