

Dear (ok) Dr. Winsemius,

I have tried  it too.
I try again now and the result is as following (similar to the results from terminal):

> install.packages("Rmpi", type="source") 
--- Please select a CRAN mirror for use in this session ---
trying URL 'http://cran.at.r-project.org/src/contrib/Rmpi_0.6-3.tar.gz'
Content type 'application/x-gzip' length 94142 bytes (91 Kb)
opened URL
==================================================
downloaded 91 Kb

* installing *source* package ‘Rmpi’ ...
** package ‘Rmpi’ successfully unpacked and MD5 sums checked
checking for gcc... llvm-gcc-4.2 -arch x86_64 -std=gnu99
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether llvm-gcc-4.2 -arch x86_64 -std=gnu99 accepts -g... yes
checking for llvm-gcc-4.2 -arch x86_64 -std=gnu99 option to accept ISO C89... none needed
checking how to run the C preprocessor... llvm-gcc-4.2 -arch x86_64 -std=gnu99 -E
checking for grep that handles long lines and -e... /usr/bin/grep
checking for egrep... /usr/bin/grep -E
checking for ANSI C header files... rm: conftest.dSYM: is a directory
rm: conftest.dSYM: is a directory
yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking mpi.h usability... no
checking mpi.h presence... no
checking for mpi.h... no
configure: error: "Cannot find mpi.h header file"
ERROR: configuration failed for package ‘Rmpi’
* removing ‘/Library/Frameworks/R.framework/Versions/3.0/Resources/library/Rmpi’

The downloaded source packages are in
‘/private/var/folders/j6/5wyr7dp55f5bq1rpwy4s4sw00000gn/T/RtmpuPV2oe/downloaded_packages’
Warning message:
In install.packages("Rmpi", type = "source") :
  installation of package ‘Rmpi’ had non-zero exit status
> 

>That does indicate the need to solve the missing Mac MPI package.


Mmm ... yes, I still try to figure out it ... and move backward to learn things that I don't understand first.

Thank you very much.

With kind regards,
Ema



________________________________
 From: David Winsemius <dwinsemius@comcast.net>

Cc: Michael Weylandt <michael.weylandt@gmail.com>; "r-sig-mac@r-project.org" <r-sig-mac@r-project.org> 
Sent: Monday, August 19, 2013 8:56 PM
Subject: Re: [R-SIG-Mac] Rmpi package



On Aug 19, 2013, at 2:15 AM, Rohmatul Fajriyah wrote:

> Dear Both,
> 
> OK.
> Try 
> install.packages("Rmpi") 

Michael should have said:

install.packages("Rmpi", type="source") 


> 
> I have done it previously (but I did not tell here), it did not work since it has no binary just a source.
> I have done sudo R CMD INSTALL Rmpi_0.6-4.tar at terminal too, and I got this message:
> ......
> checking for mpi.h... no
> configure: error: "Cannot find mpi.h header file"
> ERROR: configuration failed for package 'Rmpi',

That does indicate the need to solve the missing Mac MPI package.

> My mistake was I did not google it. Only search from r-sig-mac archives.
> 
> Now I am googling it and found some information (from R-sig-Debian and R-help archives ) that I need to give it a try.
> 
>> MPI isn't the easiest build in the world so I'd imagine it will fail, but this will at least give us a sense of how your environment is configured.
>> 
>> Needless to say: if you haven't got the compilers and command line tools available from XCode (the ones used to build R) do that first 
>> 
> I think, I already installed the Xcode, following the instruction from here: (choose Rmpi for Mac OS X) 
> http://www.stats.uwo.ca/faculty/yu/Rmpi/
> Because the Mountain Lion’s default PATH is /usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin, then --I think-- I need to change the path if I want to install Homebrew. On the other hand my current R is at /usr/bin. Which made me not sure what should I do.


> 
>>  or you have no hope ;-)

> Let me try the information that I found from google and get back here if I still have a trouble.
> 
> Prof. Winsemius: My apologise for that ... 

Heh. Not a professor, just a humble country doctor.


> 
> Thank you very much.
> 
> With kind regards,
> Ema
> 
> 
> 
> From: Michael Weylandt <michael.weylandt@gmail.com>

> Cc: David Winsemius <dwinsemius@comcast.net>; "r-sig-mac@r-project.org" <r-sig-mac@r-project.org> 
> Sent: Monday, August 19, 2013 2:19 AM
> Subject: Re: [R-SIG-Mac] Rmpi package
> 
> As David noted, it's been de-CRAN'd for pushing some check times a bit far. 
> 
> This means you'll likely need to build it from source, which home brew won't help with (well, much beyond what 'regular' R does)
> 
> Try 
> 
> install.packages("Rmpi") 
> 
> to see what happens. MPI isn't the easiest build in the world so I'd imagine it will fail, but this will at least give us a sense of how your environment is configured. 
> 
> Needless to say: if you haven't got the compilers and command line tools available from XCode (the ones used to build R) do that first or you have no hope ;-)
> 
> Michael
> 

> 
>> 
>> (Thank you Michael Weylandt, for notifying me about this. Here my previous email.)
>> 
>> Dear Sir,
>> 
>> Thank you very much for your respond.
>> 
>>  > What does this have to do with R? (Or for that matter, the directions referenced?) Generally Simon advises against using brew, fink, or other Mac/NIX package installers. 
>> 
>> Really? I don't know about it. Therefore, I should not continue to do this ...? 
>> 
>> > Rmpi is not listed as available in CRAN at the moment, apparently because it took more than 30 minutes to unload:
>> > http://www.r-project.org/nosvn/R.check/r-release-macosx-x86_64/Rmpi-00check.html
>> 
>>  I checked it and it's still there, Sir. (unless I am mistaken ...)
>> 
>> > Certainly you need to do a better job of describing your OS, your system tools, which MPI you have installed or are intending to use, and what versions of R and Rmpi that you have.  
>> > Also explain why you are not using the standard parallel package.
>> 
>> I tried to install the package to broaden my knowledge in doing parallel computing. 
>>  (Yes, I have used some R parallel packages).
>> 
>> My computer is Mac OS X 10.8.4 and R 3.0.1 (64 bit).
>> I downloaded the Rmpi_0.6-4.tar already, but I did not install it yet, due to as I have explained in my previous email.
>>  
>> Sincerely,
>> Ema
>> 
>> From: Michael Weylandt <michael.weylandt@gmail.com>

>> Cc: David Winsemius <dwinsemius@comcast.net>; "r-sig-mac@r-project.org" <r-sig-mac@r-project.org> 
>> Sent: Monday, August 19, 2013 12:52 AM
>> Subject: Re: [R-SIG-Mac] Rmpi package
>> 
>> Hi Ema,
>> 
>> Can you try resenting this -- the quoting seems to have gotten messed up. 
>> 
>> MW
>> 
>> 
>> 
>> 
> 
> 

David Winsemius
Alameda, CA, USA
	[[alternative HTML version deleted]]

