[Rd] Has the changelog for R-devel and R-patched moved?

2015-09-01 Thread Avraham Adler 
Hello.

There used to be changelog of sorts for R-devel [1] and R-release [2].
Neither have been updated since 2015-07-24. Have these moved
elsewhere, or are they no longer being updated?

Thank you,

Avi

[1] 
[2] 

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[Rd] lazy loading in SparkR

2015-09-01 Thread Tóth Zoltán 
Hi,

I'm using SparkR and R won't read the promises from the SparkR package,
only if I run lazyLoad manually.

.libPaths(c(file.path(Sys.getenv("SPARK_HOME"), "R", "lib"), .libPaths()))
print(.libPaths())
# [1] "/private/tmp/spark-1.5/spark-1.5.0-SNAPSHOT-bin-hadoop2.6/R/lib"
# [2] "/usr/local/lib/R/3.2/site-library"
# [3] "/usr/local/Cellar/r/3.2.2/R.framework/Versions/3.2/Resources/library"

library(SparkR)
# Works

if(!exists("parallelize",mode="function")){
# Here is the trick. For some reason, SparkR doesn't load it's
functions/promises automatically here.
# We can fix it with an internal function:
lazyLoad(filebase = file.path(SPARK_HOME, "R/lib/SparkR/R/SparkR"),
envir = parent.frame(), filter = function(x) TRUE)
}

# parallelize() works now

Please help me understand what goes wrong.

Here is the whole repro:
https://gist.github.com/zoltanctoth/971ae374dace93de12f0#file-sparkr-rstudio-parallelize-r-L21-L31

And the relevant files from the Spark installation:
https://www.dropbox.com/sh/0xp2wgkbrl7ov64/AAAHRWdMecGMkVdo0GUs6fmYa?dl=0

Thanks,
Best,
Zoltan

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Re: [Rd] R doesn't compile on FreeBSD 10.2

2015-09-01 Thread Davor Cubranic 
I tried compiling using GCC. First, I changed config.site to:
~/R-3.2.2$ svn diff config.site
Index: config.site
===
--- config.site (revision 69236)
+++ config.site (working copy)
@@ -278,3 +278,8 @@
 
 ## Path to the version of pkg-config to be used for locating cairographics.
 ## PKGCONF =
+F77=gfortran48
+FC=${F77}
+CC=gcc48
+CXX=g++48
+OBJC=gcc48

Then plain-vanilla configure && make worked without a hitch:

~/R-3.2.2$ ./configure
[...]
R is now configured for x86_64-unknown-freebsd10.2

  Source directory:  .
  Installation directory:/usr/local

  C compiler:gcc48 -std=gnu99  -g -O2
  Fortran 77 compiler:   gfortran48  -g -O2

  C++ compiler:  g++48  -g -O2
  C++ 11 compiler:   g++48  -std=c++11 -g -O2
  Fortran 90/95 compiler:gfortran48 -g -O2
  Obj-C compiler:gcc48 -g -O2 -fobjc-exceptions

  Interfaces supported:  X11, tcltk
  External libraries:readline, zlib, bzlib, lzma, PCRE, curl
  Additional capabilities:   PNG, JPEG, TIFF, NLS, cairo, ICU
  Options enabled:   shared BLAS, R profiling

  Capabilities skipped:  
  Options not enabled:   memory profiling

  Recommended packages:  yes

"make" completes, and "make check" again fails in datetime.R:

   > Sys.setenv(TZ = "Europe/London")  # pretty much portable.
   > (z <- as.POSIXct("1848-01-01 12:00"))
   Error in as.POSIXlt.character(x, tz, ...) : 
 character string is not in a standard unambiguous format

The next date check is fine, though:
   > (z <- as.POSIXct("2040-01-01 12:00"))
   [1] "2040-01-01 12:00:00 GMT"

as was the 1848 one when TZ="UTC":
   > Sys.setenv(TZ = "UTC")
   > (z <- as.POSIXct("1848-01-01 12:00"))
   [1] "1848-01-01 12:00:00 UTC"

This is probably a quirk of FreeBSD's datetime support, I'll see what
the port used to do for 3.0.2.

