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Failed to install rzmq #50

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jiaweih opened this Issue Dec 21, 2014 · 84 comments

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@jiaweih

jiaweih commented Dec 21, 2014

System: OS X Yosemite, R: @3.1.2_0+accelerate+cairo+gfortran48+recommended+x11

> install_github('armstrtw/rzmq')
Downloading github repo armstrtw/rzmq@master
Installing rzmq
'/opt/local/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD  \
  INSTALL  \
  '/private/var/folders/rv/wstf88ns4g16sqgg62lsz_pw0000gn/T/Rtmp5NeM5l/devtools182a058697683/armstrtw-rzmq-320891d'  \
  --library='/Users/jiaweihe/Library/R/3.1/library' --install-tests 
 installing *source* package ‘rzmq’ ...
** libs
/usr/bin/clang++ -std=c++11 -I/opt/local/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I../inst/cppzmq -I/opt/local/include    -fPIC  -pipe -Os -arch x86_64 -stdlib=libc++ -c interface.cpp -o interface.o
interface.cpp:24:10: **fatal error: 'zmq.hpp' file not found**
#include <zmq.hpp>
         ^
1 error generated.
make: *** [interface.o] Error 1
ERROR: compilation failed for package ‘rzmq’
 removing ‘/Users/jiaweihe/Library/R/3.1/library/rzmq’

Error: Command failed (1)

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rgbkrk Dec 21, 2014

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You'll need to install the libzmq3 headers too. For me I used brew and ran brew install czmq zmq.

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rgbkrk commented Dec 21, 2014

You'll need to install the libzmq3 headers too. For me I used brew and ran brew install czmq zmq.

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jiaweih Dec 21, 2014

Thank you for the tip! It turns out I also need to install cppzmq.

jiaweih commented Dec 21, 2014

Thank you for the tip! It turns out I also need to install cppzmq.

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jankatins Jan 19, 2015

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This could also be a problem in install_github as the above file is actually included via a submodule.

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jankatins commented Jan 19, 2015

This could also be a problem in install_github as the above file is actually included via a submodule.

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takluyver Jan 19, 2015

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Good point - if install_github() works by downloading a tarball/zipball from Github, any submodules will be left out.

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takluyver commented Jan 19, 2015

Good point - if install_github() works by downloading a tarball/zipball from Github, any submodules will be left out.

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everm1nd Jan 28, 2015

I have the same issue. brew install czmq zmq have no result.

I have the same issue. brew install czmq zmq have no result.

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armaneshaghi Feb 1, 2015

Same here, brew install czmq zmq does not work.

EDIT: it installs czmq but does not solve the problem. Also cppzmq is not available via brew.

Same here, brew install czmq zmq does not work.

EDIT: it installs czmq but does not solve the problem. Also cppzmq is not available via brew.

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armaneshaghi Feb 1, 2015

This solved my issue:

From terminal:

wget https://raw.githubusercontent.com/zeromq/cppzmq/master/zmq.hpp

mv zmq.hpp /usr/local/include/

From inside R:

require('devtools')

install_github('armstrtw/rzmq')

This solved my issue:

From terminal:

wget https://raw.githubusercontent.com/zeromq/cppzmq/master/zmq.hpp

mv zmq.hpp /usr/local/include/

From inside R:

require('devtools')

install_github('armstrtw/rzmq')

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everm1nd Feb 2, 2015

@armaneshaghi it works! thanks! 👍

everm1nd commented Feb 2, 2015

@armaneshaghi it works! thanks! 👍

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cosinequanon Feb 2, 2015

You can also install rzmq from CRAN which does not seem to have any of these issues.

You can also install rzmq from CRAN which does not seem to have any of these issues.

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ellisonbg Feb 4, 2015

I am seeing this as well, and there is no rzmq on CRAN for 3.1.2. This basically makes the R kernel unusable on a Mac with homebrew right now (it used to work fine). Looks like we will have to create a cppzmq package for brew. We definitely need to fix this before the 3.0 release and post working instructions for the R kernel on the main ipython install page.

I am seeing this as well, and there is no rzmq on CRAN for 3.1.2. This basically makes the R kernel unusable on a Mac with homebrew right now (it used to work fine). Looks like we will have to create a cppzmq package for brew. We definitely need to fix this before the 3.0 release and post working instructions for the R kernel on the main ipython install page.

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ellisonbg Feb 4, 2015

I should note that the manual install of the zmq.hpp header did fix it, but I don't think we can recommend that to users.

I should note that the manual install of the zmq.hpp header did fix it, but I don't think we can recommend that to users.

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armaneshaghi Feb 4, 2015

or perhaps a work-around is to force install_github to include submodules.

or perhaps a work-around is to force install_github to include submodules.

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Why not simply include the file? The Sqlite package includes the complete sqlite source, so...

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jankatins commented Feb 4, 2015

Why not simply include the file? The Sqlite package includes the complete sqlite source, so...

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cosinequanon Feb 4, 2015

@ellisonbg I was able to get rzmq for 3.1.2. but I compiled from source. I think the issue is here: http://cran.us.r-project.org/web/checks/check_results_rzmq.html

@ellisonbg I was able to get rzmq for 3.1.2. but I compiled from source. I think the issue is here: http://cran.us.r-project.org/web/checks/check_results_rzmq.html

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merqurio Feb 15, 2015

@armaneshaghi Thanks for the tip !! 👍

@armaneshaghi Thanks for the tip !! 👍

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+1 for @armaneshaghi . Gracias

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ellisonbg Feb 23, 2015

@cosinequanon can you clarify what exact steps you took to get it working?

