can't install cytofkit from bioconductor

[olivia930709]

Hello, I'm running the 'BiocManager::install("cytofkit", version = "3.8")' from bioconductor , and here came the error: arch - i386 c:/Rtools/mingw_32/bin/gcc -I"C:/PROGRA~1/R/R-35~1.2/include" -DNDEBUG -std=gnu99 -O3 -Wall -std=gnu99 -mtune=generic -c coerce.c -o coerce.o sh: c:/Rtools/mingw_32/bin/gcc: No such file or directory make: [C:/PROGRA~1/R/R-35~1.2/etc/i386/Makeconf:208: coerce.o] Error 127 ERROR: compilation failed for package 'tibble'

• removing 'C:/Users/dell/Documents/R/win-library/3.5/tibble'
• restoring previous 'C:/Users/dell/Documents/R/win-library/3.5/tibble' In R CMD INSTALL

The downloaded source packages are in ‘C:\Users\dell\AppData\Local\Temp\RtmpO4Icrx\downloaded_packages’ Warning messages: 1: package ‘cytofkit’ is not available (for R version 3.5.2) 2: In install.packages(update[instlib == l, "Package"], l, repos = repos, : installation of package ‘RANN’ had non-zero exit status 3: In install.packages(update[instlib == l, "Package"], l, repos = repos, : installation of package ‘tibble’ had non-zero exit status

Anyone has any idea why it's happening? Many thanks!

[SamGG]

Hi, It sounds odds that the compiler is 32 bits. I guess Windows is 64 bits. Nowadays all computers have more than 4GB of RAM and therefore an OS > 32 bits. Could you report the result of sessionInfo(). I would reinstall Rtools as administrator and selecting only the 64 bits stuff. If the problem persists, install tibble before cytofkit, using BiocManager::install("cytofkit"). Currently, I am still using R 3.5.1, so my answers may be inaccurate. Best.

[Remaniredd]

Trying to install Cytofkit on 3.6 version of R but always coming back with an error. not avilable for this version.

[Remaniredd]

Where can I download the cytofkit package from

[Remaniredd]

Tried installing BiocManager::install("JinmiaoChenLab/cytofkit") but end up with this error message all the time Error: .onLoad failed in loadNamespace() for 'tcltk', details: call: fun(libname, pkgname) error: X11 library is missing: install XQuartz from xquartz.macosforge.org Execution halted ERROR: lazy loading failed for package ‘cytofkit’

• removing ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library/cytofkit’ Error: Failed to install 'cytofkit' from GitHub: (converted from warning) installation of package ‘/var/folders/f2/z5d20nv12_351nfcys6xf_7m0000gp/T//RtmpgYbeTi/file1e7975842037/cytofkit_1.11.3.tar.gz’ had non-zero exit status

[Remaniredd]

How to solve this issue

[SamGG]

@olivia930709 if your issue is solved, could you close it? @Remaniredd you should start a new issue because your problem is not the same. This will avoid people getting the same problem to try Olivia's solution. Nevertheless you should install XQuartz which is a pre-requisite to R in order to use X Windows manager. Sorry I am not working on Mac and can't help you more. I think you have to follow instructions on https://www.xquartz.org.

[Remaniredd]

Thank you, SAM. After installing the Xquartz, now I am able to get the analysis done in CYTOFKIT2 but not in Cytofkit.

Thank you

[SamGG]

I forgot to mention this: I think that if you install cytofkit2, you probably won't need XQuartz as cytofkit2 use shiny instead of TclTk which requires XQuartz. Well, from the point of view of windows user :-)