Also, there is an issue tracking updating the port to the current
release: https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=195783. I've
posted the summary of this thread there, thanks for your help.

Davor


Prof Brian Ripley writes:

> On 31/08/2015 16:26, Davor Cubranic wrote:
>> Prof Brian Ripley writes:
>>
>>> Second, we don't have all the pertinent information such as the
>>> configure options used and the architecture (x86_64?).  I am going to
>>> have to guess none as none were mentioned, but using --enable-R-shlib
>>> would be pertinent.
>>>
>>> On 31/08/2015 05:47, Davor Cubranic wrote:
 On FreeBSD 10.2, I get the following error when compiling R from the
 Subversion trunk (with "configure && make"):
>>>
>>> You have not told us which revision.  A basic check is to see if you can
>>> build the latest released version, as the trunk is 'Under development'.
>>
>> As suggested, I tried compiling from Subversion tag 3.2.2 (r69054).
>> I used no command-line options to 'configure', as mentioned in my
>> previous email, and this is the output:
>>
>>R is now configured for x86_64-unknown-freebsd10.2
>>
>>  Source directory:  .
>>  Installation directory:/usr/local
>>
>>  C compiler:cc  -g -O2
>>  Fortran 77 compiler:   gfortran48  -g -O2
>>
>>  C++ compiler:  c++  -g -O2
>>  C++ 11 compiler:   c++  -std=c++11 -g -O2
>>  Fortran 90/95 compiler:gfortran48 -g -O2
>>  Obj-C compiler:  cc -g -O2 -fobjc-exceptions
>>
>>  Interfaces supported:  X11, tcltk
>>  External libraries:readline, zlib, bzlib, lzma, PCRE, curl
>>  Additional capabilities:   PNG, JPEG, TIFF, NLS, cairo, ICU
>>  Options enabled:   shared BLAS, R profiling
>>
>>  Capabilities skipped:
>>  Options not enabled:   memory profiling
>>
>>  Recommended packages:  yes
>>
>> (I thought this, and more, would be included in config.log, but please
>> let me know if there is other place to get the configuration details
>> that are relevant.)
>
> You need to tell us exactly which commands you used: nowhere records 
> everything.
>
>>
>> Still the same error:
>>
>>--- tools.so ---
>>cc -shared -L/usr/local/lib -o tools.so text.o init.o Rmd5.o md5.o 
>> signals.o install.o getfmts.o http.o gramLatex.o gramRd.o
>>--- all ---
>>--- shlib ---
>>mkdir ../../../../library/tools/libs
>>--- sysdata ---
>>installing 'sysdata.rda'
>>Error in dyn.load(file, DLLpath = DLLpath, ...) :
>>  unable to load shared object 
>> '/usr/home/davor/R-3.2.2/library/tools/libs/tools.so':
>>  /usr/home/davor/R-3.2.2/library/tools/libs/tools.so: Undefined symbol 
>> "R_ClassSymbol"
>>Error: unable to load R code in package 'tools'
>>Execution halted
>>
>>> Here is a series of checks for that symbol (results from a working Linux
>>> system):
>>>
>>> auk% nm -g bin/exec/R  | grep R_ClassSymbol
>>> 00962ec0 B R_ClassSymbol
>>>
>>> auk% nm -g src/main/main.o | grep R_ClassSymbol
>>>

Re: [Rd] Has the changelog for R-devel and R-patched moved?

2015-09-01 Thread Duncan Murdoch 
On 01/09/2015 10:21 AM, Avraham Adler wrote:
> Hello.
> 
> There used to be changelog of sorts for R-devel [1] and R-release [2].
> Neither have been updated since 2015-07-24. Have these moved
> elsewhere, or are they no longer being updated?

They haven't moved, but occasionally the updates get broken.  Thanks for
the heads up.  I'll give the process a kick.

Duncan Murdoch

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Re: [Rd] Has the changelog for R-devel and R-patched moved?

