Data.table: openMP Mac install not working
I've been trying to get timing comparisons of various file IO functions today and managed to get everything working except the OpenMP implementation of fwrite(). When I run fwrite() in my benchmark I get the following:
library(data.table)
set.seed(3-29-16)
rows <- 100000
x <- data.frame(ints = round(runif(rows, -100, 100)), stringsAsFactors = FALSE)
x$floats <- runif(rows, -100, 100)
x$bools <- sample(c(TRUE, FALSE), rows, replace = TRUE)
x$dates <- as.POSIXct(runif(rows, 100000000, 1459293171), origin = "1970-01-01")
x$categories <- as.factor(sample(c(LETTERS, 0:9), rows, replace = TRUE))
x$strings <- replicate(rows, paste0(sample(letters, sample(1:10, 1), replace = TRUE), collapse = ""))
DTCSV =fwrite(x, "x.DT.csv")
#Your platform/environment has not detected OpenMP support. fwrite() will still work, but slower in single threaded mode.
I followed the instructions here: https://github.com/Rdatatable/data.table/wiki/Installation
Created a Makevar file in ~/.R/ with the following flags:
cat ~/.R/Makevars
CC=clang-omp -fopenmp
CXX=clang-omp++ -fopenmp
Running the script above after installation and creation of Makevar file gives the above message.
When I tried to reinstall Rcpp or data.table from source (hoping that it would compile against the OpenMP capable compilier) I get an error.
install.packages("data.table", type = "source",
repos = "https://Rdatatable.github.io/data.table")
trying URL 'https://Rdatatable.github.io/data.table/src/contrib/data.table_1.9.7.tar.gz'
Content type 'application/octet-stream' length 2721566 bytes (2.6 MB)
==================================================
downloaded 2.6 MB
* installing *source* package ‘data.table’ ...
** libs
clang-omp -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c assign.c -o assign.o
In file included from assign.c:1:
In file included from ./data.table.h:1:
/Library/Frameworks/R.framework/Resources/include/R.h:45:12: fatal error: 'stdlib.h' file not found
# include <stdlib.h> /* Not used by R itself, but widely assumed in packages */
^
1 error generated.
The downloaded source packages are in
‘/private/var/folders/zg/hy0k4g312536_4l1qc1w27640000gn/T/RtmpXM09oF/downloaded_packages’
make: *** [assign.o] Error 1
ERROR: compilation failed for package ‘data.table’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/data.table’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/data.table’
Warning message:
In install.packages("data.table", type = "source", repos = "https://Rdatatable.github.io/data.table") :
installation of package ‘data.table’ had non-zero exit status
#############################
install.packages("Rcpp", type = "source")
trying URL 'http://cran.rstudio.com/src/contrib/Rcpp_0.12.4.tar.gz'
Content type 'application/x-gzip' length 2402065 bytes (2.3 MB)
==================================================
downloaded 2.3 MB
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
clang-omp++ -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c Date.cpp -o Date.o
In file included from Date.cpp:31:
In file included from ../inst/include/Rcpp.h:27:
In file included from ../inst/include/RcppCommon.h:29:
In file included from ../inst/include/Rcpp/r/headers.h:48:
In file included from ../inst/include/Rcpp/platform/compiler.h:100:
/usr/local/Cellar/clang-omp/2015-04-01/libexec/bin/../include/c++/v1/cmath:301:10: fatal error: 'math.h' file not found
#include <math.h>
^
1 error generated.
make: *** [Date.o] Error 1
ERROR: compilation failed for package ‘Rcpp’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp’
The downloaded source packages are in
‘/private/var/folders/zg/hy0k4g312536_4l1qc1w27640000gn/T/RtmpXM09oF/downloaded_packages’
Warning message:
In install.packages("Rcpp", type = "source") :
installation of package ‘Rcpp’ had non-zero exit status
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp’
I googled around and found that g++-5 on homebrew comes with openMP so I tapped it. Rcpp compiles, but then data.table does not.
cat ~/.R/Makevars
CC=g++-5 -fopenmp
CXX=g++-5 -fopenmp
install.packages("Rcpp", type = "source")
trying URL 'http://cran.rstudio.com/src/contrib/Rcpp_0.12.4.tar.gz'
Content type 'application/x-gzip' length 2402065 bytes (2.3 MB)
==================================================
downloaded 2.3 MB
* installing *source* package ‘Rcpp’ ...
