[R] R on the cloud - Windows to Linux

Whit Armstrong armstrong.whit at gmail.com
Tue Dec 20 23:22:26 CET 2011 

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 you want to be that person, then download the source and go for it.

Cheers,
Whit


On Tue, Dec 20, 2011 at 5:01 PM, Ben quant <ccquant at gmail.com> wrote:
> I just posted this on the R-hpc list. If the r-help list is the wrong list
> to use please ignore this message.  Thanks!
>
> Hello,
>
> 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
>
>
>
> Here is the entire print after install attempt (note the bolded line is the
> same as the line above):
>
>
>
> Installing package(s) into
> â/home/bnachtrieb/R/x86_64-redhat-linux-gnu-library/2.13â
>
> (as âlibâ is unspecified)
>
> trying URL
> 'http://software.rc.fas.harvard.edu/mirrors/R/src/contrib/rzmq_0.6.1.tar.gz'
>
> Content type 'application/x-gzip' length 8069 bytes
>
> opened URL
>
> ==================================================
>
> downloaded 8069 bytes
>
>
>
> Loading required package: gtools
>
> Loading required package: gdata
>
> gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
>
>
>
> gdata: read.xls support for 'XLSX' (Excel 2007+) files ENABLED.
>
>
>
> Attaching package: 'gdata'
>
>
>
> The following object(s) are masked from 'package:utils':
>
>
>
>     object.size
>
>
>
> Loading required package: stats
>
>
>
> Attaching package: 'stats'
>
>
>
> The following object(s) are masked from 'package:gdata':
>
>
>
>     nobs
>
>
>
> Loading required package: caTools
>
> Loading required package: bitops
>
> Loading required package: grid
>
> Loading required package: KernSmooth
>
> KernSmooth 2.23 loaded
>
> Copyright M. P. Wand 1997-2009
>
>
>
> Attaching package: 'gplots'
>
>
>
> The following object(s) are masked from 'package:stats':
>
>
>
>     lowess
>
>
>
> Loading required package: boot
>
> Loading required package: graphics
>
>
>
> Attaching package: 'boot'
>
>
>
> The following object(s) are masked from 'package:gtools':
>
>
>
>     inv.logit, logit
>
>
>
> Loading required package: R.methodsS3
>
> R.methodsS3 v1.2.1 (2010-09-18) successfully loaded. See ?R.methodsS3 for
> help.
>
> R.oo v1.8.3 (2011-11-01) successfully loaded. See ?R.oo for help.
>
> Loading required package: timeDate
>
> * installing *source* package ârzmqâ ...
>
> ** libs
>
> 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.
>
>

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