@cosinequanon can you clarify what exact steps you took to get it working?

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cosinequanon Feb 25, 2015

I compiled R 3.1.2 from source on my mac and then was able to install the package directly from CRAN.

I compiled R 3.1.2 from source on my mac and then was able to install the package directly from CRAN.

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ccwang002 Feb 28, 2015

Thanks for @armaneshaghi 's idea, I managed to compile it on Yosemite with brewed R by separating the git clone and installation steps since install_github doesn't support git submodule.

# manually git clone the rzmq repo
$ git clone https://github.com/armstrtw/rzmq.git --recursive 

# install through install_local()
$ R
> library(devtools)
> install_local('./rzmq')

Hope that helps :)

Thanks for @armaneshaghi 's idea, I managed to compile it on Yosemite with brewed R by separating the git clone and installation steps since install_github doesn't support git submodule.

# manually git clone the rzmq repo
$ git clone https://github.com/armstrtw/rzmq.git --recursive 

# install through install_local()
$ R
> library(devtools)
> install_local('./rzmq')

Hope that helps :)

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gdequeiroz Mar 1, 2015

I tried all the above without success. When I run:

> install_github("takluyver/IRkernel")

I get this:

Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
  namespace ‘rzmq’ 0.6.8 is being loaded, but >= 0.7.0 is required
ERROR: lazy loading failed for package ‘IRkernel’
* removing ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRkernel’

I tried all the above without success. When I run:

> install_github("takluyver/IRkernel")

I get this:

Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :
  namespace ‘rzmq’ 0.6.8 is being loaded, but >= 0.7.0 is required
ERROR: lazy loading failed for package ‘IRkernel’
* removing ‘/Library/Frameworks/R.framework/Versions/3.1/Resources/library/IRkernel’
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@gdequeiroz I'm completely new to R's packaging system, but is that an error message stating that rzmq is out of date? Maybe we can run install_github('armstrtw/rzmq'); first?

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rgbkrk commented Mar 2, 2015

@gdequeiroz I'm completely new to R's packaging system, but is that an error message stating that rzmq is out of date? Maybe we can run install_github('armstrtw/rzmq'); first?

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Not seeing any direct upgrade options at quick glance on devtools. 😒

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rgbkrk commented Mar 2, 2015

Not seeing any direct upgrade options at quick glance on devtools. 😒

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OrganicIrradiation Mar 2, 2015

I am having the same issue with Mac OS X 10.10.2.

Starting with a fresh install of Homebrew, I installed python, python3, r, and zmq installed in bash.
I get a fatal error with "'zmq.h' file not found" when I run the following:

$ brew install python python3 r zeromq
$ R
> install.packages("devtools")
> install.packages('RCurl')
> library(devtools)
> install_github('armstrtw/rzmq')

I've also tried:

$ git clone https://github.com/armstrtw/rzmq.git --recursive
$ R
> library(devtools)
> install_local('./rzmq')

To no avail.

I am having the same issue with Mac OS X 10.10.2.

Starting with a fresh install of Homebrew, I installed python, python3, r, and zmq installed in bash.
I get a fatal error with "'zmq.h' file not found" when I run the following:

$ brew install python python3 r zeromq
$ R
> install.packages("devtools")
> install.packages('RCurl')
> library(devtools)
> install_github('armstrtw/rzmq')

I've also tried:

$ git clone https://github.com/armstrtw/rzmq.git --recursive
$ R
> library(devtools)
> install_local('./rzmq')

To no avail.

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mpacer Mar 3, 2015

Hi — following @ccwang002's solution of recursively downloading it locally and then installing it worked for me. @OrganicIrradiation what were the errors that you ran into. Have you been able to successfully install the devtools?

To check, I just brewed r anew (rather than from their pkg installer on their website which was my previous incarnation) and I did not include zeromq in that install. I doubt that that could be what is causing your issues, but I figure its the only major difference I can see without being able to see the errors that are raised.

mpacer commented Mar 3, 2015

Hi — following @ccwang002's solution of recursively downloading it locally and then installing it worked for me. @OrganicIrradiation what were the errors that you ran into. Have you been able to successfully install the devtools?

To check, I just brewed r anew (rather than from their pkg installer on their website which was my previous incarnation) and I did not include zeromq in that install. I doubt that that could be what is causing your issues, but I figure its the only major difference I can see without being able to see the errors that are raised.

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OrganicIrradiation Mar 3, 2015

@michaelpacer I tried @ccwang002's solution and keep getting the same error (regardless of whether I try to install_local with the locally cloned copy or if I use the CRAN mirror). I have devtools installed (no problems there). I also have done a brew install r --build-from-source to see if that may help.

Here is the output with install.packages('rzmq'):

> install.packages('rzmq')
trying URL 'http://cran.rstudio.com/src/contrib/rzmq_0.7.7.tar.gz'
Content type 'application/x-gzip' length 16246 bytes (15 Kb)
opened URL
==================================================
downloaded 15 Kb

* installing *source* package ‘rzmq’ ...
** package ‘rzmq’ successfully unpacked and MD5 sums checked
** libs
clang++ -std=c++11 -I/usr/local/Cellar/r/3.1.2_1/R.framework/Resources/include -DNDEBUG -I../inst/cppzmq -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -fPIC -D__ACCELERATE__ -c interface.cpp -o interface.o
interface.cpp:22:10: fatal error: 'zmq.h' file not found
#include <zmq.h>
^
1 error generated.
make: *** [interface.o] Error 1
ERROR: compilation failed for package ‘rzmq’
* removing ‘/usr/local/Cellar/r/3.1.2_1/R.framework/Versions/3.1/Resources/library/rzmq’