** package ‘Rcpp’ successfully unpacked and MD5 sums checked
** libs
g++-5 -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c Date.cpp -o Date.o
g++-5 -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c Module.cpp -o Module.o
g++-5 -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c Rcpp_init.cpp -o Rcpp_init.o
g++-5 -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c api.cpp -o api.o
g++-5 -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c attributes.cpp -o attributes.o
g++-5 -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/include/ -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c barrier.cpp -o barrier.o
g++-5 -fopenmp -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o Rcpp.so Date.o Module.o Rcpp_init.o api.o attributes.o barrier.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/3.3/Resources/library/Rcpp/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rcpp)
The downloaded source packages are in
‘/private/var/folders/zg/hy0k4g312536_4l1qc1w27640000gn/T/RtmpXM09oF/downloaded_packages’
############################
install.packages("data.table", type = "source",
repos = "https://Rdatatable.github.io/data.table")
trying URL 'https://Rdatatable.github.io/data.table/src/contrib/data.table_1.9.7.tar.gz'
Content type 'application/octet-stream' length 2721566 bytes (2.6 MB)
==================================================
downloaded 2.6 MB
* installing *source* package ‘data.table’ ...
** libs
g++-5 -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c assign.c -o assign.o
In file included from assign.c:1:0:
data.table.h:73:29: error: two or more data types in declaration of 'parameter'
SEXP which(SEXP x, Rboolean bool);
^
assign.c: In function 'int _selfrefok(SEXP, Rboolean, Rboolean)':
assign.c:115:26: error: invalid conversion from 'void*' to 'SEXP {aka SEXPREC*}' [-fpermissive]
p = R_ExternalPtrAddr(v);
^
The downloaded source packages are in
‘/private/var/folders/zg/hy0k4g312536_4l1qc1w27640000gn/T/RtmpXM09oF/downloaded_packages’
Warning message:
In install.packages("data.table", type = "source", repos = "https://Rdatatable.github.io/data.table") :
installation of package ‘data.table’ had non-zero exit status
assign.c: In function 'Rboolean selfrefok(SEXP, Rboolean)':
assign.c:137:44: error: cannot convert 'bool' to 'Rboolean' in return
return(_selfrefok(x, FALSE, verbose)==1);
^
assign.c: In function 'Rboolean selfrefnamesok(SEXP, Rboolean)':
assign.c:140:43: error: cannot convert 'bool' to 'Rboolean' in return
return(_selfrefok(x, TRUE, verbose)==1);
^
assign.c: In function 'SEXPREC* alloccol(SEXP, R_len_t, Rboolean)':
assign.c:195:17: error: expected unqualified-id before 'class'
SEXP names, class;
^
assign.c:199:5: error: expected primary-expression before 'class'
class = getAttrib(dt, R_ClassSymbol);
^
In file included from data.table.h:3:0,
from assign.c:1:
assign.c:200:16: error: expected primary-expression before 'class'
if (isNull(class)) error("dt passed to alloccol has no class attribute. Please report result of traceback() to datatable-help.");
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:303:21: note: in definition of macro 'TYPEOF'
#define TYPEOF(x) ((x)->sxpinfo.type)
^
assign.c:200:9: note: in expansion of macro 'isNull'
if (isNull(class)) error("dt passed to alloccol has no class attribute. Please report result of traceback() to datatable-help.");
^
assign.c:200:16: error: expected ')' before 'class'
if (isNull(class)) error("dt passed to alloccol has no class attribute. Please report result of traceback() to datatable-help.");
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:303:21: note: in definition of macro 'TYPEOF'
#define TYPEOF(x) ((x)->sxpinfo.type)
^
assign.c:200:9: note: in expansion of macro 'isNull'
if (isNull(class)) error("dt passed to alloccol has no class attribute. Please report result of traceback() to datatable-help.");
^
assign.c:200:133: error: expected ')' before ';' token
if (isNull(class)) error("dt passed to alloccol has no class attribute. Please report result of traceback() to datatable-help.");
^
assign.c:200:133: error: expected ')' before ';' token
assign.c:200:133: error: expected ')' before ';' token
In file included from data.table.h:3:0,
from assign.c:1:
assign.c: In function 'SEXPREC* alloccolwrapper(SEXP, SEXP, SEXP)':
assign.c:227:76: error: invalid conversion from 'int' to 'Rboolean' [-fpermissive]
SEXP ans = PROTECT(alloccol(dt, INTEGER(newncol)[0], LOGICAL(verbose)[0]));
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:661:31: note: in definition of macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
assign.c:193:6: note: initializing argument 3 of 'SEXPREC* alloccol(SEXP, R_len_t, Rboolean)'
SEXP alloccol(SEXP dt, R_len_t n, Rboolean verbose)
^
