[R] R on the cloud - Windows to Linux

[Peter Langfelder]

On Tue, Dec 20, 2011 at 2:22 PM, Whit Armstrong
<armstrong.whit at gmail.com> wrote:
> Ben,
>
> You can email me directly if you have problems.
>
> You can see the build status here:
> http://cran.r-project.org/web/checks/check_results_rzmq.html
>
> I don't use windows at all, so I'm hoping for some help from the
> community for windows compatibility.

If I understand correctly he is trying to compile the package on linux
 My guess is that he does not have the "development" version of a
required library installed. My guess is library zmq.

Ben, you probably need to install the library zeromq, which is a
system library (not an R package). Make sure you also install the
zeromq-devel package as that contains the header files which is what
your compilation is missing.

The installation procedure depends on the linux flavor/distribution
you use. You may need to ask your system admin to install it for you
if the system is not under your control.

HTH,

Peter
>

>> Hopefully I have the correct server list. I'm new'ish to R and very new to
>> Linux. I'm looking to do work using AWS and the rzmq package is a dependency
>> to some other packages/code I want to use (deathstar). I can't seem to get
>> rzmq installed on our linux machine. Here are the details:
>>
>> I'm attempting to do:
>>
>> install.packages("rzmq", dependencies = TRUE)
>>
>>
>>
>> And it looks like it errors out on this line:
>>
>> g++ -m64 -I/usr/include/R  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
>> --param=ssp-buffer-size=4 -m64 -mtune=generic -c interface.cpp -o
>> interface.o