The downloaded source packages are in
‘/private/var/folders/_r/7xdg4v39247_259q1qjjktbc0000gn/T/Rtmpcc2gyE/downloaded_packages’
Warning message:
In install.packages("rzmq") :
installation of package ‘rzmq’ had non-zero exit status

Here is the output with library(devtools) and install_github('armstrtw/rzmq'):

> library(devtools)
> install_github('armstrtw/rzmq')
Downloading github repo armstrtw/rzmq@master
Installing rzmq
'/usr/local/Cellar/r/3.1.2_1/R.framework/Resources/bin/R' --vanilla CMD \
INSTALL \
'/private/var/folders/_r/7xdg4v39247_259q1qjjktbc0000gn/T/Rtmpc2mGvD/devtools10f0d7f8d4715/armstrtw-rzmq-320891d' \
--library='/usr/local/Cellar/r/3.1.2_1/R.framework/Versions/3.1/Resources/library' \
--install-tests 

* installing *source* package ‘rzmq’ ...
** libs
clang++ -std=c++11 -I/usr/local/Cellar/r/3.1.2_1/R.framework/Resources/include -DNDEBUG -I../inst/cppzmq -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -fPIC -D__ACCELERATE__ -c interface.cpp -o interface.o
interface.cpp:22:10: fatal error: 'zmq.h' file not found
#include <zmq.h>
^
1 error generated.
make: *** [interface.o] Error 1
ERROR: compilation failed for package ‘rzmq’
* removing ‘/usr/local/Cellar/r/3.1.2_1/R.framework/Versions/3.1/Resources/library/rzmq’
Error: Command failed (1)

@michaelpacer I tried @ccwang002's solution and keep getting the same error (regardless of whether I try to install_local with the locally cloned copy or if I use the CRAN mirror). I have devtools installed (no problems there). I also have done a brew install r --build-from-source to see if that may help.

Here is the output with install.packages('rzmq'):

> install.packages('rzmq')
trying URL 'http://cran.rstudio.com/src/contrib/rzmq_0.7.7.tar.gz'
Content type 'application/x-gzip' length 16246 bytes (15 Kb)
opened URL
==================================================
downloaded 15 Kb

* installing *source* package ‘rzmq’ ...
** package ‘rzmq’ successfully unpacked and MD5 sums checked
** libs
clang++ -std=c++11 -I/usr/local/Cellar/r/3.1.2_1/R.framework/Resources/include -DNDEBUG -I../inst/cppzmq -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -fPIC -D__ACCELERATE__ -c interface.cpp -o interface.o
interface.cpp:22:10: fatal error: 'zmq.h' file not found
#include <zmq.h>
^
1 error generated.
make: *** [interface.o] Error 1
ERROR: compilation failed for package ‘rzmq’
* removing ‘/usr/local/Cellar/r/3.1.2_1/R.framework/Versions/3.1/Resources/library/rzmq’

The downloaded source packages are in
‘/private/var/folders/_r/7xdg4v39247_259q1qjjktbc0000gn/T/Rtmpcc2gyE/downloaded_packages’
Warning message:
In install.packages("rzmq") :
installation of package ‘rzmq’ had non-zero exit status

Here is the output with library(devtools) and install_github('armstrtw/rzmq'):

> library(devtools)
> install_github('armstrtw/rzmq')
Downloading github repo armstrtw/rzmq@master
Installing rzmq
'/usr/local/Cellar/r/3.1.2_1/R.framework/Resources/bin/R' --vanilla CMD \
INSTALL \
'/private/var/folders/_r/7xdg4v39247_259q1qjjktbc0000gn/T/Rtmpc2mGvD/devtools10f0d7f8d4715/armstrtw-rzmq-320891d' \
--library='/usr/local/Cellar/r/3.1.2_1/R.framework/Versions/3.1/Resources/library' \
--install-tests 

* installing *source* package ‘rzmq’ ...
** libs
clang++ -std=c++11 -I/usr/local/Cellar/r/3.1.2_1/R.framework/Resources/include -DNDEBUG -I../inst/cppzmq -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -fPIC -D__ACCELERATE__ -c interface.cpp -o interface.o
interface.cpp:22:10: fatal error: 'zmq.h' file not found
#include <zmq.h>
^
1 error generated.
make: *** [interface.o] Error 1
ERROR: compilation failed for package ‘rzmq’
* removing ‘/usr/local/Cellar/r/3.1.2_1/R.framework/Versions/3.1/Resources/library/rzmq’
Error: Command failed (1)
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ccwang002 Mar 3, 2015

Could you try to output your cpp header search paths by

$ clang++ -E -x c++ - -v < /dev/null
Apple LLVM version 6.0 (clang-600.0.56) (based on LLVM 3.5svn)
# ...
#include "..." search starts here:
#include <...> search starts here:
 /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1
 /usr/local/include
# ...

$ ls -l /usr/local/include/zmq.h
/usr/local/include/zmq.h -> ../Cellar/zeromq/4.0.5_2/include/zmq.h

You should find /usr/local/include in the search path and zmq.h under that folder.

Adding -v at the following line in rzmq/src/Makevars

PKG_CPPFLAGS = -I../inst/cppzmq   # add -v here

will show the search path during install_local(...). Sorry I didn't figure out how to use the more proper install_local(args='...') way to pass the verbosity flag.