assign.c: In function 'Rboolean isDatatable(SEXP)':
assign.c:252:10: error: expected primary-expression before 'class'
SEXP class = getAttrib(x, R_ClassSymbol);
^
In file included from data.table.h:3:0,
from assign.c:1:
assign.c:253:28: error: expected primary-expression before 'class'
for (int i=0; i<length(class); i++) {
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:1222:30: note: in definition of macro 'length'
#define length(x) Rf_length(x)
^
assign.c:254:36: error: expected primary-expression before 'class'
if (strcmp(CHAR(STRING_ELT(class, i)), "data.table") == 0) return(TRUE);
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:382:41: note: in definition of macro 'DATAPTR'
#define DATAPTR(x) (((SEXPREC_ALIGN *) (x)) + 1)
^
assign.c:254:20: note: in expansion of macro 'CHAR'
if (strcmp(CHAR(STRING_ELT(class, i)), "data.table") == 0) return(TRUE);
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:389:35: note: in expansion of macro 'DATAPTR'
#define STRING_ELT(x,i) ((SEXP *) DATAPTR(x))[i]
^
assign.c:254:25: note: in expansion of macro 'STRING_ELT'
if (strcmp(CHAR(STRING_ELT(class, i)), "data.table") == 0) return(TRUE);
^
assign.c:254:36: error: expected ')' before 'class'
if (strcmp(CHAR(STRING_ELT(class, i)), "data.table") == 0) return(TRUE);
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:382:41: note: in definition of macro 'DATAPTR'
#define DATAPTR(x) (((SEXPREC_ALIGN *) (x)) + 1)
^
assign.c:254:20: note: in expansion of macro 'CHAR'
if (strcmp(CHAR(STRING_ELT(class, i)), "data.table") == 0) return(TRUE);
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:389:35: note: in expansion of macro 'DATAPTR'
#define STRING_ELT(x,i) ((SEXP *) DATAPTR(x))[i]
^
assign.c:254:25: note: in expansion of macro 'STRING_ELT'
if (strcmp(CHAR(STRING_ELT(class, i)), "data.table") == 0) return(TRUE);
^
assign.c:254:80: error: expected ')' before ';' token
if (strcmp(CHAR(STRING_ELT(class, i)), "data.table") == 0) return(TRUE);
^
assign.c:254:80: error: expected ')' before ';' token
assign.c:254:80: error: expected ')' before ';' token
assign.c:254:80: error: expected ')' before ';' token
assign.c:254:80: error: expected ')' before ';' token
assign.c:254:80: error: expected ')' before ';' token
assign.c:254:80: error: expected ')' before ';' token
assign.c:254:80: error: expected ')' before ';' token
assign.c: In function 'SEXPREC* selfrefokwrapper(SEXP, SEXP)':
assign.c:272:63: error: invalid conversion from 'int' to 'Rboolean' [-fpermissive]
return ScalarInteger(_selfrefok(x,FALSE,LOGICAL(verbose)[0]));
^
assign.c:104:12: note: initializing argument 3 of 'int _selfrefok(SEXP, Rboolean, Rboolean)'
static int _selfrefok(SEXP x, Rboolean checkNames, Rboolean verbose) {
^
assign.c: In function 'SEXPREC* assign(SEXP, SEXP, SEXP, SEXP, SEXP, SEXP)':
assign.c:285:93: error: expected unqualified-id before 'class'
SEXP targetcol, RHS, names, nullint, thisvalue, thisv, targetlevels, newcol, s, colnam, class, tmp, colorder, key, index, a;
^
assign.c:287:39: error: invalid conversion from 'int' to 'Rboolean' [-fpermissive]
Rboolean verbose = LOGICAL(verb)[0], anytodelete=FALSE, isDataTable=FALSE;
^
assign.c:297:5: error: expected primary-expression before 'class'
class = getAttrib(dt, R_ClassSymbol);
^
In file included from data.table.h:3:0,
from assign.c:1:
assign.c:298:16: error: expected primary-expression before 'class'
if (isNull(class)) error("Input passed to assign has no class attribute. Must be a data.table or data.frame.");
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:303:21: note: in definition of macro 'TYPEOF'
#define TYPEOF(x) ((x)->sxpinfo.type)
^
assign.c:298:9: note: in expansion of macro 'isNull'
if (isNull(class)) error("Input passed to assign has no class attribute. Must be a data.table or data.frame.");
^
assign.c:298:16: error: expected ')' before 'class'
if (isNull(class)) error("Input passed to assign has no class attribute. Must be a data.table or data.frame.");
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:303:21: note: in definition of macro 'TYPEOF'
#define TYPEOF(x) ((x)->sxpinfo.type)
^
assign.c:298:9: note: in expansion of macro 'isNull'
if (isNull(class)) error("Input passed to assign has no class attribute. Must be a data.table or data.frame.");
^
assign.c:298:115: error: expected ')' before ';' token
if (isNull(class)) error("Input passed to assign has no class attribute. Must be a data.table or data.frame.");
^
assign.c:298:115: error: expected ')' before ';' token
assign.c:298:115: error: expected ')' before ';' token
In file included from data.table.h:3:0,
from assign.c:1:
assign.c:303:24: error: expected primary-expression before 'class'
for (i=0; i<length(class); i++) { // There doesn't seem to be an R API interface to inherits(), but manually here isn't too bad.
