Errors installing from source - MAC OS M1 and R 4.1/Rstudio daily build

kgoldfeld · April 16, 2021, 10:43pm

I am occasionally running into some difficulties installing from source. This my setup, in addition to Rstudio Version 1.4.1674

R Under development (unstable) (2021-04-08 r80148)
Platform: aarch64-apple-darwin20.0 (64-bit)
Running under: macOS Big Sur 11.2.3

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/lib/libRlapack.dylib

Here is what I get when I try to install package lubridate (though I run into similar problems with some - not all - pacakges):

installing the source package ‘lubridate’

trying URL 'https://cran.rstudio.com/src/contrib/lubridate_1.7.10.tar.gz'
Content type 'application/x-gzip' length 473547 bytes (462 KB)
==================================================
downloaded 462 KB

* installing *source* package ‘lubridate’ ...
** package ‘lubridate’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./cctz/src/ -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c cctz/src/time_zone_fixed.cc -o cctz/src/time_zone_fixed.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./cctz/src/ -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c cctz/src/time_zone_if.cc -o cctz/src/time_zone_if.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./cctz/src/ -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/R/arm64/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c cctz/src/time_zone_impl.cc -o cctz/src/time_zone_impl.o
In file included from cctz/src/time_zone_impl.cc:21:
In file included from /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/unordered_map:409:
In file included from /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__hash_table:18:
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/cmath:317:9: error: no member named 'signbit' in the global namespace
using ::signbit;
      ~~^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/cmath:318:9: error: no member named 'fpclassify' in the global namespace
using ::fpclassify;
      ~~^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/cmath:319:9: error: no member named 'isfinite' in the global namespace
using ::isfinite;
      ~~^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/cmath:320:9: error: no member named 'isinf' in the global namespace
using ::isinf;
      ~~^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/cmath:321:9: error: no member named 'isnan' in the global namespace
using ::isnan;
      ~~^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/cmath:322:9: error: no member named 'isnormal' in the global namespace
using ::isnormal;
      ~~^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/cmath:323:7: error: no member named 'isgreater' in the global namespace; did you mean '::std::greater'?
using ::isgreater;
      ^~
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/functional:738:29: note: '::std::greater' declared here
struct _LIBCPP_TEMPLATE_VIS greater : binary_function<_Tp, _Tp, bool>
                            ^
In file included from cctz/src/time_zone_impl.cc:21:
In file included from /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/unordered_map:409:
In file included from /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__hash_table:18:
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/cmath:324:7: error: no member named 'isgreaterequal' in the global namespace; did you mean '::std::greater_equal'?
using ::isgreaterequal;
      ^~
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/functional:767:29: note: '::std::greater_equal' declared here
struct _LIBCPP_TEMPLATE_VIS greater_equal : binary_function<_Tp, _Tp, bool>
                            ^
In file included from cctz/src/time_zone_impl.cc:21:
In file included from /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/unordered_map:409:
In file included from /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__hash_table:18:
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/cmath:325:9: error: no member named 'isless' in the global namespace
using ::isless;
      ~~^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/cmath:326:9: error: no member named 'islessequal' in the global namespace
using ::islessequal;
      ~~^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/cmath:327:9: error: no member named 'islessgreater' in the global namespace
using ::islessgreater;
      ~~^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/cmath:328:9: error: no member named 'isunordered' in the global namespace
using ::isunordered;
      ~~^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/cmath:329:9: error: no member named 'isunordered' in the global namespace
using ::isunordered;
      ~~^
13 errors generated.
make: *** [cctz/src/time_zone_impl.o] Error 1
ERROR: compilation failed for package ‘lubridate’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/lubridate’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/lubridate’
Warning in install.packages :
  installation of package ‘lubridate’ had non-zero exit status

The downloaded source packages are in
	‘/private/var/folders/jr/19fz7v9976gbf62sf66f7zz40000gq/T/RtmpNeEkUk/downloaded_packages’
> start <- Sys.time()
> summary_stats <- rbindlist(lapply(scenarios, function(a) s_replicate(a, nsim = 2000)))
> Sys.time() - start
Time difference of 9.373234 mins
> s_replicate <- function(argsvec, nsim) {
+   
+   list_of_defs <- s_define()
+   
+   model_results <- rbindlist(
+     parallel::mclapply(
+       X = 1 : nsim, 
+       FUN = function(x) s_single_rep(list_of_defs, argsvec), 
+       mc.cores = 8)
+   )
+   
+   #--- summary statistics ---#
+   
+   power <- model_results[, mean(pval <= 0.05)]
+   summary_stats <- data.table(t(argsvec), power)
+   
+   return(summary_stats) # summary_stats is a data.table
+ }
> start <- Sys.time()
> summary_stats <- rbindlist(lapply(scenarios, function(a) s_replicate(a, nsim = 2000)))
> Sys.time() - start
Time difference of 4.344438 mins
> parallel::detectCores()
[1] 8
> install.packages("lubridate")

