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.w...@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 <ccqu...@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]]
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