Non-zero exit status when trying to install CellChat from Github

[mbarnes20]

Hi there!

I am using the devtools::install_github("sqjin/CellChat") to install CellChat after following the installation of NMF and circlize packages from the GitHub page. I am still getting the following warning message:

Warning message:
In i.p(...) :
installation of package ‘C:/Users/mvb19/AppData/Local/Temp/RtmpU9WRMh/file215c7e405f62/CellChat_2.1.2.tar.gz’ had non-zero exit status

I have RTools installed, and I have tried installing the package using the zip file and tar.gz files from my local drive, but neither of those work either. Please help!

Thanks so much :)

[gchen605]

I think I have a related problem, here is what I see:

devtools::install_github("jinworks/CellChat")
Downloading GitHub repo jinworks/CellChat@HEAD
Skipping 3 packages not available: Biobase, BiocNeighbors, BiocGenerics
── R CMD build ───────────────────────────────────────────────────────────────────
✔ checking for file ‘/private/var/folders/d_/498ljjl95lb3gk4fqc7kjgxxn8j52f/T/RtmpZiLYPu/remotes562719560337/jinworks-CellChat-b05405a/DESCRIPTION’ ...
─ preparing ‘CellChat’:
✔ checking DESCRIPTION meta-information
─ cleaning src
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ building ‘CellChat_2.1.2.tar.gz’
Warning: invalid uid value replaced by that for user 'nobody'
Warning: invalid gid value replaced by that for user 'nobody'

Installing package into ‘/Users/user/Library/R/arm64/4.4/library’
(as ‘lib’ is unspecified)

• installing source package ‘CellChat’ ...
  ** using staged installation
  ** libs
  using C++ compiler: ‘Apple clang version 16.0.0 (clang-1600.0.26.3)’
  using SDK: ‘MacOSX15.0.sdk’
  clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Users/user/Library/R/arm64/4.4/library/Rcpp/include' -I'/Users/user/Library/R/arm64/4.4/library/RcppEigen/include' -I/opt/R/arm64/include -fPIC -falign-functions=64 -Wall -g -O2 -c CellChat_Rcpp.cpp -o CellChat_Rcpp.o
  In file included from CellChat_Rcpp.cpp:1:
  In file included from /Users/user/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigen.h:25:
  /Users/user/Library/R/arm64/4.4/library/RcppEigen/include/RcppEigenForward.h:25:10: fatal error: 'iterator' file not found
  25 | #include
  | ^~~~~~~~~~
  1 error generated.
  make: *** [CellChat_Rcpp.o] Error 1
  ERROR: compilation failed for package ‘CellChat’
• removing ‘/Users/user/Library/R/arm64/4.4/library/CellChat’
  Warning message:
  In i.p(...) :
  installation of package ‘/var/folders/d_/498ljjl95lb3gk4fqc7kjgxxn8j52f/T//RtmpZiLYPu/file56276d4c46e7/CellChat_2.1.2.tar.gz’ had non-zero exit status

[mbarnes20]

@gchen605 it looks like your problem may be slightly different from mine, as I did not have any other error messages other than 'lazy loading failed' after the compiling of the package etc.
With your error, an issue with compiling may be linked to Rtools not being detected? Have you tried running pkgbuild::find_rtools() to see if Rtools is detected? If it is, then I'm not sure what else to suggest for you.

I have finally managed to get it installed on R v4.4.1 by creating a new personal library and basically starting from scratch and installing everything from there.

[Lulu0015]

I met the same issue as @gchen605. Are any solutions being found? Thanks!

[Lulu0015]

I met the same issue as @gchen605. Are any solutions being found? Thanks!

Reinstalling xcode solved the issue for me.

[gchen605]

I met the same issue as @gchen605. Are any solutions being found? Thanks!

Reinstalling xcode solved the issue for me.

This worked for me! Thank you!