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:1222:30: note: in definition of macro 'length'
#define length(x) Rf_length(x)
^
assign.c:304:36: error: expected primary-expression before 'class'
if (strcmp(CHAR(STRING_ELT(class, i)), "data.table") == 0) break;
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:382:41: note: in definition of macro 'DATAPTR'
#define DATAPTR(x) (((SEXPREC_ALIGN *) (x)) + 1)
^
assign.c:304:20: note: in expansion of macro 'CHAR'
if (strcmp(CHAR(STRING_ELT(class, i)), "data.table") == 0) break;
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:389:35: note: in expansion of macro 'DATAPTR'
#define STRING_ELT(x,i) ((SEXP *) DATAPTR(x))[i]
^
assign.c:304:25: note: in expansion of macro 'STRING_ELT'
if (strcmp(CHAR(STRING_ELT(class, i)), "data.table") == 0) break;
^
assign.c:304:36: error: expected ')' before 'class'
if (strcmp(CHAR(STRING_ELT(class, i)), "data.table") == 0) break;
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:382:41: note: in definition of macro 'DATAPTR'
#define DATAPTR(x) (((SEXPREC_ALIGN *) (x)) + 1)
^
assign.c:304:20: note: in expansion of macro 'CHAR'
if (strcmp(CHAR(STRING_ELT(class, i)), "data.table") == 0) break;
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:389:35: note: in expansion of macro 'DATAPTR'
#define STRING_ELT(x,i) ((SEXP *) DATAPTR(x))[i]
^
assign.c:304:25: note: in expansion of macro 'STRING_ELT'
if (strcmp(CHAR(STRING_ELT(class, i)), "data.table") == 0) break;
^
assign.c:304:73: error: expected ')' before ';' token
if (strcmp(CHAR(STRING_ELT(class, i)), "data.table") == 0) break;
^
assign.c:304:73: error: expected ')' before ';' token
assign.c:304:73: error: expected ')' before ';' token
assign.c:304:73: error: expected ')' before ';' token
assign.c:304:73: error: expected ')' before ';' token
assign.c:304:73: error: expected ')' before ';' token
assign.c:304:73: error: expected ')' before ';' token
assign.c:304:73: error: expected ')' before ';' token
In file included from data.table.h:3:0,
from assign.c:1:
assign.c:306:18: error: expected primary-expression before 'class'
if (i<length(class))
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:1222:30: note: in definition of macro 'length'
#define length(x) Rf_length(x)
^
assign.c:309:28: error: expected primary-expression before 'class'
for (i=0; i<length(class); i++) {
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:1222:30: note: in definition of macro 'length'
#define length(x) Rf_length(x)
^
assign.c:310:40: error: expected primary-expression before 'class'
if (strcmp(CHAR(STRING_ELT(class, i)), "data.frame") == 0) break;
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:382:41: note: in definition of macro 'DATAPTR'
#define DATAPTR(x) (((SEXPREC_ALIGN *) (x)) + 1)
^
assign.c:310:24: note: in expansion of macro 'CHAR'
if (strcmp(CHAR(STRING_ELT(class, i)), "data.frame") == 0) break;
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:389:35: note: in expansion of macro 'DATAPTR'
#define STRING_ELT(x,i) ((SEXP *) DATAPTR(x))[i]
^
assign.c:310:29: note: in expansion of macro 'STRING_ELT'
if (strcmp(CHAR(STRING_ELT(class, i)), "data.frame") == 0) break;
^
assign.c:310:40: error: expected ')' before 'class'
if (strcmp(CHAR(STRING_ELT(class, i)), "data.frame") == 0) break;
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:382:41: note: in definition of macro 'DATAPTR'
#define DATAPTR(x) (((SEXPREC_ALIGN *) (x)) + 1)
^
assign.c:310:24: note: in expansion of macro 'CHAR'
if (strcmp(CHAR(STRING_ELT(class, i)), "data.frame") == 0) break;
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:389:35: note: in expansion of macro 'DATAPTR'
#define STRING_ELT(x,i) ((SEXP *) DATAPTR(x))[i]
^
assign.c:310:29: note: in expansion of macro 'STRING_ELT'
if (strcmp(CHAR(STRING_ELT(class, i)), "data.frame") == 0) break;
^
assign.c:310:77: error: expected ')' before ';' token
if (strcmp(CHAR(STRING_ELT(class, i)), "data.frame") == 0) break;
^
assign.c:310:77: error: expected ')' before ';' token
assign.c:310:77: error: expected ')' before ';' token
assign.c:310:77: error: expected ')' before ';' token
assign.c:310:77: error: expected ')' before ';' token
assign.c:310:77: error: expected ')' before ';' token
assign.c:310:77: error: expected ')' before ';' token
assign.c:310:77: error: expected ')' before ';' token
In file included from data.table.h:3:0,
from assign.c:1:
assign.c:312:25: error: expected primary-expression before 'class'
