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
ā/home/bnachtrieb/R/x86_64-redhat-linux-gnu-library/2.13ā

(as ālibā 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 ārzmqā ...

** 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 āint string_to_socket_type(std::string)ā:

interface.cpp:25: error: āZMQ_PAIRā was not declared in this scope

interface.cpp:27: error: āZMQ_PUBā was not declared in this scope

interface.cpp:29: error: āZMQ_SUBā was not declared in this scope

interface.cpp:31: error: āZMQ_REQā was not declared in this scope

interface.cpp:33: error: āZMQ_REPā was not declared in this scope

interface.cpp:35: error: āZMQ_DEALERā was not declared in this scope

interface.cpp:37: error: āZMQ_ROUTERā was not declared in this scope

interface.cpp:39: error: āZMQ_PULLā was not declared in this scope

interface.cpp:41: error: āZMQ_PUSHā was not declared in this scope

interface.cpp:43: error: āZMQ_XPUBā was not declared in this scope

interface.cpp:45: error: āZMQ_XSUBā was not declared in this scope

interface.cpp: In function āvoid contextFinalizer(SEXPREC*)ā:

interface.cpp:52: error: āzmqā has not been declared

interface.cpp:52: error: ācontextā was not declared in this scope

interface.cpp:52: error: expected type-specifier before āzmqā

interface.cpp:52: error: expected `>' before āzmqā

interface.cpp:52: error: expected `(' before āzmqā

interface.cpp:52: error: āzmqā has not been declared

interface.cpp:52: error: expected primary-expression before ā>ā token

interface.cpp:52: error: expected `)' before ā;ā token

interface.cpp:53: error: type ā<type error>ā argument given to ādeleteā,
expected pointer

interface.cpp: In function āvoid socketFinalizer(SEXPREC*)ā:

interface.cpp:58: error: āzmqā has not been declared

interface.cpp:58: error: āsocketā was not declared in this scope

interface.cpp:58: error: expected type-specifier before āzmqā

interface.cpp:58: error: expected `>' before āzmqā

interface.cpp:58: error: expected `(' before āzmqā

interface.cpp:58: error: āzmqā has not been declared

interface.cpp:58: error: expected primary-expression before ā>ā token

interface.cpp:58: error: expected `)' before ā;ā token

interface.cpp:59: error: type ā<type error>ā argument given to ādeleteā,
expected pointer

interface.cpp: In function āSEXPREC* initContext()ā:

interface.cpp:65: error: āzmqā has not been declared

interface.cpp:65: error: ācontextā was not declared in this scope

interface.cpp:65: error: expected type-specifier before āzmqā

interface.cpp:65: error: expected `;' before āzmqā

interface.cpp: In function āSEXPREC* initSocket(SEXPREC*, SEXPREC*)ā:

interface.cpp:86: error: āzmqā has not been declared

interface.cpp:86: error: ācontextā was not declared in this scope

interface.cpp:86: error: expected type-specifier before āzmqā

interface.cpp:86: error: expected `>' before āzmqā

interface.cpp:86: error: expected `(' before āzmqā

interface.cpp:86: error: āzmqā has not been declared

interface.cpp:86: error: expected primary-expression before ā>ā token

interface.cpp:86: error: expected `)' before ā;ā token

interface.cpp:87: error: āzmqā has not been declared

interface.cpp:87: error: āsocketā was not declared in this scope

interface.cpp:87: error: expected type-specifier before āzmqā

interface.cpp:87: error: expected `;' before āzmqā

interface.cpp: In function āSEXPREC* bindSocket(SEXPREC*, SEXPREC*)ā:

interface.cpp:101: error: āzmqā has not been declared

interface.cpp:101: error: āsocketā was not declared in this scope

interface.cpp:101: error: expected type-specifier before āzmqā

interface.cpp:101: error: expected `>' before āzmqā

interface.cpp:101: error: expected `(' before āzmqā

interface.cpp:101: error: āzmqā has not been declared

interface.cpp:101: error: expected primary-expression before ā>ā token

interface.cpp:101: error: expected `)' before ā;ā token

interface.cpp: In function āSEXPREC* connectSocket(SEXPREC*, SEXPREC*)ā:

interface.cpp:122: error: āzmqā has not been declared

interface.cpp:122: error: āsocketā was not declared in this scope

interface.cpp:122: error: expected type-specifier before āzmqā

interface.cpp:122: error: expected `>' before āzmqā

interface.cpp:122: error: expected `(' before āzmqā

interface.cpp:122: error: āzmqā has not been declared

interface.cpp:122: error: expected primary-expression before ā>ā token

interface.cpp:122: error: expected `)' before ā;ā token

interface.cpp: In function āSEXPREC* sendSocket(SEXPREC*, SEXPREC*)ā:

