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.
