[R-SIG-Mac] Issues Compiling Post-Yosemite

Amos B. Elberg amos.elberg at gmail.com
Sat Oct 18 21:58:53 CEST 2014

Has anyone else had compilation issues after the yosemite upgrade?  My already-compiled R is running fine, after reinstalling Xquartz.  I’m seeing a pair of issues trying to rebuild, though.  

First, configure is having trouble with external BLASes.  The check for double complex BLAS returns “no” with the Apple BLAS, MKL, and openblas.  I’ve traced the issue to lines 30313-14 ( output=`./conftest${ac_exeext} 2>&5` ) but I can’t seem to get any guiding diagnostic information.  

Second, with external BLAS disabled, during compilation I get this error, either linking tools.so or immediately after:

 *** caught segfault ***
address 0x53e, cause 'memory not mapped'

 1: sub("[[:blank:]]*([[:alnum:]]+)", "\\1", dp)
 2: eval(expr, envir, enclos)
 3: eval(quote({    dp <- Sys.getenv("R_DEFAULT_PACKAGES")    if (identical(dp, "")) dp <- c("datasets", "utils", "grDevices",         "graphics", "stats", "methods") else if (identical(dp,         "NULL")) dp <- character(0) else dp <- strsplit(dp, ",")[[1]]    dp <- sub("[[:blank:]]*([[:alnum:]]+)", "\\1", dp)    options(defaultPackages = dp)}), new.env())
 4: eval(expr, envir, enclos)
 5: eval(expr, p)
 6: eval.parent(substitute(eval(quote(expr), envir)))
 7: local({    dp <- Sys.getenv("R_DEFAULT_PACKAGES")    if (identical(dp, ""))         dp <- c("datasets", "utils", "grDevices", "graphics",             "stats", "methods")    else if (identical(dp, "NULL"))         dp <- character(0)    else dp <- strsplit(dp, ",")[[1]]    dp <- sub("[[:blank:]]*([[:alnum:]]+)", "\\1", dp)    options(defaultPackages = dp)})
aborting ...
/bin/sh: line 1: 71430 Done                    echo "tools:::.install_package_description('.', '"../../../library/tools"')"
     71431 Segmentation fault: 11  | R_DEFAULT_PACKAGES=NULL ../../../bin/R --vanilla --slave > /dev/null
make[3]: *** [all] Error 139
make[2]: *** [R] Error 1
make[1]: *** [R] Error 1
make: *** [R] Error 1

I don’t doubt that at least the second issue has to do with the changed toolchain, but I’m lost as to the first.  

Can anyone suggest a direction to go in?

Amos Elberg
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