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Issues installing #305

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clairexqu opened this issue Feb 5, 2025 · 2 comments
Open

Issues installing #305

clairexqu opened this issue Feb 5, 2025 · 2 comments

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@clairexqu
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This is the message I get when I try to install CellChat:

installing source package ‘CellChat’ ...
** using staged installation
** libs
using C++ compiler: ‘Apple clang version 16.0.0 (clang-1600.0.26.6)’
using SDK: ‘MacOSX15.2.sdk’
clang++ -arch arm64 -std=gnu++17 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/Rcpp/include' -I'/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/RcppEigen/include/RcppEigen.h:25:
/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/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 ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library/CellChat’
    Warning message:
    In i.p(...) :
    installation of package ‘/var/folders/tz/t159gbm56bd2661pwf1l9nfr0000gn/T//RtmprN8pth/filee79723aba7c/CellChat_2.1.2.tar.gz’ had non-zero exit status

Someone else had this issue a month ago, but I'm still not sure how to resolve it. I know its related to the compiler and Xcode, but I tried to update it just now and am still getting the same message.

@clairexqu
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I have an M1 chip if that helps

@clairexqu
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When I updated to the most recent version of R, I get this

ERROR: dependency ‘BiocNeighbors’ is not available for package ‘CellChat’

  • removing ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/CellChat’
    Warning messages:
    1: packages ‘Biobase’, ‘BiocNeighbors’ are not available for this version of R

Versions of these packages 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
2: In i.p(...) :
installation of package ‘/var/folders/tz/t159gbm56bd2661pwf1l9nfr0000gn/T//RtmpoGng6D/file10cf7c5f00ba/CellChat_2.1.2.tar.gz’ had non-zero exit status

What version of R is ideal for CellChat?

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