Problems with installation of cytofkit

[irenesarkar30]

Hi,

I have been trying to install cytofkit and every time it comes up with an error message. I have tied from Bioconductor and also from Github.

Error: Failed to install 'cytofkit' from GitHub:
Could not find tools necessary to compile a package
Call pkgbuild::check_build_tools(debug = TRUE) to diagnose the problem.

I am very new to coding so it will be really nice if you can tell me how to install this, as I really want to use it. Thanks.

[SamGG]

Hi,
Windows, Mac or Linux?

[irenesarkar30]

Hi, Thank you for replying so fast. I have been stuck witht his for the last 2 days!! I have Windows 10 and R version 3.6.1. Thanks a lot. Irene

…

________________________________ From: Samuel Granjeaud <[email protected]> Sent: Thursday, October 31, 2019 3:03:19 PM To: JinmiaoChenLab/cytofkit Cc: Irene Sarkar; Author Subject: Re: [JinmiaoChenLab/cytofkit] Problems with installation of cytofkit (#76) Hi, Windows, Mac or Linux? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#76?email_source=notifications&email_token=AM7BU2HY7FX6HGTSOD7FPW3QRLQSPA5CNFSM4JHKMUBKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOECX4L2I#issuecomment-548390377>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AM7BU2GEJTC47ZLYLQZVMRDQRLQSPANCNFSM4JHKMUBA>.

[SamGG]

I think Rtools should be installed to compile the Rphenograph code.
You could find a short howto at http://jtleek.com/modules/01_DataScientistToolbox/02_10_rtools/#1
Usually you must be administrator to install Rtools because you have to modify the PATH variable at on point of the installation. We got a detailed procedure in french at http://impact-cyto.inserm.fr/installation-r/. Please do find below a quick translation with deepl.
Hope this help,
Samuel

The installation consists of two parts: the first part where it is recommended to act as the administrator of the machine, the second part where user rights are sufficient.

For the first part (as administrator), here are the software and extensions that we recommend to install:

R (choose your system): install the 64-bit version (uncheck the 32-bit version); moreover, I do not select any translation in order to obtain error messages in English that are more documented on the Internet.
RStudio Desktop (choose your system): follow the steps.
The most up-to-date versions often require a computer-specific installation (compilation step). For Windows, you must install in addition:

Rtools (windows): download and follow the steps; choose the 64-bit version, because R is installed in 64 bits (uncheck the installation of the 32-bit version of Rtools). Important point: tick the box to add programs to the PATH (without this, R does not find make); this option only appears if the installation is performed as an administrator (if you do not see it, repeat the installation in administrator mode by clicking with the right button on the installer and selecting "Run year while..."). Complete the installation.

For the second part, administrator rights are not necessary, as packages adding functionality to R will be installed in the user folder. So, run Rstudio, and then install the following packages/library that will be useful to install the different analysis methods:
devtools allows you to install packages from github to use the latest updates:
install.packages("devtools")

Translated with www.DeepL.com/Translator

[irenesarkar30]

Hi,

I just followed your instrauctions but the same error is coming. It is first saying that i need some additional tools, which I installed and tried running again. It again says I need additional tools and gives the same error message " Error: Failed to install 'cytofkit' from GitHub:
Could not find tools necessary to compile a package
Call pkgbuild::check_build_tools(debug = TRUE) to diagnose the problem.'

I am very confused as my colleague could install in R 3.6.1 but I cannot.

[SamGG]

Quite weird. Could you do a copy of the output of the R console/terminal and paste it in your reply? After that, try to reinstall devtools, and then cytofkit. But before, you should ensure that you are working in an empty RStudio project, either doing:

• start a new project, close all other projects, quit RStudio and restart it
• close all the scripts, clear all data, , quit RStudio and restart it

[irenesarkar30]

install.packages("devtools")
Installing package into ‘C:/Users/irene/OneDrive/Documents/R/win-library/3.6’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/bin/windows/contrib/3.6/devtools_2.2.1.zip'
Content type 'application/zip' length 342318 bytes (334 KB)
downloaded 334 KB

package ‘devtools’ successfully unpacked and MD5 sums checked

The downloaded binary packages are in
C:\Users\irene\AppData\Local\Temp\RtmpEpK5jc\downloaded_packages

BiocManager::install("cytofkit")
Bioconductor version 3.9 (BiocManager 1.30.9), R 3.6.1 (2019-07-05)
Installing package(s) 'cytofkit'
Warning message:
package ‘cytofkit’ is not available (for R version 3.6.1)
BiocManager::install("JinmiaoChenLab/cytofkit")
Bioconductor version 3.9 (BiocManager 1.30.9), R 3.6.1 (2019-07-05)
Installing github package(s) 'JinmiaoChenLab/cytofkit'
Downloading GitHub repo JinmiaoChenLab/cytofkit@master
trying URL 'https://cran.rstudio.com/bin/windows/Rtools/Rtools35.exe'
Content type 'application/x-msdownload' length 108622512 bytes (103.6 MB)
downloaded 103.6 MB

Error: Failed to install 'cytofkit' from GitHub:
Could not find tools necessary to compile a package
Call pkgbuild::check_build_tools(debug = TRUE) to diagnose the problem.

[SamGG]

OK, it fails clearly at cytofkit.
Try directly
devtools::install_github("JinmiaoChenLab/cytofkit")

[SamGG]

Copy/paste the result from the recommended command
pkgbuild::check_build_tools(debug = TRUE)

[Sheseira]

I have problems with the installation as well. I used a code you mentioned in another post, but unfortunately it still doesn't work. I just started with coding a couple days ago, so please bear with me.

Copy/paste the result from the recommended command
pkgbuild::check_build_tools(debug = TRUE)

[SamGG]

Hi,
The error has nothing to do with the installation of cytofkit. Skip updates. If it fails, then the problem has to do with installing cytofkit. Then open a new issue please.
Best.