install fail using dev tools

[ptsii]

This is on an apple laptop (intel), running the latest operating system

Here's the output:

── R CMD build ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file ‘/private/var/folders/mk/9_clkwx513df94kdv85c25m80000gn/T/RtmpeSwXX1/remotes24173c198763/bbuchsbaum-neuroim2-6c134a3/DESCRIPTION’ (395ms)
─ preparing ‘neuroim2’: (1s)
Warning: /private/var/folders/mk/9_clkwx513df94kdv85c25m80000gn/T/Rtmp7vQmKC/Rbuild266f13276152/neuroim2/man/LatentNeuroVec-class.Rd:23: unknown macro '\linkS4Class'
─ checking for empty or unneeded directoriesn/LatentNeuroVec-class.Rd:23: unknown macro '\linkS4Class'

• installing source package ‘neuroim2’ ...
  ** using staged installation
  ** libs
  clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include -fPIC "-mtune=native -g O2 -Wall -pedantic -Wconversion" -c RcppExports.cpp -o RcppExports.o
  error: unknown target CPU 'native -g O2 -Wall -pedantic -Wconversion'
  note: valid target CPU values are: i386, i486, winchip-c6, winchip2, c3, i586, pentium, pentium-mmx, pentiumpro, i686, pentium2, pentium3, pentium3m, pentium-m, c3-2, yonah, pentium4, pentium4m, prescott, nocona, core2, penryn, bonnell, atom, silvermont, slm, goldmont, goldmont-plus, tremont, nehalem, corei7, westmere, sandybridge, corei7-avx, ivybridge, core-avx-i, haswell, core-avx2, broadwell, skylake, skylake-avx512, skx, cascadelake, cooperlake, cannonlake, icelake-client, rocketlake, icelake-server, tigerlake, sapphirerapids, alderlake, knl, knm, lakemont, k6, k6-2, k6-3, athlon, athlon-tbird, athlon-xp, athlon-mp, athlon-4, k8, athlon64, athlon-fx, opteron, k8-sse3, athlon64-sse3, opteron-sse3, amdfam10, barcelona, btver1, btver2, bdver1, bdver2, bdver3, bdver4, znver1, znver2, znver3, x86-64, geode
  make: *** [RcppExports.o] Error 1
  ERROR: compilation failed for package ‘neuroim2’
• removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/neuroim2’
  Warning message:
  In i.p(...) :
  installation of package ‘/var/folders/mk/9_clkwx513df94kdv85c25m80000gn/T//RtmpeSwXX1/file24177264035f/neuroim2_0.7.0.tar.gz’ had non-zero exit status

[bbuchsbaum]

\linkS4Class mispelled in neuroim2, have just fixed in neuroim2 repository.

[ptsii]

Thanks for the quick assessment!

However, I still get an error:

> install_github("bbuchsbaum/neuroim2")
Downloading GitHub repo bbuchsbaum/neuroim2@HEAD
── R CMD build ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────────
✔  checking for file ‘/private/var/folders/mk/9_clkwx513df94kdv85c25m80000gn/T/RtmpeSwXX1/remotes2417639f99a8/bbuchsbaum-neuroim2-8177731/DESCRIPTION’ (1.8s)
✔  checking DESCRIPTION meta-information ...
─  cleaning src
   
* installing *source* package ‘neuroim2’ ...
** using staged installation
** libs
clang++ -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG  -I'/Library/Frameworks/R.framework/Versions/4.2/Resources/library/Rcpp/include' -I/usr/local/include   -fPIC  "-mtune=native -g O2 -Wall -pedantic -Wconversion" -c RcppExports.cpp -o RcppExports.o
error: unknown target CPU 'native -g O2 -Wall -pedantic -Wconversion'
note: valid target CPU values are: i386, i486, winchip-c6, winchip2, c3, i586, pentium, pentium-mmx, pentiumpro, i686, pentium2, pentium3, pentium3m, pentium-m, c3-2, yonah, pentium4, pentium4m, prescott, nocona, core2, penryn, bonnell, atom, silvermont, slm, goldmont, goldmont-plus, tremont, nehalem, corei7, westmere, sandybridge, corei7-avx, ivybridge, core-avx-i, haswell, core-avx2, broadwell, skylake, skylake-avx512, skx, cascadelake, cooperlake, cannonlake, icelake-client, rocketlake, icelake-server, tigerlake, sapphirerapids, alderlake, knl, knm, lakemont, k6, k6-2, k6-3, athlon, athlon-tbird, athlon-xp, athlon-mp, athlon-4, k8, athlon64, athlon-fx, opteron, k8-sse3, athlon64-sse3, opteron-sse3, amdfam10, barcelona, btver1, btver2, bdver1, bdver2, bdver3, bdver4, znver1, znver2, znver3, x86-64, geode
make: *** [RcppExports.o] Error 1
ERROR: compilation failed for package ‘neuroim2’
* removing ‘/Library/Frameworks/R.framework/Versions/4.2/Resources/library/neuroim2’
Warning message:
In i.p(...) :
  installation of package ‘/var/folders/mk/9_clkwx513df94kdv85c25m80000gn/T//RtmpeSwXX1/file241732117b1/neuroim2_0.7.0.tar.gz’ had non-zero exit status

I'm wondering if this is the problem: "error: unknown target CPU"?

[bbuchsbaum]

I'm afraid this one is in your court. You need a working R build toolchain for your mac laptop.

see:

https://stackoverflow.com/questions/70638118/configuring-compilers-on-apple-silicon-big-sur-monterey-ventura-for-rcpp-and

[ptsii]

Can you elaborate? My laptop isn't apple silicon, it is intel. But the link you provided references apple silicon. Also, I've compiled many R libraries successfully (e.g., recently ANTsR). What is the issue with rMVPA that is different from these other libraries?

[bbuchsbaum]

I don't know the issue, but I know compiling R sources on Mac can be tricky. can you compile the following?

Rcpp::sourceCpp(code='
#include <Rcpp.h>

// [[Rcpp::export]]
int fibonacci(const int x) {
if (x == 0) return(0);
if (x == 1) return(1);
return (fibonacci(x - 1)) + fibonacci(x - 2);
}'
,verbose=T)

see:
https://discourse.mc-stan.org/t/problem-compling-rstan-models-on-mac-m1-with-clang-13-0-0/26184