2015-09-01 Thread peter dalgaard 

On 01 Sep 2015, at 16:21 , Avraham Adler  wrote:

> Hello.
> 
> There used to be changelog of sorts for R-devel [1] and R-release [2].
> Neither have been updated since 2015-07-24. Have these moved
> elsewhere, or are they no longer being updated?

Presumably, something that used to happen daily on the hosting machine (or 
elsewhere) isn't happening any more

If the functionality is easily restored, it will probably be restored soon; if 
not, probably somewhat later.

Meanwhile, the link to the latest NEWS file (one line above!) appears to be 
up-to-yesterday's date.

-pd

> 
> Thank you,
> 
> Avi
> 
> [1] 
> [2] 
> 
> __
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> https://stat.ethz.ch/mailman/listinfo/r-devel

-- 
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Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Office: A 4.23
Email: pd@cbs.dk  Priv: pda...@gmail.com

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Re: [Rd] Has the changelog for R-devel and R-patched moved?

2015-09-01 Thread Avraham Adler 
On Tue, Sep 1, 2015 at 10:57 AM, peter dalgaard  wrote:
>
> On 01 Sep 2015, at 16:21 , Avraham Adler  wrote:
>
>> Hello.
>>
>> There used to be changelog of sorts for R-devel [1] and R-release [2].
>> Neither have been updated since 2015-07-24. Have these moved
>> elsewhere, or are they no longer being updated?
>
> Presumably, something that used to happen daily on the hosting machine (or 
> elsewhere) isn't happening any more
>
> If the functionality is easily restored, it will probably be restored soon; 
> if not, probably somewhat later.
>
> Meanwhile, the link to the latest NEWS file (one line above!) appears to be 
> up-to-yesterday's date.
>
> -pd
>
>>
>> Thank you,
>>
>> Avi
>>
>> [1] 
>> [2] 
>>
>> __
>> R-devel@r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>
> --
> Peter Dalgaard, Professor,
> Center for Statistics, Copenhagen Business School
> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
> Phone: (+45)38153501
> Office: A 4.23
> Email: pd@cbs.dk  Priv: pda...@gmail.com
>

Yes, understood. The reason the changlog is prefereable is that the
NEWS is cumulative, and does not indicate changes between
R-patched_2015-08-26 and R-patched_2015-08-27. Whereas more
information can be gleaned from the changelog entries.


Obviously, this is of very low priority, and if the server refuses to
acknowledge Dr. Murdoch's well-placed steel-toe reminders, getting it
restarted should be deferred as long as is necessary. 8-)

Thank you,

Avi

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Re: [Rd] R doesn't compile on FreeBSD 10.2

2015-09-01 Thread Prof Brian Ripley 
The datetime.R issue looks familiar.  Darwin (the basis for OS X) copied 
a lot of things from FreeBSD, bugs and all.  So I expect the same remedy 
applies (http://cran.r-project.org/doc/manuals/r-patched/R-admin.html#OS-X):


'Configure option --with-internal-tzcode is the default on OS X, as the 
system implementation of time zones does not work correctly for times 
before 1902 or after 2037 (despite using a 64-bit time_t).'



On 01/09/2015 15:40, Davor Cubranic wrote:

I tried compiling using GCC. First, I changed config.site to:
~/R-3.2.2$ svn diff config.site
Index: config.site
===
--- config.site (revision 69236)
+++ config.site (working copy)
@@ -278,3 +278,8 @@

  ## Path to the version of pkg-config to be used for locating cairographics.
  ## PKGCONF =
+F77=gfortran48
+FC=${F77}
+CC=gcc48
+CXX=g++48
+OBJC=gcc48

Then plain-vanilla configure && make worked without a hitch:

~/R-3.2.2$ ./configure
[...]
R is now configured for x86_64-unknown-freebsd10.2

   Source directory:  .
   Installation directory:/usr/local

   C compiler:gcc48 -std=gnu99  -g -O2
   Fortran 77 compiler:   gfortran48  -g -O2

   C++ compiler:  g++48  -g -O2
   C++ 11 compiler:   g++48  -std=c++11 -g -O2
   Fortran 90/95 compiler:gfortran48 -g -O2
   Obj-C compiler:   gcc48 -g -O2 -fobjc-exceptions