>> g++ -m64 -I/usr/include/R  -I/usr/local/include    -fpic  -O2 -g -pipe -Wall
>> -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector
>> --param=ssp-buffer-size=4 -m64 -mtune=generic -c interface.cpp -o
>> interface.o
>>
>> interface.cpp:20:19: error: zmq.hpp: No such file or directory
>>
>> interface.cpp: In function âint string_to_socket_type(std::string)â:
>>
>> interface.cpp:25: error: âZMQ_PAIRâ was not declared in this scope
>>
>> interface.cpp:27: error: âZMQ_PUBâ was not declared in this scope
>>
>> interface.cpp:29: error: âZMQ_SUBâ was not declared in this scope
>>
>> interface.cpp:31: error: âZMQ_REQâ was not declared in this scope
>>
>> interface.cpp:33: error: âZMQ_REPâ was not declared in this scope
>>
>> interface.cpp:35: error: âZMQ_DEALERâ was not declared in this scope
>>
>> interface.cpp:37: error: âZMQ_ROUTERâ was not declared in this scope
>>
>> interface.cpp:39: error: âZMQ_PULLâ was not declared in this scope
>>
>> interface.cpp:41: error: âZMQ_PUSHâ was not declared in this scope
>>
>> interface.cpp:43: error: âZMQ_XPUBâ was not declared in this scope
>>
>> interface.cpp:45: error: âZMQ_XSUBâ was not declared in this scope
>>
>> interface.cpp: In function âvoid contextFinalizer(SEXPREC*)â:
>>
>> interface.cpp:52: error: âzmqâ has not been declared
>>
>> interface.cpp:52: error: âcontextâ was not declared in this scope
>>
>> interface.cpp:52: error: expected type-specifier before âzmqâ
>>
>> interface.cpp:52: error: expected `>' before âzmqâ
>>
>> interface.cpp:52: error: expected `(' before âzmqâ
>>
>> interface.cpp:52: error: âzmqâ has not been declared
>>
>> interface.cpp:52: error: expected primary-expression before â>â token
>>
>> interface.cpp:52: error: expected `)' before â;â token
>>
>> interface.cpp:53: error: type â<type error>â argument given to âdeleteâ,
>> expected pointer
>>
>> interface.cpp: In function âvoid socketFinalizer(SEXPREC*)â:
>>
>> interface.cpp:58: error: âzmqâ has not been declared
>>
>> interface.cpp:58: error: âsocketâ was not declared in this scope
>>
>> interface.cpp:58: error: expected type-specifier before âzmqâ
>>
>> interface.cpp:58: error: expected `>' before âzmqâ
>>
>> interface.cpp:58: error: expected `(' before âzmqâ
>>
>> interface.cpp:58: error: âzmqâ has not been declared
>>
>> interface.cpp:58: error: expected primary-expression before â>â token
>>
>> interface.cpp:58: error: expected `)' before â;â token
>>
>> interface.cpp:59: error: type â<type error>â argument given to âdeleteâ,
>> expected pointer
>>
>> interface.cpp: In function âSEXPREC* initContext()â:
>>
>> interface.cpp:65: error: âzmqâ has not been declared
>>
>> interface.cpp:65: error: âcontextâ was not declared in this scope
>>
>> interface.cpp:65: error: expected type-specifier before âzmqâ
>>
>> interface.cpp:65: error: expected `;' before âzmqâ
>>
>> interface.cpp: In function âSEXPREC* initSocket(SEXPREC*, SEXPREC*)â:
>>
>> interface.cpp:86: error: âzmqâ has not been declared
>>
>> interface.cpp:86: error: âcontextâ was not declared in this scope
>>
>> interface.cpp:86: error: expected type-specifier before âzmqâ
>>
>> interface.cpp:86: error: expected `>' before âzmqâ
>>
>> interface.cpp:86: error: expected `(' before âzmqâ
>>
>> interface.cpp:86: error: âzmqâ has not been declared
>>
>> interface.cpp:86: error: expected primary-expression before â>â token
>>
>> interface.cpp:86: error: expected `)' before â;â token
>>
>> interface.cpp:87: error: âzmqâ has not been declared
>>
>> interface.cpp:87: error: âsocketâ was not declared in this scope
>>
>> interface.cpp:87: error: expected type-specifier before âzmqâ
>>
>> interface.cpp:87: error: expected `;' before âzmqâ
>>
>> interface.cpp: In function âSEXPREC* bindSocket(SEXPREC*, SEXPREC*)â:
>>
>> interface.cpp:101: error: âzmqâ has not been declared
>>
>> interface.cpp:101: error: âsocketâ was not declared in this scope
>>
>> interface.cpp:101: error: expected type-specifier before âzmqâ
>>
>> interface.cpp:101: error: expected `>' before âzmqâ
>>
>> interface.cpp:101: error: expected `(' before âzmqâ
>>
>> interface.cpp:101: error: âzmqâ has not been declared
>>
>> interface.cpp:101: error: expected primary-expression before â>â token
>>
>> interface.cpp:101: error: expected `)' before â;â token
>>