interface.cpp:149: error: āzmqā has not been declared

interface.cpp:149: error: āsocketā was not declared in this scope

interface.cpp:149: error: expected type-specifier before āzmqā

interface.cpp:149: error: expected `>' before āzmqā

interface.cpp:149: error: expected `(' before āzmqā

interface.cpp:149: error: āzmqā has not been declared

interface.cpp:149: error: expected primary-expression before ā>ā token

interface.cpp:149: error: expected `)' before ā;ā token

interface.cpp:150: error: āzmqā has not been declared

interface.cpp:150: error: expected `;' before āmsgā

interface.cpp:151: error: āmsgā was not declared in this scope

interface.cpp: In function āSEXPREC* sendNullMsg(SEXPREC*)ā:

interface.cpp:166: error: āzmqā has not been declared

interface.cpp:166: error: āsocketā was not declared in this scope

interface.cpp:166: error: expected type-specifier before āzmqā

interface.cpp:166: error: expected `>' before āzmqā

interface.cpp:166: error: expected `(' before āzmqā

interface.cpp:166: error: āzmqā has not been declared

interface.cpp:166: error: expected primary-expression before ā>ā token

interface.cpp:166: error: expected `)' before ā;ā token

interface.cpp:167: error: āzmqā has not been declared

interface.cpp:167: error: expected `;' before āmsgā

interface.cpp:169: error: āmsgā was not declared in this scope

interface.cpp: In function āSEXPREC* receiveSocket(SEXPREC*)ā:

interface.cpp:181: error: āzmqā has not been declared

interface.cpp:181: error: expected `;' before āmsgā

interface.cpp:182: error: āzmqā has not been declared

interface.cpp:182: error: āsocketā was not declared in this scope

interface.cpp:182: error: expected type-specifier before āzmqā

interface.cpp:182: error: expected `>' before āzmqā

interface.cpp:182: error: expected `(' before āzmqā

interface.cpp:182: error: āzmqā has not been declared

interface.cpp:182: error: expected primary-expression before ā>ā token

interface.cpp:182: error: expected `)' before ā;ā token

interface.cpp:184: error: āmsgā was not declared in this scope

interface.cpp:189: error: āmsgā was not declared in this scope

interface.cpp: In function āSEXPREC* receiveString(SEXPREC*)ā:

interface.cpp:201: error: āzmqā has not been declared

interface.cpp:201: error: expected `;' before āmsgā

interface.cpp:202: error: āzmqā has not been declared

interface.cpp:202: error: āsocketā was not declared in this scope

interface.cpp:202: error: expected type-specifier before āzmqā

interface.cpp:202: error: expected `>' before āzmqā

interface.cpp:202: error: expected `(' before āzmqā

interface.cpp:202: error: āzmqā has not been declared

interface.cpp:202: error: expected primary-expression before ā>ā token

interface.cpp:202: error: expected `)' before ā;ā token

interface.cpp:204: error: āmsgā was not declared in this scope

interface.cpp:210: error: āmsgā was not declared in this scope

interface.cpp: In function āSEXPREC* receiveInt(SEXPREC*)ā:

interface.cpp:227: error: āzmqā has not been declared

interface.cpp:227: error: expected `;' before āmsgā

interface.cpp:228: error: āzmqā has not been declared

interface.cpp:228: error: āsocketā was not declared in this scope

interface.cpp:228: error: expected type-specifier before āzmqā

interface.cpp:228: error: expected `>' before āzmqā

interface.cpp:228: error: expected `(' before āzmqā

interface.cpp:228: error: āzmqā has not been declared

interface.cpp:228: error: expected primary-expression before ā>ā token

interface.cpp:228: error: expected `)' before ā;ā token

interface.cpp:230: error: āmsgā was not declared in this scope

interface.cpp:235: error: āmsgā was not declared in this scope

interface.cpp:240: error: āmsgā was not declared in this scope

interface.cpp: In function āSEXPREC* receiveDouble(SEXPREC*)ā:

interface.cpp:250: error: āzmqā has not been declared

interface.cpp:250: error: expected `;' before āmsgā

interface.cpp:251: error: āzmqā has not been declared

interface.cpp:251: error: āsocketā was not declared in this scope

interface.cpp:251: error: expected type-specifier before āzmqā

interface.cpp:251: error: expected `>' before āzmqā

interface.cpp:251: error: expected `(' before āzmqā

interface.cpp:251: error: āzmqā has not been declared

interface.cpp:251: error: expected primary-expression before ā>ā token

interface.cpp:251: error: expected `)' before ā;ā token

interface.cpp:253: error: āmsgā was not declared in this scope

interface.cpp:258: error: āmsgā was not declared in this scope

interface.cpp:263: error: āmsgā was not declared in this scope

make: *** [interface.o] Error 1

ERROR: compilation failed for package ārzmqā

* removing ā/home/bnachtrieb/R/x86_64-redhat-linux-gnu-library/2.13/rzmqā



The downloaded packages are in

        ā/tmp/RtmpoTdDMm/downloaded_packagesā

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@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@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@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.
>

	[[alternative HTML version deleted]]