   Interfaces supported:  X11, tcltk
   External libraries:readline, zlib, bzlib, lzma, PCRE, curl
   Additional capabilities:   PNG, JPEG, TIFF, NLS, cairo, ICU
   Options enabled:   shared BLAS, R profiling

   Capabilities skipped:
   Options not enabled:   memory profiling

   Recommended packages:  yes

"make" completes, and "make check" again fails in datetime.R:

> Sys.setenv(TZ = "Europe/London")  # pretty much portable.
> (z <- as.POSIXct("1848-01-01 12:00"))
Error in as.POSIXlt.character(x, tz, ...) :
  character string is not in a standard unambiguous format

The next date check is fine, though:
> (z <- as.POSIXct("2040-01-01 12:00"))
[1] "2040-01-01 12:00:00 GMT"

as was the 1848 one when TZ="UTC":
> Sys.setenv(TZ = "UTC")
> (z <- as.POSIXct("1848-01-01 12:00"))
[1] "1848-01-01 12:00:00 UTC"

This is probably a quirk of FreeBSD's datetime support, I'll see what
the port used to do for 3.0.2.

Also, there is an issue tracking updating the port to the current
release: https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=195783. I've
posted the summary of this thread there, thanks for your help.

Davor


Prof Brian Ripley writes:


On 31/08/2015 16:26, Davor Cubranic wrote:

Prof Brian Ripley writes:


Second, we don't have all the pertinent information such as the
configure options used and the architecture (x86_64?).  I am going to
have to guess none as none were mentioned, but using --enable-R-shlib
would be pertinent.

On 31/08/2015 05:47, Davor Cubranic wrote:

On FreeBSD 10.2, I get the following error when compiling R from the
Subversion trunk (with "configure && make"):


You have not told us which revision.  A basic check is to see if you can
build the latest released version, as the trunk is 'Under development'.


As suggested, I tried compiling from Subversion tag 3.2.2 (r69054).
I used no command-line options to 'configure', as mentioned in my
previous email, and this is the output:

R is now configured for x86_64-unknown-freebsd10.2

  Source directory:  .
  Installation directory:/usr/local

  C compiler:cc  -g -O2
  Fortran 77 compiler:   gfortran48  -g -O2

  C++ compiler:  c++  -g -O2
  C++ 11 compiler:   c++  -std=c++11 -g -O2
  Fortran 90/95 compiler:gfortran48 -g -O2
  Obj-C compiler:cc -g -O2 -fobjc-exceptions

  Interfaces supported:  X11, tcltk
  External libraries:readline, zlib, bzlib, lzma, PCRE, curl
  Additional capabilities:   PNG, JPEG, TIFF, NLS, cairo, ICU
  Options enabled:   shared BLAS, R profiling

  Capabilities skipped:
  Options not enabled:   memory profiling

  Recommended packages:  yes

(I thought this, and more, would be included in config.log, but please
let me know if there is other place to get the configuration details
that are relevant.)


You need to tell us exactly which commands you used: nowhere records
everything.



Still the same error:

--- tools.so ---
cc -shared -L/usr/local/lib -o tools.so text.o init.o Rmd5.o md5.o 
signals.o install.o getfmts.o http.o gramLatex.o gramRd.o
--- all ---
--- shlib ---
mkdir ../../../../library/tools/libs
--- sysdata ---
installing 'sysdata.rda'
Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared object 
'/usr/home/davor/R-3.2.2/library/tools/libs/tools.so':
  /usr/home/davor/R-3.2.2/library/tools/libs/tools.so: Undefined symbol 
"R_C

Re: [Rd] Has the changelog for R-devel and R-patched moved?

2015-09-01 Thread peter dalgaard 

> On 01 Sep 2015, at 17:05 , Avraham Adler  wrote:
>> 
> 
> Yes, understood. The reason the changlog is prefereable is that the
> NEWS is cumulative, and does not indicate changes between
> R-patched_2015-08-26 and R-patched_2015-08-27. Whereas more
> information can be gleaned from the changelog entries.
> 

You mean like 

svn diff -x -w -r '{2015-08-26}':'{2015-08-27}' 
https://svn.r-project.org/R/branches/R-3-2-branch/doc/NEWS.Rd

;-)

(Not that anything actually happened that day.)