if (i == length(class)) error("Input is not a data.table, data.frame or an object that inherits from either.");
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:1222:30: note: in definition of macro 'length'
#define length(x) Rf_length(x)
^
assign.c:350:17: error: 'tmp' was not declared in this scope
PROTECT(tmp = chmatch(cols, names, 0, FALSE));
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:661:31: note: in definition of macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
assign.c:598:54: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
if (isReal(thisvalue)) s3="; may have truncated precision"; else s3="";
^
assign.c:598:96: warning: deprecated conversion from string constant to 'char*' [-Wwrite-strings]
if (isReal(thisvalue)) s3="; may have truncated precision"; else s3="";
^
assign.c:607:5: error: 'key' was not declared in this scope
key = getAttrib(dt,install("sorted"));
^
In file included from data.table.h:3:0,
from assign.c:1:
assign.c:611:17: error: 'tmp' was not declared in this scope
PROTECT(tmp = allocVector(STRSXP, LENGTH(cols)));
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:661:31: note: in definition of macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
assign.c:625:11: error: assignment of function 'char* index(const char*, int)'
index = getAttrib(dt,install("index"));
^
assign.c:625:11: error: cannot convert 'SEXP {aka SEXPREC*}' to 'char*(const char*, int)' in assignment
assign.c:626:18: error: comparison between distinct pointer types 'char* (*)(const char*, int)' and 'SEXP {aka SEXPREC*}' lacks a cast [-fpermissive]
if (index != R_NilValue) {
^
In file included from data.table.h:3:0,
from assign.c:1:
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:300:25: error: request for member 'attrib' in 'index', which is of non-class type 'char*(const char*, int)'
#define ATTRIB(x) ((x)->attrib)
^
assign.c:627:13: note: in expansion of macro 'ATTRIB'
s = ATTRIB(index);
^
assign.c:629:13: error: 'a' was not declared in this scope
a = TAG(s);
^
In file included from data.table.h:3:0,
from assign.c:1:
assign.c:666:17: error: 'colorder' was not declared in this scope
PROTECT(colorder = duplicate(cols));
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:661:31: note: in definition of macro 'PROTECT'
#define PROTECT(s) Rf_protect(s)
^
assign.c: At global scope:
assign.c:876:42: error: expected ',' or '...' before 'new'
SEXP setcharvec(SEXP x, SEXP which, SEXP new)
^
In file included from data.table.h:3:0,
from assign.c:1:
assign.c: In function 'SEXPREC* setcharvec(SEXP, SEXP, SEXP)':
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:303:22: error: expected type-specifier before ')' token
#define TYPEOF(x) ((x)->sxpinfo.type)
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:1374:22: note: in expansion of macro 'TYPEOF'
#define isString(s) (TYPEOF(s) == STRSXP)
^
assign.c:881:10: note: in expansion of macro 'isString'
if (!isString(new)) error("'new' must be a character vector");
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:338:44: error: expected type-specifier before ')' token
# define SHORT_VEC_LENGTH(x) (((VECSEXP) (x))->vecsxp.length)
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:337:26: note: in expansion of macro 'SHORT_VEC_LENGTH'
# define IS_LONG_VEC(x) (SHORT_VEC_LENGTH(x) == R_LONG_VEC_TOKEN)
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:344:21: note: in expansion of macro 'IS_LONG_VEC'
# define LENGTH(x) (IS_LONG_VEC(x) ? R_BadLongVector(x, __FILE__, __LINE__) : SHORT_VEC_LENGTH(x))
^
assign.c:882:9: note: in expansion of macro 'LENGTH'
if (LENGTH(new)!=LENGTH(which)) error("'new' is length %d. Should be the same as length of 'which' (%d)",LENGTH(new),LENGTH(which));
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:344:55: error: expected type-specifier before ',' token
# define LENGTH(x) (IS_LONG_VEC(x) ? R_BadLongVector(x, __FILE__, __LINE__) : SHORT_VEC_LENGTH(x))
^
assign.c:882:9: note: in expansion of macro 'LENGTH'
if (LENGTH(new)!=LENGTH(which)) error("'new' is length %d. Should be the same as length of 'which' (%d)",LENGTH(new),LENGTH(which));
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:338:44: error: expected type-specifier before ')' token
# define SHORT_VEC_LENGTH(x) (((VECSEXP) (x))->vecsxp.length)
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:344:79: note: in expansion of macro 'SHORT_VEC_LENGTH'