Could you try to output your cpp header search paths by

$ clang++ -E -x c++ - -v < /dev/null
Apple LLVM version 6.0 (clang-600.0.56) (based on LLVM 3.5svn)
# ...
#include "..." search starts here:
#include <...> search starts here:
 /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1
 /usr/local/include
# ...

$ ls -l /usr/local/include/zmq.h
/usr/local/include/zmq.h -> ../Cellar/zeromq/4.0.5_2/include/zmq.h

You should find /usr/local/include in the search path and zmq.h under that folder.

Adding -v at the following line in rzmq/src/Makevars

PKG_CPPFLAGS = -I../inst/cppzmq   # add -v here

will show the search path during install_local(...). Sorry I didn't figure out how to use the more proper install_local(args='...') way to pass the verbosity flag.

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ellisonbg Mar 3, 2015

I think the solution is to create a brew package for zmqcpp.

On Tue, Mar 3, 2015 at 8:59 AM, Liang Bo Wang notifications@github.com
wrote:

Could you try to output your cpp header search paths by

$ clang++ -E -x c++ - -v < /dev/null
Apple LLVM version 6.0 (clang-600.0.56) (based on LLVM 3.5svn)# ...#include "..." search starts here:#include <...> search starts here:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1
/usr/local/include# ...

$ ls -l /usr/local/include/zmq.h
/usr/local/include/zmq.h -> ../Cellar/zeromq/4.0.5_2/include/zmq.h

You should find /usr/local/include in the search path and zmq.h under
that folder.

Adding -v at the following line in rzmq/src/Makevars

PKG_CPPFLAGS = -I../inst/cppzmq # add -v here

will show the search path during install_local(...). Sorry I didn't
figure out how to use the more proper install_local(args='...') way to
pass the verbosity flag.


Reply to this email directly or view it on GitHub
#50 (comment).

Brian E. Granger
Cal Poly State University, San Luis Obispo
@ellisonbg on Twitter and GitHub
bgranger@calpoly.edu and ellisonbg@gmail.com

I think the solution is to create a brew package for zmqcpp.

On Tue, Mar 3, 2015 at 8:59 AM, Liang Bo Wang notifications@github.com
wrote:

Could you try to output your cpp header search paths by

$ clang++ -E -x c++ - -v < /dev/null
Apple LLVM version 6.0 (clang-600.0.56) (based on LLVM 3.5svn)# ...#include "..." search starts here:#include <...> search starts here:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1
/usr/local/include# ...

$ ls -l /usr/local/include/zmq.h
/usr/local/include/zmq.h -> ../Cellar/zeromq/4.0.5_2/include/zmq.h

You should find /usr/local/include in the search path and zmq.h under
that folder.

Adding -v at the following line in rzmq/src/Makevars

PKG_CPPFLAGS = -I../inst/cppzmq # add -v here

will show the search path during install_local(...). Sorry I didn't
figure out how to use the more proper install_local(args='...') way to
pass the verbosity flag.


Reply to this email directly or view it on GitHub
#50 (comment).

Brian E. Granger
Cal Poly State University, San Luis Obispo
@ellisonbg on Twitter and GitHub
bgranger@calpoly.edu and ellisonbg@gmail.com

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OrganicIrradiation Mar 4, 2015

@ccwang002 Here are the search header info and library info:

$ clang++ -E -x c++ - -v < /dev/null
Apple LLVM version 6.0 (clang-600.0.56) (based on LLVM 3.5svn)
#include "..." search starts here:
#include <...> search starts here:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/6.0/include
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks (framework directory)
End of search list.

$ ls -l /usr/local/include/zmq.h
/usr/local/include/zmq.h -> ../Cellar/zeromq/4.0.5_2/include/zmq.h

So it looks like I needed to install the xcode command line tools to get /usr/local/include into the clang++ search path (not sure why the command line tools were not already installed on this computer). I ran xcode-select --install and TADA! installation of rzmq worked and I was able to get IRkernel up and running. Thanks for all of your help!

@ellisonbg There is a homebrew tap that has cppzmq:

$ brew tap bertjwregeer/compat
$ brew install cppzmq

This did not fix my issue though, it looks like only the installation of zeromq was necessary (along with the xcode command line tools).

Just to summarize, here were the steps necessary to get IRkernel setup on this machine:

# Install Xcode Command Line Tools if not already installed
$ xcode-select --install

# Install python, r, and zmq via homebrew
$ brew install python python3 r zeromq

# Install iPython/Jupyter
$ pip install ipython[all]

# Install IRkernel
$ r
> install.packages("devtools")
> install.packages('rzmq')
# Need RCurl for install_github
> install.packages('RCurl')
> library(devtools)
> install_github("takluyver/IRdisplay")
> install_github("takluyver/IRkernel")
# Only if you have IPython 3 or above installed:
> IRkernel::installspec()

@ccwang002 Here are the search header info and library info:

$ clang++ -E -x c++ - -v < /dev/null
Apple LLVM version 6.0 (clang-600.0.56) (based on LLVM 3.5svn)
#include "..." search starts here:
#include <...> search starts here:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/6.0/include
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks (framework directory)
End of search list.

$ ls -l /usr/local/include/zmq.h
/usr/local/include/zmq.h -> ../Cellar/zeromq/4.0.5_2/include/zmq.h

So it looks like I needed to install the xcode command line tools to get /usr/local/include into the clang++ search path (not sure why the command line tools were not already installed on this computer). I ran xcode-select --install and TADA! installation of rzmq worked and I was able to get IRkernel up and running. Thanks for all of your help!

