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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