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&type=printable | 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 | 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 | 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 | https://cran.rstudio.com/bin/windows/contrib/3.5 ] : cannot open URL ' [ https://cran.rstudio.com/bin/windows/contrib/3.5/PACKAGES | 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 | 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 | 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 | 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 | 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 | 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
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