  There is a binary version available but the source version is later:
           binary source needs_compilation
lubridate 1.7.9.2 1.7.10              TRUE

Do you want to install from sources the package which needs compilation? (Yes/no/cancel) Yes
installing the source package ‘lubridate’

trying URL 'https://cran.rstudio.com/src/contrib/lubridate_1.7.10.tar.gz'
Content type 'application/x-gzip' length 473547 bytes (462 KB)
==================================================
downloaded 462 KB

* installing *source* package ‘lubridate’ ...
** package ‘lubridate’ successfully unpacked and MD5 sums checked
** using staged installation
** libs
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./cctz/src/ -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c cctz/src/time_zone_fixed.cc -o cctz/src/time_zone_fixed.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./cctz/src/ -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c cctz/src/time_zone_if.cc -o cctz/src/time_zone_if.o
clang++ -arch arm64 -std=gnu++11 -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I. -I./cctz/src/ -I'/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/Rcpp/include' -I/opt/homebrew/Cellar/gettext/0.21/include -I/opt/homebrew/opt/llvm/include   -fPIC  -falign-functions=64 -Wall -g -O2  -c cctz/src/time_zone_impl.cc -o cctz/src/time_zone_impl.o
In file included from cctz/src/time_zone_impl.cc:21:
In file included from /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/unordered_map:409:
In file included from /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__hash_table:18:
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/cmath:317:9: error: no member named 'signbit' in the global namespace
using ::signbit;
      ~~^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/cmath:318:9: error: no member named 'fpclassify' in the global namespace
using ::fpclassify;
      ~~^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/cmath:319:9: error: no member named 'isfinite' in the global namespace
using ::isfinite;
      ~~^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/cmath:320:9: error: no member named 'isinf' in the global namespace
using ::isinf;
      ~~^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/cmath:321:9: error: no member named 'isnan' in the global namespace
using ::isnan;
      ~~^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/cmath:322:9: error: no member named 'isnormal' in the global namespace
using ::isnormal;
      ~~^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/cmath:323:7: error: no member named 'isgreater' in the global namespace; did you mean '::std::greater'?
using ::isgreater;
      ^~
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/functional:738:29: note: '::std::greater' declared here
struct _LIBCPP_TEMPLATE_VIS greater : binary_function<_Tp, _Tp, bool>
                            ^
In file included from cctz/src/time_zone_impl.cc:21:
In file included from /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/unordered_map:409:
In file included from /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__hash_table:18:
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/cmath:324:7: error: no member named 'isgreaterequal' in the global namespace; did you mean '::std::greater_equal'?
using ::isgreaterequal;
      ^~
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/functional:767:29: note: '::std::greater_equal' declared here
struct _LIBCPP_TEMPLATE_VIS greater_equal : binary_function<_Tp, _Tp, bool>
                            ^
In file included from cctz/src/time_zone_impl.cc:21:
In file included from /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/unordered_map:409:
In file included from /Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/__hash_table:18:
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/cmath:325:9: error: no member named 'isless' in the global namespace
using ::isless;
      ~~^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/cmath:326:9: error: no member named 'islessequal' in the global namespace
using ::islessequal;
      ~~^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/cmath:327:9: error: no member named 'islessgreater' in the global namespace
using ::islessgreater;
      ~~^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/cmath:328:9: error: no member named 'isunordered' in the global namespace
using ::isunordered;
      ~~^
/Library/Developer/CommandLineTools/usr/bin/../include/c++/v1/cmath:329:9: error: no member named 'isunordered' in the global namespace
using ::isunordered;
      ~~^
13 errors generated.
make: *** [cctz/src/time_zone_impl.o] Error 1
ERROR: compilation failed for package ‘lubridate’
* removing ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/lubridate’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/4.1-arm64/Resources/library/lubridate’
Warning in install.packages :
  installation of package ‘lubridate’ had non-zero exit status

The downloaded source packages are in
	‘/private/var/folders/jr/19fz7v9976gbf62sf66f7zz40000gq/T/RtmpNeEkUk/downloaded_packages’

Any ideas?

technocrat · April 16, 2021, 11:20pm

Installing to macOS from source has always been, and is likely always to be, problematic because Apple uses a non-standard compiler. If it doesn't work the first time, it won't work unless the user edits the source code. It is always better to install the binary version.

system · May 7, 2021, 11:21pm

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