# define LENGTH(x) (IS_LONG_VEC(x) ? R_BadLongVector(x, __FILE__, __LINE__) : SHORT_VEC_LENGTH(x))
^
assign.c:882:9: note: in expansion of macro 'LENGTH'
if (LENGTH(new)!=LENGTH(which)) error("'new' is length %d. Should be the same as length of 'which' (%d)",LENGTH(new),LENGTH(which));
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:338:44: error: expected type-specifier before ')' token
# define SHORT_VEC_LENGTH(x) (((VECSEXP) (x))->vecsxp.length)
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:337:26: note: in expansion of macro 'SHORT_VEC_LENGTH'
# define IS_LONG_VEC(x) (SHORT_VEC_LENGTH(x) == R_LONG_VEC_TOKEN)
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:344:21: note: in expansion of macro 'IS_LONG_VEC'
# define LENGTH(x) (IS_LONG_VEC(x) ? R_BadLongVector(x, __FILE__, __LINE__) : SHORT_VEC_LENGTH(x))
^
assign.c:882:110: note: in expansion of macro 'LENGTH'
if (LENGTH(new)!=LENGTH(which)) error("'new' is length %d. Should be the same as length of 'which' (%d)",LENGTH(new),LENGTH(which));
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:344:55: error: expected type-specifier before ',' token
# define LENGTH(x) (IS_LONG_VEC(x) ? R_BadLongVector(x, __FILE__, __LINE__) : SHORT_VEC_LENGTH(x))
^
assign.c:882:110: note: in expansion of macro 'LENGTH'
if (LENGTH(new)!=LENGTH(which)) error("'new' is length %d. Should be the same as length of 'which' (%d)",LENGTH(new),LENGTH(which));
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:338:44: error: expected type-specifier before ')' token
# define SHORT_VEC_LENGTH(x) (((VECSEXP) (x))->vecsxp.length)
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:344:79: note: in expansion of macro 'SHORT_VEC_LENGTH'
# define LENGTH(x) (IS_LONG_VEC(x) ? R_BadLongVector(x, __FILE__, __LINE__) : SHORT_VEC_LENGTH(x))
^
assign.c:882:110: note: in expansion of macro 'LENGTH'
if (LENGTH(new)!=LENGTH(which)) error("'new' is length %d. Should be the same as length of 'which' (%d)",LENGTH(new),LENGTH(which));
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:382:42: error: expected type-specifier before ')' token
#define DATAPTR(x) (((SEXPREC_ALIGN *) (x)) + 1)
^
/Library/Frameworks/R.framework/Resources/include/Rinternals.h:389:35: note: in expansion of macro 'DATAPTR'
#define STRING_ELT(x,i) ((SEXP *) DATAPTR(x))[i]
^
assign.c:886:32: note: in expansion of macro 'STRING_ELT'
SET_STRING_ELT(x, w-1, STRING_ELT(new, i));
^
make: *** [assign.o] Error 1
ERROR: compilation failed for package ‘data.table’
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/data.table’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/data.table’
openmp
bhive01
All 17 comments
This has come up before in #1652. What's your OS X version? Assuming you've updated homebrew before installing clang-omp, do you have xcode command line tools installed as well?
arunsrinivasan
on 6 May 2016
If this is going to keep resurfacing, I guess we should include something about it in the start-up banner?
MichaelChirico
on 6 May 2016
👍1
Should be good on both of those things. Did brew update before clang-omp tap. Command line tools installed.
Brandons-iMac:~ brandonhurr$ xcode-select -version
xcode-select version 2343.
Brandons-iMac:~ brandonhurr$ xcode-select -p
/Applications/Xcode.app/Contents/Developer
Brandons-iMac:~ brandonhurr$ brew update
==> Migrating Homebrew to v0.9.9
warning: no common commits
remote: Counting objects: 469, done.
remote: Compressing objects: 100% (426/426), done.
remote: Total 469 (delta 27), reused 262 (delta 17), pack-reused 0
Receiving objects: 100% (469/469), 759.83 KiB | 254.00 KiB/s, done.
Resolving deltas: 100% (27/27), done.
From https://github.com/Homebrew/brew
+ 21ce7a5...d887dd3 master -> origin/master (forced update)
HEAD is now at d887dd3 brew install: make -s apply only to given formula, not deps (#205)
==> Homebrew has enabled anonymous aggregate user behaviour analytics
Read the analytics documentation (and how to opt-out) here:
https://git.io/brew-analytics
==> Tapping homebrew/core
Cloning into '/usr/local/Library/Taps/homebrew/homebrew-core'...
remote: Counting objects: 3697, done.
remote: Compressing objects: 100% (3585/3585), done.
remote: Total 3697 (delta 14), reused 641 (delta 1), pack-reused 0
Receiving objects: 100% (3697/3697), 2.83 MiB | 407.00 KiB/s, done.
Resolving deltas: 100% (14/14), done.
Checking connectivity... done.
Tapped 3573 formulae (3,723 files, 8.8M)
Already up-to-date.