>> interface.cpp: In function âSEXPREC* connectSocket(SEXPREC*, SEXPREC*)â:
>>
>> interface.cpp:122: error: âzmqâ has not been declared
>>
>> interface.cpp:122: error: âsocketâ was not declared in this scope
>>
>> interface.cpp:122: error: expected type-specifier before âzmqâ
>>
>> interface.cpp:122: error: expected `>' before âzmqâ
>>
>> interface.cpp:122: error: expected `(' before âzmqâ
>>
>> interface.cpp:122: error: âzmqâ has not been declared
>>
>> interface.cpp:122: error: expected primary-expression before â>â token
>>
>> interface.cpp:122: error: expected `)' before â;â token
>>
>> interface.cpp: In function âSEXPREC* sendSocket(SEXPREC*, SEXPREC*)â:
>>
>> interface.cpp:149: error: âzmqâ has not been declared
>>
>> interface.cpp:149: error: âsocketâ was not declared in this scope
>>
>> interface.cpp:149: error: expected type-specifier before âzmqâ
>>
>> interface.cpp:149: error: expected `>' before âzmqâ
>>
>> interface.cpp:149: error: expected `(' before âzmqâ
>>
>> interface.cpp:149: error: âzmqâ has not been declared
>>
>> interface.cpp:149: error: expected primary-expression before â>â token
>>
>> interface.cpp:149: error: expected `)' before â;â token
>>
>> interface.cpp:150: error: âzmqâ has not been declared
>>
>> interface.cpp:150: error: expected `;' before âmsgâ
>>
>> interface.cpp:151: error: âmsgâ was not declared in this scope
>>
>> interface.cpp: In function âSEXPREC* sendNullMsg(SEXPREC*)â:
>>
>> interface.cpp:166: error: âzmqâ has not been declared
>>
>> interface.cpp:166: error: âsocketâ was not declared in this scope
>>
>> interface.cpp:166: error: expected type-specifier before âzmqâ
>>
>> interface.cpp:166: error: expected `>' before âzmqâ
>>
>> interface.cpp:166: error: expected `(' before âzmqâ
>>
>> interface.cpp:166: error: âzmqâ has not been declared
>>
>> interface.cpp:166: error: expected primary-expression before â>â token
>>
>> interface.cpp:166: error: expected `)' before â;â token
>>
>> interface.cpp:167: error: âzmqâ has not been declared
>>
>> interface.cpp:167: error: expected `;' before âmsgâ
>>
>> interface.cpp:169: error: âmsgâ was not declared in this scope
>>
>> interface.cpp: In function âSEXPREC* receiveSocket(SEXPREC*)â:
>>
>> interface.cpp:181: error: âzmqâ has not been declared
>>
>> interface.cpp:181: error: expected `;' before âmsgâ
>>
>> interface.cpp:182: error: âzmqâ has not been declared
>>
>> interface.cpp:182: error: âsocketâ was not declared in this scope
>>
>> interface.cpp:182: error: expected type-specifier before âzmqâ
>>
>> interface.cpp:182: error: expected `>' before âzmqâ
>>
>> interface.cpp:182: error: expected `(' before âzmqâ
>>
>> interface.cpp:182: error: âzmqâ has not been declared
>>
>> interface.cpp:182: error: expected primary-expression before â>â token
>>
>> interface.cpp:182: error: expected `)' before â;â token
>>
>> interface.cpp:184: error: âmsgâ was not declared in this scope
>>
>> interface.cpp:189: error: âmsgâ was not declared in this scope
>>
>> interface.cpp: In function âSEXPREC* receiveString(SEXPREC*)â:
>>
>> interface.cpp:201: error: âzmqâ has not been declared
>>
>> interface.cpp:201: error: expected `;' before âmsgâ
>>
>> interface.cpp:202: error: âzmqâ has not been declared
>>
>> interface.cpp:202: error: âsocketâ was not declared in this scope
>>
>> interface.cpp:202: error: expected type-specifier before âzmqâ
>>
>> interface.cpp:202: error: expected `>' before âzmqâ
>>
>> interface.cpp:202: error: expected `(' before âzmqâ
>>
>> interface.cpp:202: error: âzmqâ has not been declared
>>
>> interface.cpp:202: error: expected primary-expression before â>â token
>>
>> interface.cpp:202: error: expected `)' before â;â token
>>
>> interface.cpp:204: error: âmsgâ was not declared in this scope
>>
>> interface.cpp:210: error: âmsgâ was not declared in this scope
>>
>> interface.cpp: In function âSEXPREC* receiveInt(SEXPREC*)â:
>>
>> interface.cpp:227: error: âzmqâ has not been declared
>>
>> interface.cpp:227: error: expected `;' before âmsgâ
>>
>> interface.cpp:228: error: âzmqâ has not been declared
>>
>> interface.cpp:228: error: âsocketâ was not declared in this scope
>>
>> interface.cpp:228: error: expected type-specifier before âzmqâ
>>
>> interface.cpp:228: error: expected `>' before âzmqâ
>>