-- 
Peter Dalgaard, Professor,
Center for Statistics, Copenhagen Business School
Solbjerg Plads 3, 2000 Frederiksberg, Denmark
Phone: (+45)38153501
Email: pd@cbs.dk  Priv: pda...@gmail.com

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Re: [Rd] Has the changelog for R-devel and R-patched moved?

2015-09-01 Thread Duncan Murdoch 
On 01/09/2015 11:05 AM, Avraham Adler wrote:
> On Tue, Sep 1, 2015 at 10:57 AM, peter dalgaard  wrote:
>>
>> On 01 Sep 2015, at 16:21 , Avraham Adler  wrote:
>>
>>> Hello.
>>>
>>> There used to be changelog of sorts for R-devel [1] and R-release [2].
>>> Neither have been updated since 2015-07-24. Have these moved
>>> elsewhere, or are they no longer being updated?
>>
>> Presumably, something that used to happen daily on the hosting machine (or 
>> elsewhere) isn't happening any more
>>
>> If the functionality is easily restored, it will probably be restored soon; 
>> if not, probably somewhat later.
>>
>> Meanwhile, the link to the latest NEWS file (one line above!) appears to be 
>> up-to-yesterday's date.
>>
>> -pd
>>
>>>
>>> Thank you,
>>>
>>> Avi
>>>
>>> [1] 
>>> [2] 
>>>
>>> __
>>> R-devel@r-project.org mailing list
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>>
>> --
>> Peter Dalgaard, Professor,
>> Center for Statistics, Copenhagen Business School
>> Solbjerg Plads 3, 2000 Frederiksberg, Denmark
>> Phone: (+45)38153501
>> Office: A 4.23
>> Email: pd@cbs.dk  Priv: pda...@gmail.com
>>
> 
> Yes, understood. The reason the changlog is prefereable is that the
> NEWS is cumulative, and does not indicate changes between
> R-patched_2015-08-26 and R-patched_2015-08-27. Whereas more
> information can be gleaned from the changelog entries.
> 
> 
> Obviously, this is of very low priority, and if the server refuses to
> acknowledge Dr. Murdoch's well-placed steel-toe reminders, getting it
> restarted should be deferred as long as is necessary. 8-)

Nobody ignores my steel-toe boots ;-). It's going again.

Duncan Murdoch

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Re: [Rd] R doesn't compile on FreeBSD 10.2

2015-09-01 Thread Davor Cubranic 

I tried "./configure --with-internal-tzcode && make", but it caused
problems seemingly with any parsing of time. Example:

  ~/R-3.2.2$ make check
  Testing examples for package ‘base’
  Testing examples for package ‘tools’
  Warning in as.POSIXlt.POSIXct(x, tz) : unknown timezone ''
  Warning in as.POSIXlt.POSIXct(x, tz) : unknown timezone 'GMT'
  Warning in as.POSIXlt.POSIXct(x, tz) :
unknown timezone 'America/New_York'
comparing ‘tools-Ex.Rout’ to ‘tools-Ex.Rout.save’ ... OK
  [...]
  running code in 'simple-true.R' ... OK
comparing 'simple-true.Rout' to './simple-true.Rout.save' ...231,237d230
  < Warning messages:
  < 1: In strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  <   unknown timezone ''
  < 2: In strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  <   unknown timezone 'GMT'
  < 3: In strptime(xx, f <- "%Y-%m-%d %H:%M:%OS", tz = tz) :
  <   unknown timezone 'America/New_York'
  *** Error code 1

  Stop.
  [...]

Interestingly, doing the same (using option "--with-internal-tzcode")
with r69235 from the trunk, everything works fine and "make check"
completes with no errors.

