Installation issues

[taxkourel]

## I install bioconductor

if (!requireNamespace("BiocManager", quietly = TRUE))

• install.packages("BiocManager")
  

BiocManager::install(version = "3.13")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
CRAN: https://cran.rstudio.com/

Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18)

##But then I can't install cytofkit2

if (!requireNamespace("BiocManager", quietly = TRUE))

• install.packages("BiocManager")
  

BiocManager::install("cytofkit2")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
CRAN: https://cran.rstudio.com/

Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18)
Installing package(s) 'cytofkit2'
Warning message:
In .inet_warning(msg) :
package ‘cytofkit2’ is not available for Bioconductor version '3.13'

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages

#what am I doing wrong? Thank you.

[raman91]

Hi, please install cytofkit2 using these commands:

if(!require(devtools)){
install.packages("devtools") # If not already installed
}
devtools::install_github("JinmiaoChenLab/cytofkit2")

Thanks

[taxkourel]

Did not work. After it installs some packages I get this The downloaded binary packages are in C:\Users\m099097\AppData\Local\Temp\RtmpWgBjb2\downloaded_packages installing the source packages ‘matrixStats’, ‘ALL’, ‘e1071’ trying URL 'https://cran.rstudio.com/src/contrib/matrixStats_0.60.0.tar.gz' Content type 'application/x-gzip' length 204940 bytes (200 KB) downloaded 200 KB trying URL 'https://bioconductor.org/packages/3.13/data/experiment/src/contrib/ALL_1.34.0.tar.gz' Content type 'application/x-gzip' length 11401609 bytes (10.9 MB) downloaded 10.9 MB trying URL 'https://cran.rstudio.com/src/contrib/e1071_1.7-8.tar.gz' Content type 'application/x-gzip' length 581347 bytes (567 KB) downloaded 567 KB * installing *source* package 'matrixStats' ... ** package 'matrixStats' successfully unpacked and MD5 sums checked ** using staged installation ** libs *** arch - i386 "c:/rtools40/mingw32/bin/"gcc -I"C:/PROGRA~1/R/R-41~1.0/include" -DNDEBUG -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c 000.init.c -o 000.init.o sh: c:/rtools40/mingw32/bin/gcc: No such file or directory make: *** [C:/PROGRA~1/R/R-41~1.0/etc/i386/Makeconf:238: 000.init.o] Error 127 ERROR: compilation failed for package 'matrixStats' * removing 'C:/Users/m099097/Documents/R/win-library/4.1/matrixStats' * installing *source* package 'ALL' ... ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices converting help for package 'ALL' finding HTML links ... done ALL html tojulian html ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location *** arch - i386 *** arch - x64 ** testing if installed package can be loaded from final location *** arch - i386 *** arch - x64 ** testing if installed package keeps a record of temporary installation path * DONE (ALL) * installing *source* package 'e1071' ... ** package 'e1071' successfully unpacked and MD5 sums checked ** using staged installation ********************************************** WARNING: this package has a configure script It probably needs manual configuration ********************************************** ** libs *** arch - i386 "c:/rtools40/mingw32/bin/"gcc -I"C:/PROGRA~1/R/R-41~1.0/include" -DNDEBUG -O2 -Wall -std=gnu99 -mfpmath=sse -msse2 -mstackrealign -c Rsvm.c -o Rsvm.o sh: c:/rtools40/mingw32/bin/gcc: No such file or directory make: *** [C:/PROGRA~1/R/R-41~1.0/etc/i386/Makeconf:238: Rsvm.o] Error 127 ERROR: compilation failed for package 'e1071' * removing 'C:/Users/m099097/Documents/R/win-library/4.1/e1071' The downloaded source packages are in ‘C:\Users\m099097\AppData\Local\Temp\RtmpWgBjb2\downloaded_packages’ √ checking for file 'C:\Users\m099097\AppData\Local\Temp\RtmpWgBjb2\remotes509861af585f\JinmiaoChenLab-cytofkit2-8ec6b91/DESCRIPTION' (486ms) - preparing 'cytofkit2': (749ms) √ checking DESCRIPTION meta-information ... - cleaning src - checking for LF line-endings in source and make files and shell scripts (363ms) - checking for empty or unneeded directories - building 'cytofkit2_0.99.75.tar.gz' Installing package into ‘C:/Users/m099097/Documents/R/win-library/4.1’ (as ‘lib’ is unspecified) ERROR: dependency 'e1071' is not available for package 'cytofkit2' * removing 'C:/Users/m099097/Documents/R/win-library/4.1/cytofkit2' Warning messages: 1: In i.p(...) : installation of package ‘matrixStats’ had non-zero exit status 2: In i.p(...) : installation of package ‘e1071’ had non-zero exit status 3: In i.p(...) : installation of package ‘C:/Users/m099097/AppData/Local/Temp/RtmpWgBjb2/file50981d242ec2/cytofkit2_0.99.75.tar.gz’ had non-zero exit status and then

cytofkit_shiny_dashboard()

Error in cytofkit_shiny_dashboard() : could not find function "cytofkit_shiny_dashboard" From: raman91 ***@***.***> Sent: Wednesday, July 28, 2021 8:32 PM To: JinmiaoChenLab/cytofkit2 ***@***.***> Cc: Kourelis, Taxiarchis, M.D. ***@***.***>; Author ***@***.***> Subject: [EXTERNAL] Re: [JinmiaoChenLab/cytofkit2] Installation issues (#37) Hi, please install cytofkit2 using these commands: if(!require(devtools)){ install.packages("devtools") # If not already installed } devtools::install_github("JinmiaoChenLab/cytofkit2") Thanks — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#37 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AKDS2EHAZVEWO7SRL7EGKBDT2CVRTANCNFSM5BE7T7SA>.

[raman91]

Hi, you will have to install 'e1071' package individually first using:
install.packages('e1071')

and then install cytofkit2 package using:

if(!require(devtools)){
install.packages("devtools") # If not already installed
}
devtools::install_github("JinmiaoChenLab/cytofkit2")

[taxkourel]

Thank you! I did that and had to instal. 5 more packages but it worked eventually 😊 From: raman91 ***@***.***> Sent: Friday, July 30, 2021 12:39 AM To: JinmiaoChenLab/cytofkit2 ***@***.***> Cc: Kourelis, Taxiarchis, M.D. ***@***.***>; Author ***@***.***> Subject: [EXTERNAL] Re: [JinmiaoChenLab/cytofkit2] Installation issues (#37) Hi, you will have to install 'e1071' package individually first using: install.packages('e1071') and then install cytofkit2 package using: if(!require(devtools)){ install.packages("devtools") # If not already installed } devtools::install_github("JinmiaoChenLab/cytofkit2") — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#37 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AKDS2ECXUKMNUDSCETDETKLT2I3JDANCNFSM5BE7T7SA>.