Cannot install on arm64

[skilpinen]

Hi,

Any attempt to install this package (same with master and develop) to Arm64 Mac leads to error below. What is this about?

remotes::install_github("satijalab/sctransform", ref="develop") Downloading GitHub repo satijalab/sctransform@develop ✔ checking for file ‘/private/var/folders/jb/8nrbz8jx5v78ly5_0kvgx49c0000gn/T/RtmpQBcrbr/remotes1132274ac8bdc/satijalab-sctransform-e9e52a4/DESCRIPTION’ (442ms) ─ preparing ‘sctransform’: ✔ checking DESCRIPTION meta-information ... ─ cleaning src ─ installing the package to process help pages

─ installing source package ‘sctransform’ ... using staged installation libs arm64-apple-darwin20.0.0-clang++ -std=gnu++11 -I"/opt/homebrew/Caskroom/miniforge/base/envs/r412_arm/lib/R/include" -DNDEBUG -I'/opt/homebrew/Caskroom/miniforge/base/envs/r412_arm/lib/R/library/RcppArmadillo/include' -I'/opt/homebrew/Caskroom/miniforge/base/envs/r412_arm/lib/R/library/Rcpp/include' -D_FORTIFY_SOURCE=2 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/r412_arm/include -mmacosx-version-min=11.0 -I/opt/homebrew/Caskroom/miniforge/base/envs/r412_arm/include -fPIC -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -stdlib=libc++ -fvisibility-inlines-hidden -fmessage-length=0 -isystem /opt/homebrew/Caskroom/miniforge/base/envs/r412_arm/include -fdebug-prefix-map=/Users/runner/miniforge3/conda-bld/r-base-split_1642327593909/work=/usr/local/src/conda/r-base-4.1.2 -fdebug-prefix-map=/opt/homebrew/Caskroom/miniforge/base/envs/r412_arm=/usr/local/src/conda-prefix -Wall -pedantic -fdiagnostics-color=always -c RcppExports.cpp -o RcppExports.o In file included from RcppExports.cpp:4: In file included from /opt/homebrew/Caskroom/miniforge/base/envs/r412_arm/lib/R/library/RcppArmadillo/include/RcppArmadillo.h:29: In file included from /opt/homebrew/Caskroom/miniforge/base/envs/r412_arm/lib/R/library/RcppArmadillo/include/RcppArmadilloForward.h:48: In file included from /opt/homebrew/Caskroom/miniforge/base/envs/r412_arm/lib/R/library/RcppArmadillo/include/armadillo:380: /opt/homebrew/Caskroom/miniforge/base/envs/r412_arm/lib/R/library/RcppArmadillo/include/armadillo_bits/eop_aux.hpp:99:124: error: no member named 'Rlog1p' in namespace 'std'; did you mean 'log1p'? template arma_inline static typename arma_integral_only::result log1p (const eT x) { return eT( std::log1p(double(x)) ); }

                                                                                                                              log1p
   /opt/homebrew/Caskroom/miniforge/base/envs/r412_arm/lib/R/include/Rmath.h:71:15: note: expanded from macro 'log1p'
   #define log1p Rlog1p
                 ^
   /opt/homebrew/Caskroom/miniforge/base/envs/r412_arm/bin/../include/c++/v1/cmath:433:9: note: 'log1p' declared here
   using ::log1p _LIBCPP_USING_IF_EXISTS;
           ^
   In file included from RcppExports.cpp:4:
   In file included from /opt/homebrew/Caskroom/miniforge/base/envs/r412_arm/lib/R/library/RcppArmadillo/include/RcppArmadillo.h:29:
   In file included from /opt/homebrew/Caskroom/miniforge/base/envs/r412_arm/lib/R/library/RcppArmadillo/include/RcppArmadilloForward.h:48:
   In file included from /opt/homebrew/Caskroom/miniforge/base/envs/r412_arm/lib/R/library/RcppArmadillo/include/armadillo:380:
   /opt/homebrew/Caskroom/miniforge/base/envs/r412_arm/lib/R/library/RcppArmadillo/include/armadillo_bits/eop_aux.hpp:100:115: error: no member named 'Rlog1p' in namespace 'std'; did you mean simply 'Rlog1p'?
     template<typename eT> arma_inline static typename       arma_real_only<eT>::result log1p (const eT  x) { return std::log1p(x);               }
                                                                                                                     ^~~~~~~~~~
                                                                                                                     Rlog1p
   /opt/homebrew/Caskroom/miniforge/base/envs/r412_arm/lib/R/library/RcppArmadillo/include/armadillo_bits/eop_aux.hpp:101:86: note: 'Rlog1p' declared here
     template<typename eT> arma_inline static typename         arma_cx_only<eT>::result log1p (const eT& x) { arma_ignore(x); return eT(0);       }
                                                                                        ^
   /opt/homebrew/Caskroom/miniforge/base/envs/r412_arm/lib/R/include/Rmath.h:71:15: note: expanded from macro 'log1p'
   #define log1p Rlog1p
                 ^
   In file included from RcppExports.cpp:4:
   In file included from /opt/homebrew/Caskroom/miniforge/base/envs/r412_arm/lib/R/library/RcppArmadillo/include/RcppArmadillo.h:29:
   In file included from /opt/homebrew/Caskroom/miniforge/base/envs/r412_arm/lib/R/library/RcppArmadillo/include/RcppArmadilloForward.h:48:
   In file included from /opt/homebrew/Caskroom/miniforge/base/envs/r412_arm/lib/R/library/RcppArmadillo/include/armadillo:440:
   /opt/homebrew/Caskroom/miniforge/base/envs/r412_arm/lib/R/library/RcppArmadillo/include/armadillo_bits/fn_misc.hpp:172:21: error: no member named 'Rlog1p' in namespace 'std'; did you mean simply 'Rlog1p'?
       return (log_a + std::log1p(std::exp(negdelta)));
                       ^~~~~~~~~~
                       Rlog1p
   /opt/homebrew/Caskroom/miniforge/base/envs/r412_arm/lib/R/include/Rmath.h:70:9: note: 'Rlog1p' declared here
   double  Rlog1p(double);
           ^
   3 errors generated.
   make: *** [/opt/homebrew/Caskroom/miniforge/base/envs/r412_arm/lib/R/etc/Makeconf:177: RcppExports.o] Error 1
   ERROR: compilation failed for package ‘sctransform’
─  removing ‘/private/var/folders/jb/8nrbz8jx5v78ly5_0kvgx49c0000gn/T/RtmpTGatHe/Rinst11eaa7cedd496/sctransform’
         -----------------------------------
   ERROR: package installation failed
Error: Failed to install 'sctransform' from GitHub:
  System command 'R' failed, exit status: 1, stdout & stderr were printed

[saketkc]

This appears to be arising from your installed version of Rcpparmadillo not having required flags set for arm64, see related issue, though it seems to have been fixed upstream. I would recommend creating a new conda environment with updated packages or updating packages in your current enironment before installing sctransform.

[genecell]

As mentioned in https://github.com/conda-forge/r-base-feedstock/issues/163#issuecomment-1172913391, I successfully installed sctransform in Mac silicon M1 Max by first run export PKG_CPPFLAGS="-DHAVE_WORKING_LOG1P in the terminal and then install the package in R.