Brandons-iMac:~ brandonhurr$ brew list
brew-cask gdal graphicsmagick libiomp opencv3 readline
cairo gdbm harfbuzz liblwgeom openexr sdl2
clang-omp geos icu4c libmpc openssl sqlite
cmake gettext ilmbase libpng optipng tcl-tk
eigen ghostscript imagemagick libspatialite pango v8-315
ffmpeg giflib isl libtiff pdflib-lite webp
fftw gist isl014 libtool pixman wget
fontconfig git jbig2dec libvo-aacenc pkg-config wxmac
freetype glew jpeg libxml2 proj x264
freexl glib json-c little-cms2 protobuf xvid
gcc gmp lame lzlib pymol xz
gcc5 gnuplot libffi mpfr python zeromq
gd gobject-introspection libgeotiff numpy qt
OK, so I read the other issue and realized I didn't get the Makevar quite right for gcc5. With the Makevar below it compiles but then can't load. I installed gcc 5 from brew via these instructions.
cat ~/.R/Makevars
CC=gcc-5 -fopenmp
CXX=g++-5 -fopenmp
I had g++-5 in both places. now it's gcc-5 and g++-5.
install.packages("data.table", type = "source",
repos = "https://Rdatatable.github.io/data.table")
trying URL 'https://Rdatatable.github.io/data.table/src/contrib/data.table_1.9.7.tar.gz'
Content type 'application/octet-stream' length 2721566 bytes (2.6 MB)
==================================================
downloaded 2.6 MB
* installing *source* package ‘data.table’ ...
** libs
gcc-5 -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c assign.c -o assign.o
gcc-5 -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c bmerge.c -o bmerge.o
gcc-5 -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c chmatch.c -o chmatch.o
gcc-5 -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c dogroups.c -o dogroups.o
gcc-5 -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c fastmean.c -o fastmean.o
gcc-5 -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c fcast.c -o fcast.o
gcc-5 -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c fmelt.c -o fmelt.o
gcc-5 -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c forder.c -o forder.o
gcc-5 -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c frank.c -o frank.o
gcc-5 -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c fread.c -o fread.o
gcc-5 -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c fwrite.c -o fwrite.o
gcc-5 -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c gsumm.c -o gsumm.o
gcc-5 -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c ijoin.c -o ijoin.o
gcc-5 -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c init.c -o init.o
gcc-5 -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c openmp-utils.c -o openmp-utils.o
gcc-5 -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c quickselect.c -o quickselect.o
gcc-5 -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c rbindlist.c -o rbindlist.o
gcc-5 -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c reorder.c -o reorder.o
gcc-5 -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c shift.c -o shift.o
gcc-5 -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c subset.c -o subset.o
gcc-5 -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c transpose.c -o transpose.o
gcc-5 -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c uniqlist.c -o uniqlist.o
gcc-5 -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c vecseq.c -o vecseq.o
gcc-5 -fopenmp -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include -fPIC -Wall -mtune=core2 -g -O2 -c wrappers.c -o wrappers.o
gcc-5 -fopenmp -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o data.table.so assign.o bmerge.o chmatch.o dogroups.o fastmean.o fcast.o fmelt.o forder.o frank.o fread.o fwrite.o gsumm.o ijoin.o init.o openmp-utils.o quickselect.o rbindlist.o reorder.o shift.o subset.o transpose.o uniqlist.o vecseq.o wrappers.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
mv data.table.so datatable.so
if [ `uname -s` = 'Darwin' ]; then install_name_tool -id datatable.so datatable.so; fi
installing to /Library/Frameworks/R.framework/Versions/3.3/Resources/library/data.table/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/Library/Frameworks/R.framework/Versions/3.3/Resources/library/data.table/libs/datatable.so':
dlopen(/Library/Frameworks/R.framework/Versions/3.3/Resources/library/data.table/libs/datatable.so, 6): Symbol not found: _GOMP_parallel
Referenced from: /Library/Frameworks/R.framework/Versions/3.3/Resources/library/data.table/libs/datatable.so
Expected in: flat namespace
in /Library/Frameworks/R.framework/Versions/3.3/Resources/library/data.table/libs/datatable.so
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/data.table’
The downloaded source packages are in
‘/private/var/folders/zg/hy0k4g312536_4l1qc1w27640000gn/T/RtmpXM09oF/downloaded_packages’
* restoring previous ‘/Library/Frameworks/R.framework/Versions/3.3/Resources/library/data.table’
Warning message:
In install.packages("data.table", type = "source", repos = "https://Rdatatable.github.io/data.table") :
installation of package ‘data.table’ had non-zero exit status
I'm not sure how you figure if command line tools is installed by that statement. Looking at this issue, it seems you need to run xcode-select --install from the terminal. I don't know your OS X version. So it's hard to search for OS specific ways to get Xcode up and running correctly.
arunsrinivasan
on 6 May 2016
Well, in Xcode it shows that I have them, which should be the case. I build nearly every package from source and you can't do that without them. When I tell it to install it tries to get them, which will take a while because of my quite slow connection. I will try a reinstallation of the tools and then data.table with gcc-5 and clang-omp again.
The latest error suggests that gcc-5 is able to build it, but something is not right with _GOMP_parallel.
bhive01
on 6 May 2016
In that case, I don't know yet what's the issue as well. Once again, what's your OS X version?
arunsrinivasan
on 6 May 2016
Well, good news is that reinstallation of the tools worked. I don't understand why because I was already compiling things using them. But, when I paste the following from here I got:
No receipt for 'com.apple.pkg.CLTools_Executables' found at '/'.