Davor


Prof Brian Ripley writes:

> The datetime.R issue looks familiar.  Darwin (the basis for OS X) copied 
> a lot of things from FreeBSD, bugs and all.  So I expect the same remedy 
> applies (http://cran.r-project.org/doc/manuals/r-patched/R-admin.html#OS-X):
>
> 'Configure option --with-internal-tzcode is the default on OS X, as the 
> system implementation of time zones does not work correctly for times 
> before 1902 or after 2037 (despite using a 64-bit time_t).'
>
>
> On 01/09/2015 15:40, Davor Cubranic wrote:
>> I tried compiling using GCC. First, I changed config.site to:
>> ~/R-3.2.2$ svn diff config.site
>> Index: config.site
>> ===
>> --- config.site  (revision 69236)
>> +++ config.site  (working copy)
>> @@ -278,3 +278,8 @@
>>
>>   ## Path to the version of pkg-config to be used for locating cairographics.
>>   ## PKGCONF =
>> +F77=gfortran48
>> +FC=${F77}
>> +CC=gcc48
>> +CXX=g++48
>> +OBJC=gcc48
>>
>> Then plain-vanilla configure && make worked without a hitch:
>>
>> ~/R-3.2.2$ ./configure
>> [...]
>> R is now configured for x86_64-unknown-freebsd10.2
>>
>>Source directory:  .
>>Installation directory:/usr/local
>>
>>C compiler:gcc48 -std=gnu99  -g -O2
>>Fortran 77 compiler:   gfortran48  -g -O2
>>
>>C++ compiler:  g++48  -g -O2
>>C++ 11 compiler:   g++48  -std=c++11 -g -O2
>>Fortran 90/95 compiler:gfortran48 -g -O2
>>Obj-C compiler:gcc48 -g -O2 -fobjc-exceptions
>>
>>Interfaces supported:  X11, tcltk
>>External libraries:readline, zlib, bzlib, lzma, PCRE, curl
>>Additional capabilities:   PNG, JPEG, TIFF, NLS, cairo, ICU
>>Options enabled:   shared BLAS, R profiling
>>
>>Capabilities skipped:
>>Options not enabled:   memory profiling
>>
>>Recommended packages:  yes
>>
>> "make" completes, and "make check" again fails in datetime.R:
>>
>> > Sys.setenv(TZ = "Europe/London")  # pretty much portable.
>> > (z <- as.POSIXct("1848-01-01 12:00"))
>> Error in as.POSIXlt.character(x, tz, ...) :
>>   character string is not in a standard unambiguous format
>>
>> The next date check is fine, though:
>> > (z <- as.POSIXct("2040-01-01 12:00"))
>> [1] "2040-01-01 12:00:00 GMT"
>>
>> as was the 1848 one when TZ="UTC":
>> > Sys.setenv(TZ = "UTC")
>> > (z <- as.POSIXct("1848-01-01 12:00"))
>> [1] "1848-01-01 12:00:00 UTC"
>>
>> This is probably a quirk of FreeBSD's datetime support, I'll see what
>> the port used to do for 3.0.2.
>>
>> Also, there is an issue tracking updating the port to the current
>> release: https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=195783. I've
>> posted the summary of this thread there, thanks for your help.
>>
>> Davor
>>
>>
>> Prof Brian Ripley writes:
>>
>>> On 31/08/2015 16:26, Davor Cubranic wrote:
 Prof Brian Ripley writes:

> Second, we don't have all the pertinent information such as the
> configure options used and the architecture (x86_64?).  I am going to
> have to guess none as none were mentioned, but using --enable-R-shlib
> would be pertinent.
>
> On 31/08/2015 05:47, Davor Cubranic wrote:
>> On FreeBSD 10.2, I get the following error when compiling R from the
>> Subversion trunk (with "configure && make"):
>
> You have not told us which revision.  A basic check is to see if you can
> build the latest released version, as the trunk is 'Under development'.

 As suggested, I tried compiling from Subversion tag 3.2.2 (r69054).
 I used no command-line options to 'configure', as mentioned in my
 previous email, and this is the output:

 R is now configured for x86_64-unknown-freebsd10.2

   Source directory:  .