@ellisonbg There is a homebrew tap that has cppzmq:

$ brew tap bertjwregeer/compat
$ brew install cppzmq

This did not fix my issue though, it looks like only the installation of zeromq was necessary (along with the xcode command line tools).

Just to summarize, here were the steps necessary to get IRkernel setup on this machine:

# Install Xcode Command Line Tools if not already installed
$ xcode-select --install

# Install python, r, and zmq via homebrew
$ brew install python python3 r zeromq

# Install iPython/Jupyter
$ pip install ipython[all]

# Install IRkernel
$ r
> install.packages("devtools")
> install.packages('rzmq')
# Need RCurl for install_github
> install.packages('RCurl')
> library(devtools)
> install_github("takluyver/IRdisplay")
> install_github("takluyver/IRkernel")
# Only if you have IPython 3 or above installed:
> IRkernel::installspec()
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ellisonbg Mar 4, 2015

Hmm, this explanation doesn't match up with what other's have found. I had
XCode command line tools installed, but it didn't work until I installed
the zmpcpp header.

On Wed, Mar 4, 2015 at 2:04 AM, OrganicIrradiation <notifications@github.com

wrote:

@ccwang002 https://github.com/ccwang002 Here are the search header info
and library info:

$ clang++ -E -x c++ - -v < /dev/null
Apple LLVM version 6.0 (clang-600.0.56) (based on LLVM 3.5svn)
#include "..." search starts here:
#include <...> search starts here:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/6.0/include
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks (framework directory)
End of search list.

$ ls -l /usr/local/include/zmq.h
/usr/local/include/zmq.h -> ../Cellar/zeromq/4.0.5_2/include/zmq.h

So it looks like I needed to install the xcode command line tools to get
/usr/local/include into the clang++ search path (not sure why the command
line tools were not already installed on this computer). I ran xcode-select
--install and TADA! installation of rzmq worked and I was able to get
IRkernel up and running. Thanks for all of your help!

@ellisonbg https://github.com/ellisonbg There is a homebrew tap that
has cppzmq:

$ brew tap bertjwregeer/compat
$ brew install cppzmq

This did not fix my issue though, it looks like only the installation of
zeromq was necessary (along with the xcode command line tools).

Just to summarize, here were the steps necessary to get IRkernel setup on
this machine:

Install Xcode Command Line Tools if not already installed

$ xcode-select --install

Install python, r, and zmq via homebrew

$ brew install python python3 r zeromq

Install iPython/Jupyter

$ pip install ipython[all]

Install IRkernel

$ r

install.packages("devtools")
install.packages('rzmq')

Need RCurl for install_github

install.packages('RCurl')
library(devtools)
install_github("takluyver/IRdisplay")
install_github("takluyver/IRkernel")

Only if you have IPython 3 or above installed:

IRkernel::installspec()


Reply to this email directly or view it on GitHub
#50 (comment).

Brian E. Granger
Cal Poly State University, San Luis Obispo
@ellisonbg on Twitter and GitHub
bgranger@calpoly.edu and ellisonbg@gmail.com

Hmm, this explanation doesn't match up with what other's have found. I had
XCode command line tools installed, but it didn't work until I installed
the zmpcpp header.

On Wed, Mar 4, 2015 at 2:04 AM, OrganicIrradiation <notifications@github.com

wrote:

@ccwang002 https://github.com/ccwang002 Here are the search header info
and library info:

$ clang++ -E -x c++ - -v < /dev/null
Apple LLVM version 6.0 (clang-600.0.56) (based on LLVM 3.5svn)
#include "..." search starts here:
#include <...> search starts here:
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../include/c++/v1
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/../lib/clang/6.0/include
/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/include
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/usr/include
/Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX10.10.sdk/System/Library/Frameworks (framework directory)
End of search list.

$ ls -l /usr/local/include/zmq.h
/usr/local/include/zmq.h -> ../Cellar/zeromq/4.0.5_2/include/zmq.h

So it looks like I needed to install the xcode command line tools to get
/usr/local/include into the clang++ search path (not sure why the command
line tools were not already installed on this computer). I ran xcode-select
--install and TADA! installation of rzmq worked and I was able to get
IRkernel up and running. Thanks for all of your help!

@ellisonbg https://github.com/ellisonbg There is a homebrew tap that
has cppzmq:

$ brew tap bertjwregeer/compat
$ brew install cppzmq

This did not fix my issue though, it looks like only the installation of
zeromq was necessary (along with the xcode command line tools).

Just to summarize, here were the steps necessary to get IRkernel setup on
this machine:

Install Xcode Command Line Tools if not already installed

$ xcode-select --install

Install python, r, and zmq via homebrew

$ brew install python python3 r zeromq

Install iPython/Jupyter

$ pip install ipython[all]

Install IRkernel

$ r

install.packages("devtools")
install.packages('rzmq')

Need RCurl for install_github

install.packages('RCurl')
library(devtools)
install_github("takluyver/IRdisplay")
install_github("takluyver/IRkernel")

Only if you have IPython 3 or above installed:

IRkernel::installspec()


Reply to this email directly or view it on GitHub
#50 (comment).

Brian E. Granger
Cal Poly State University, San Luis Obispo
@ellisonbg on Twitter and GitHub
bgranger@calpoly.edu and ellisonbg@gmail.com

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ccwang002 Mar 4, 2015

To be clear, zmq.h not found and zmq.hpp not found are different situations.

For zmq.h, it's probably due to the installation of the normal zeromq library.

For zmq.hpp, since you can see the compiler looking for headers under -I../inst/cppzmq during the compilation, if the git repo is fully cloned, the compiler should always find it.