After reinstall:
pkgutil --pkg-info=com.apple.pkg.CLTools_Executables
package-id: com.apple.pkg.CLTools_Executables
version: 7.3.1.0.1.1461711523
volume: /
location: /
install-time: 1462568157
groups: com.apple.FindSystemFiles.pkg-group com.apple.DevToolsBoth.pkg-group com.apple.DevToolsNonRelocatableShared.pkg-group
data.table installation with those flags and clang-omp works fine. It does not work with gcc-5 still, but that's irrelevant.
I'm sorry that's my fault. I did not follow instructions. I skipped the first line because I thought I had the tools already.
OSX version 10.11.4
bhive01
on 6 May 2016
Great! IIUC xcode-select --install should be run _after_ installing clang-omp seems to be the issue?
arunsrinivasan
on 6 May 2016
👍1
Nope, exactly how you have them. Sorry again for not running everything as it was written.
bhive01
on 6 May 2016
👍1
Thanks. Updated https://github.com/Rdatatable/data.table/wiki/Installation with a note that this step is essential.
arunsrinivasan
on 6 May 2016
👍1
Yes, if you do have it installed, it will tell you so there is no harm in running it anyway:
Brandons-iMac:~ brandonhurr$ xcode-select --install
xcode-select: error: command line tools are already installed, use "Software Update" to install updates
👍1
Thanks. Clarified it further.
arunsrinivasan
on 6 May 2016
The brew clang-omp formula has been moved to the bone-yard (deleted). It looks like llvm is the replacement formula (https://github.com/Homebrew/homebrew-core/issues/3266). Anyone have Mac build tips for llvm?
botanize
on 3 Aug 2016
Hi,
Following the installation instructions on https://github.com/Rdatatable/data.table/wiki/Installation works fine for data.table. But the configuration conflicts with compiling other packages (e.g. "stringi"):
* installing *source* package ‘stringi’ ...
** package ‘stringi’ successfully unpacked and MD5 sums checked
checking for local ICUDT_DIR... icu55/data
checking for R_HOME... /Library/Frameworks/R.framework/Resources
checking for R... /Library/Frameworks/R.framework/Resources/bin/R
checking for R >= 3.1.0... yes
checking for cat... /bin/cat
checking for gcc... /usr/local/opt/llvm/bin/clang -fopenmp
checking whether the C compiler works... no
configure: error: in `/private/var/folders/4c/p9cf0m8n5mj254pwzm9bwwf80000gn/T/Rtmp1AQfuU/R.INSTALL16441b46a3ea/stringi':
configure: error: C compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘stringi’
* removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/stringi’
Removing the .R directory containing the Makevars file with the build instructions then uses Xcode's clang and it works fine. Maybe it is worth mentioning unless there is another issue specific to my environment?
macOS 10.12 (16A323)
xcode-select version 2345.1.
R Under development (unstable) (2016-10-22 r71573)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12
kmakat
on 24 Oct 2016
I just ran into that problem myself. Unfortunately I can't find a way to pass compiler options to install.packages that results in an OpenMP build without the -fopenmp tag in Makevars. I added a note on the wiki.
On Oct 23, 2016, at 21:03, kmakat [email protected] wrote:
Hi,
Following the installation instructions on https://github.com/Rdatatable/data.table/wiki/Installation works fine for data.table. But the configuration conflicts with compiling other packages (e.g. "stringi"):
- installing _source_ package ‘stringi’ ...
** package ‘stringi’ successfully unpacked and MD5 sums checked
checking for local ICUDT_DIR... icu55/data
checking for R_HOME... /Library/Frameworks/R.framework/Resources
checking for R... /Library/Frameworks/R.framework/Resources/bin/R
checking for R >= 3.1.0... yes
checking for cat... /bin/cat
checking for gcc... /usr/local/opt/llvm/bin/clang -fopenmp
checking whether the C compiler works... no
configure: error: in/private/var/folders/4c/p9cf0m8n5mj254pwzm9bwwf80000gn/T/Rtmp1AQfuU/R.INSTALL16441b46a3ea/stringi': configure: error: C compiler cannot create executables Seeconfig.log' for more details
ERROR: configuration failed for package ‘stringi’- removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/stringi’
Removing the .R directory containing the Makevars file with the build instructions then uses Xcode's clang and it works fine. Maybe it is worth mentioning unless there is another issue specific to my environment?macOS 10.12 (16A323)
xcode-select version 2345.1.
R Under development (unstable) (2016-10-22 r71573)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS Sierra 10.12
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botanize
on 25 Oct 2016
I realize this issue is closed, but I wanted to provide an update related to R 3.4. I am doing a fresh install on Sierra for R 3.4. I followed the instructions here to enable OpenMP support: http://thecoatlessprofessor.com/programming/openmp-in-r-on-os-x/#gui-clang4
The development package of data.table installed flawlessly. This is not my area of expertise, but it may be an easier path for some.
markdanese
on 3 Sep 2017
👍1
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