>> interface.cpp:228: error: expected `(' before âzmqâ
>>
>> interface.cpp:228: error: âzmqâ has not been declared
>>
>> interface.cpp:228: error: expected primary-expression before â>â token
>>
>> interface.cpp:228: error: expected `)' before â;â token
>>
>> interface.cpp:230: error: âmsgâ was not declared in this scope
>>
>> interface.cpp:235: error: âmsgâ was not declared in this scope
>>
>> interface.cpp:240: error: âmsgâ was not declared in this scope
>>
>> interface.cpp: In function âSEXPREC* receiveDouble(SEXPREC*)â:
>>
>> interface.cpp:250: error: âzmqâ has not been declared
>>
>> interface.cpp:250: error: expected `;' before âmsgâ
>>
>> interface.cpp:251: error: âzmqâ has not been declared
>>
>> interface.cpp:251: error: âsocketâ was not declared in this scope
>>
>> interface.cpp:251: error: expected type-specifier before âzmqâ
>>
>> interface.cpp:251: error: expected `>' before âzmqâ
>>
>> interface.cpp:251: error: expected `(' before âzmqâ
>>
>> interface.cpp:251: error: âzmqâ has not been declared
>>
>> interface.cpp:251: error: expected primary-expression before â>â token
>>
>> interface.cpp:251: error: expected `)' before â;â token
>>
>> interface.cpp:253: error: âmsgâ was not declared in this scope
>>
>> interface.cpp:258: error: âmsgâ was not declared in this scope
>>
>> interface.cpp:263: error: âmsgâ was not declared in this scope
>>
>> make: *** [interface.o] Error 1
>>
>> ERROR: compilation failed for package ârzmqâ
>>
>> * removing â/home/bnachtrieb/R/x86_64-redhat-linux-gnu-library/2.13/rzmqâ
>>
>>
>>
>> The downloaded packages are in
>>
>>         â/tmp/RtmpoTdDMm/downloaded_packagesâ
>>
>> Warning message:
>>
>> In install.packages("rzmq", dependencies = TRUE) :
>>
>>   installation of package 'rzmq' had non-zero exit status
>>
>>
>>>
>>
>>
>>
>> Thank you for your help!
>>
>>
>> Ben
>>
>> On Wed, Dec 7, 2011 at 7:00 PM, Whit Armstrong <armstrong.whit at gmail.com>
>> wrote:
>>>
>>> subscribe to R-hpc.
>>>
>>> and check out these:
>>> https://github.com/armstrtw/rzmq
>>> https://github.com/armstrtw/AWS.tools
>>> https://github.com/armstrtw/deathstar
>>>
>>> and this:
>>> http://code.google.com/p/segue/
>>>
>>> If you're willing to work, you can probably get deathstar to work
>>> using a local windows box and remote linux nodes.
>>>
>>> -Whit
>>>
>>>
>>> On Wed, Dec 7, 2011 at 6:02 PM, Ben quant <ccquant at gmail.com> wrote:
>>> > Hello,
>>> >
>>> > I'm working with the gam function and due to the amount of data I am
>>> > working with it is taking a long time to run. I looked at the tips to
>>> > get
>>> > it to run faster, but none have acceptable side effects. That is the
>>> > real
>>> > problem.
>>> >
>>> > I have accepted that gam will run a long time. I will be running gam
>>> > many
>>> > times for many different models. To make gam useable I am looking at
>>> > splitting the work up and putting all of it on an Amazon EC2 cloud. I
>>> > have
>>> > a Windows machine and I'm (planning on) running Linux EC2 instances via
>>> > Amazon.
>>> >
>>> > I have R running on one EC2 instance now. Now I'm looking to:
>>> >
>>> > 1) division of processing
>>> > 2) creating/terminating instances via R
>>> > 3) porting code and data to the cloud
>>> > 4) producing plots on the cloud and getting them back on my (Windows)
>>> > computer for review
>>> > 5) do all of the above programmically (over night)
>>> >
>>> > I am new'ish to R, brand new to the cloud, and I am new to Linux (but I
>>> > have access to a Linux expert at my company). I'm looking for 1)
>>> > guidance
>>> > so I am headed in the best direction from the start, 2) any gotchas I
>>> > can
>>> > learn from, 3) package suggestions.
>>> >
>>> > Thank you very much for your assistance!
>>> >
>>> > Regards,
>>> >
>>> > Ben
>>> >
>>> >        [[alternative HTML version deleted]]
>>> >
>>> > ______________________________________________
>>> > R-help at r-project.org mailing list
>>> > https://stat.ethz.ch/mailman/listinfo/r-help
>>> > PLEASE do read the posting guide
>>> > http://www.R-project.org/posting-guide.html
>>> > and provide commented, minimal, self-contained, reproducible code.
>>
>>
>
> ______________________________________________
> R-help at r-project.org mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.