To be clear, zmq.h not found and zmq.hpp not found are different situations.

For zmq.h, it's probably due to the installation of the normal zeromq library.

For zmq.hpp, since you can see the compiler looking for headers under -I../inst/cppzmq during the compilation, if the git repo is fully cloned, the compiler should always find it.

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ellisonbg Mar 4, 2015

Ahh, thanks! As we find solutions for these things, can someone update the
README for the IRkernel so other users will have it easier?

On Wed, Mar 4, 2015 at 9:09 AM, Liang Bo Wang notifications@github.com
wrote:

To be clear, zmq.h not found and zmq.hpp not found are different
situations.

For zmq.h, it's probably due to the installation of the normal zeromq
library.

For zmq.hpp, since you can see the compiler looking for headers under
-I../inst/cppzmq during the compilation, if the git repo is fully cloned,
the compiler should always find it.


Reply to this email directly or view it on GitHub
#50 (comment).

Brian E. Granger
Cal Poly State University, San Luis Obispo
@ellisonbg on Twitter and GitHub
bgranger@calpoly.edu and ellisonbg@gmail.com

Ahh, thanks! As we find solutions for these things, can someone update the
README for the IRkernel so other users will have it easier?

On Wed, Mar 4, 2015 at 9:09 AM, Liang Bo Wang notifications@github.com
wrote:

To be clear, zmq.h not found and zmq.hpp not found are different
situations.

For zmq.h, it's probably due to the installation of the normal zeromq
library.

For zmq.hpp, since you can see the compiler looking for headers under
-I../inst/cppzmq during the compilation, if the git repo is fully cloned,
the compiler should always find it.


Reply to this email directly or view it on GitHub
#50 (comment).

Brian E. Granger
Cal Poly State University, San Luis Obispo
@ellisonbg on Twitter and GitHub
bgranger@calpoly.edu and ellisonbg@gmail.com

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takluyver Mar 4, 2015

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Anyone having trouble installing this: you might like to try r2_kernel, an experimental alternative approach using rpy2 to drive R. This might be easier to install.

Member

takluyver commented Mar 4, 2015

Anyone having trouble installing this: you might like to try r2_kernel, an experimental alternative approach using rpy2 to drive R. This might be easier to install.

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ellisonbg Mar 4, 2015

Nice! But I do think that in the long run, the native R kernel is
absolutely critical.

On Wed, Mar 4, 2015 at 2:33 PM, Thomas Kluyver notifications@github.com
wrote:

Anyone having trouble installing this: you might like to try r2_kernel
https://github.com/takluyver/r2_kernel, an experimental alternative
approach using rpy2 to drive R. This might be easier to install.


Reply to this email directly or view it on GitHub
#50 (comment).

Brian E. Granger
Cal Poly State University, San Luis Obispo
@ellisonbg on Twitter and GitHub
bgranger@calpoly.edu and ellisonbg@gmail.com

Nice! But I do think that in the long run, the native R kernel is
absolutely critical.

On Wed, Mar 4, 2015 at 2:33 PM, Thomas Kluyver notifications@github.com
wrote:

Anyone having trouble installing this: you might like to try r2_kernel
https://github.com/takluyver/r2_kernel, an experimental alternative
approach using rpy2 to drive R. This might be easier to install.


Reply to this email directly or view it on GitHub
#50 (comment).

Brian E. Granger
Cal Poly State University, San Luis Obispo
@ellisonbg on Twitter and GitHub
bgranger@calpoly.edu and ellisonbg@gmail.com

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takluyver Mar 4, 2015

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I don't know that it is. Python is a much, much nicer language to write the kind of infrastructure that a kernel needs - (de)serialisation and messaging. The idea of having a native kernel was that R programmers would be involved with developing it, but as we discussed on Friday, there's a substantial overlap between R and Python programmers. So I don't think there's a reason why it can't be developed in Python by people who care about R.

For the time being, I intend to keep both alive and see what happens.

Member

takluyver commented Mar 4, 2015

I don't know that it is. Python is a much, much nicer language to write the kind of infrastructure that a kernel needs - (de)serialisation and messaging. The idea of having a native kernel was that R programmers would be involved with developing it, but as we discussed on Friday, there's a substantial overlap between R and Python programmers. So I don't think there's a reason why it can't be developed in Python by people who care about R.

For the time being, I intend to keep both alive and see what happens.

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ellisonbg Mar 4, 2015

Personally, I completely agree with your statement that Python is a much
better language for this type of thing. But, in the long run, if we want
this to be used, accepted, adopted and maintained by the the R community it
has to be native R code. Also, there are some kernel features (Comms and
Widgets) that I think will be easier to write natively than trying to proxy
through rpy2.

On Wed, Mar 4, 2015 at 2:51 PM, Thomas Kluyver notifications@github.com
wrote:

I don't know that it is. Python is a much, much nicer language to write
the kind of infrastructure that a kernel needs - (de)serialisation and
messaging. The idea of having a native kernel was that R programmers would
be involved with developing it, but as we discussed on Friday, there's a
substantial overlap between R and Python programmers. So I don't think
there's a reason why it can't be developed in Python by people who care
about R.

For the time being, I intend to keep both alive and see what happens.


Reply to this email directly or view it on GitHub
#50 (comment).

Brian E. Granger
Cal Poly State University, San Luis Obispo
@ellisonbg on Twitter and GitHub
bgranger@calpoly.edu and ellisonbg@gmail.com

Personally, I completely agree with your statement that Python is a much
better language for this type of thing. But, in the long run, if we want
this to be used, accepted, adopted and maintained by the the R community it
has to be native R code. Also, there are some kernel features (Comms and
Widgets) that I think will be easier to write natively than trying to proxy
through rpy2.

On Wed, Mar 4, 2015 at 2:51 PM, Thomas Kluyver notifications@github.com
wrote:

I don't know that it is. Python is a much, much nicer language to write
the kind of infrastructure that a kernel needs - (de)serialisation and
messaging. The idea of having a native kernel was that R programmers would
be involved with developing it, but as we discussed on Friday, there's a
substantial overlap between R and Python programmers. So I don't think
there's a reason why it can't be developed in Python by people who care
about R.

For the time being, I intend to keep both alive and see what happens.


Reply to this email directly or view it on GitHub
#50 (comment).

Brian E. Granger
Cal Poly State University, San Luis Obispo
@ellisonbg on Twitter and GitHub
bgranger@calpoly.edu and ellisonbg@gmail.com

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I'm not sure that that assertion is warranted. The 'R community' is not a distinct thing, there are plenty of programmers who do both R and Python. And if having a Python layer makes it easier to maintain, I don't see any reason to avoid that.

r2_kernel is not pure Python - a fair component of the guts is still in R, it's really just using Python to deal with the messaging protocol.

I'm not sure what a good interface to widgets/comms in R would be, but whatever it is, I don't think there should be any great obstacle to doing it via rpy2. Ultimately, you just need an interface to send and receive messages, which is what we use for the kernel in general, and that's perfectly possible.

Member

takluyver commented Mar 4, 2015

I'm not sure that that assertion is warranted. The 'R community' is not a distinct thing, there are plenty of programmers who do both R and Python. And if having a Python layer makes it easier to maintain, I don't see any reason to avoid that.

r2_kernel is not pure Python - a fair component of the guts is still in R, it's really just using Python to deal with the messaging protocol.

I'm not sure what a good interface to widgets/comms in R would be, but whatever it is, I don't think there should be any great obstacle to doing it via rpy2. Ultimately, you just need an interface to send and receive messages, which is what we use for the kernel in general, and that's perfectly possible.

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dennisobrien Mar 6, 2015

I had this same issue on Ubuntu 14.04 using R 3.0.2 (the version that is included in the standard packages). It was fixed by adding my local CRAN repository to sources.list and installing R 3.1.2.

A similar issue was mentioned in the github project armstrtw/rzmq regarding the CXX1XSTD flag missing from /etc/R/Makevars.

I had this same issue on Ubuntu 14.04 using R 3.0.2 (the version that is included in the standard packages). It was fixed by adding my local CRAN repository to sources.list and installing R 3.1.2.

A similar issue was mentioned in the github project armstrtw/rzmq regarding the CXX1XSTD flag missing from /etc/R/Makevars.

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pylang Mar 10, 2015

@armaneshaghi's solution fixed the first issue - "header missing" error after install_github('armstrtw/rzmq'). Now I get:

Downloading github repo armstrtw/rzmq@master
Installing rzmq
"C:/PROGRA~1/R/R-31~1.2/bin/x64/R" --vanilla CMD INSTALL  \
  "~/AppData/Local/Temp/RtmpIhAeOL/devtools1efc4ce53fcd/armstrtw-rzmq-45f0d94"  \
  --library="C:/Anaconda/Lib/site-packages/rpy2/R/win-library/3.1"  \
  --install-tests 

* installing *source* package 'rzmq' ...
** libs
g++ -m64 -std=c++0x -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -I../inst/cppzmq    -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c interface.cpp -o interface.o
interface.cpp:22:17: fatal error: zmq.h: No such file or directory
compilation terminated.
make: *** [interface.o] Error 1
Warning: running command 'make -f "Makevars" -f "C:/PROGRA~1/R/R-31~1.2/etc/x64/Makeconf" -f "C:/PROGRA~1/R/R-31~1.2/share/make/winshlib.mk" CXX='$(CXX1X) $(CXX1XSTD)' CXXFLAGS='$(CXX1XFLAGS)' CXXPICFLAGS='$(CXX1XPICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX1XLDFLAGS)' SHLIB_LD='$(SHLIB_CXX1XLD)' SHLIB="rzmq.dll" WIN=64 TCLBIN=64 OBJECTS="interface.o"' had status 2
ERROR: compilation failed for package 'rzmq'
* removing 'C:/Anaconda/Lib/site-packages/rpy2/R/win-library/3.1/rzmq'
Error: Command failed (1)

[Win7-64, Anaconda, python2 (default), python3 (virtualenv), IPython3, R3.1.2, Rtools 3.1, ZeroMQ-4.0.4 rc]

pylang commented Mar 10, 2015

@armaneshaghi's solution fixed the first issue - "header missing" error after install_github('armstrtw/rzmq'). Now I get:

Downloading github repo armstrtw/rzmq@master
Installing rzmq
"C:/PROGRA~1/R/R-31~1.2/bin/x64/R" --vanilla CMD INSTALL  \
  "~/AppData/Local/Temp/RtmpIhAeOL/devtools1efc4ce53fcd/armstrtw-rzmq-45f0d94"  \
  --library="C:/Anaconda/Lib/site-packages/rpy2/R/win-library/3.1"  \
  --install-tests 

* installing *source* package 'rzmq' ...
** libs
g++ -m64 -std=c++0x -I"C:/PROGRA~1/R/R-31~1.2/include" -DNDEBUG -I../inst/cppzmq    -I"d:/RCompile/CRANpkg/extralibs64/local/include"     -O2 -Wall  -mtune=core2 -c interface.cpp -o interface.o
interface.cpp:22:17: fatal error: zmq.h: No such file or directory
compilation terminated.
make: *** [interface.o] Error 1
Warning: running command 'make -f "Makevars" -f "C:/PROGRA~1/R/R-31~1.2/etc/x64/Makeconf" -f "C:/PROGRA~1/R/R-31~1.2/share/make/winshlib.mk" CXX='$(CXX1X) $(CXX1XSTD)' CXXFLAGS='$(CXX1XFLAGS)' CXXPICFLAGS='$(CXX1XPICFLAGS)' SHLIB_LDFLAGS='$(SHLIB_CXX1XLDFLAGS)' SHLIB_LD='$(SHLIB_CXX1XLD)' SHLIB="rzmq.dll" WIN=64 TCLBIN=64 OBJECTS="interface.o"' had status 2
ERROR: compilation failed for package 'rzmq'
* removing 'C:/Anaconda/Lib/site-packages/rpy2/R/win-library/3.1/rzmq'
Error: Command failed (1)

[Win7-64, Anaconda, python2 (default), python3 (virtualenv), IPython3, R3.1.2, Rtools 3.1, ZeroMQ-4.0.4 rc]

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Hopefully one of the Mac users will enlighten us both :)

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takluyver commented Apr 23, 2015

Hopefully one of the Mac users will enlighten us both :)

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The main part is done here. What IMO needs to be done is getting rzmq to build under install_github, which AFAIK fails due to the submodule. But IMO thats a bug in rzmq (ropensci/rzmq#15)

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jankatins commented Apr 26, 2015

The main part is done here. What IMO needs to be done is getting rzmq to build under install_github, which AFAIK fails due to the submodule. But IMO thats a bug in rzmq (ropensci/rzmq#15)

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OK, closing this in the hope that the repo we provide will solve these issues.

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takluyver commented Apr 26, 2015

OK, closing this in the hope that the repo we provide will solve these issues.

@takluyver takluyver closed this Apr 26, 2015

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xiaoweiz May 13, 2015

Just to be clear, rzmq must be built from source, correct? On OSX with R 3.2, I tried install.packages('rzmq', repos = 'http://irkernel.github.io/') and got

Warning: unable to access index for repository http://irkernel.github.io/bin/macosx/mavericks/contrib/3.2
Package which is only available in source form, and may need
  compilation of C/C++/Fortran:rzmqDo you want to attempt to install these from sources?

and continuing further led to

installing the source package ‘rzmq’

trying URL 'http://irkernel.github.io/src/contrib/rzmq_0.7.7.tar.gz'
Content type 'application/octet-stream' length 897372 bytes (876 KB)
==================================================
downloaded 876 KB

* installing *source* package ‘rzmq’ ...
** libs
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include    -I../inst/cppzmq -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2 -c interface.cpp -o interface.o
interface.cpp:22:10: fatal error: 'zmq.h' file not found
#include <zmq.h>
         ^
1 error generated.
make: *** [interface.o] Error 1
ERROR: compilation failed for package ‘rzmq’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rzmq’

The downloaded source packages are in
    ‘/private/var/folders/qt/mlwd3rvn26v0ydgk4yvm21jm0000gn/T/RtmphSc8jc/downloaded_packages’
Warning message:
In install.packages("rzmq", repos = "http://irkernel.github.io/") :
  installation of package ‘rzmq’ had non-zero exit status

Just to be clear, rzmq must be built from source, correct? On OSX with R 3.2, I tried install.packages('rzmq', repos = 'http://irkernel.github.io/') and got

Warning: unable to access index for repository http://irkernel.github.io/bin/macosx/mavericks/contrib/3.2
Package which is only available in source form, and may need
  compilation of C/C++/Fortran:rzmqDo you want to attempt to install these from sources?

and continuing further led to

installing the source package ‘rzmq’

trying URL 'http://irkernel.github.io/src/contrib/rzmq_0.7.7.tar.gz'
Content type 'application/octet-stream' length 897372 bytes (876 KB)
==================================================
downloaded 876 KB

* installing *source* package ‘rzmq’ ...
** libs
clang++ -std=c++11 -I/Library/Frameworks/R.framework/Resources/include    -I../inst/cppzmq -I/usr/local/include -I/usr/local/include/freetype2 -I/opt/X11/include    -fPIC  -Wall -mtune=core2 -g -O2 -c interface.cpp -o interface.o
interface.cpp:22:10: fatal error: 'zmq.h' file not found
#include <zmq.h>
         ^
1 error generated.
make: *** [interface.o] Error 1
ERROR: compilation failed for package ‘rzmq’
* removing ‘/Library/Frameworks/R.framework/Versions/3.2/Resources/library/rzmq’

The downloaded source packages are in
    ‘/private/var/folders/qt/mlwd3rvn26v0ydgk4yvm21jm0000gn/T/RtmphSc8jc/downloaded_packages’
Warning message:
In install.packages("rzmq", repos = "http://irkernel.github.io/") :
  installation of package ‘rzmq’ had non-zero exit status
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well, it’s at

http://irkernel.github.io/bin/macosx/contrib/3.2, not

http://irkernel.github.io/bin/macosx/mavericks/contrib/3.2

i tried to just symlink those: does it work now for you?

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flying-sheep commented May 13, 2015

well, it’s at

http://irkernel.github.io/bin/macosx/contrib/3.2, not

http://irkernel.github.io/bin/macosx/mavericks/contrib/3.2

i tried to just symlink those: does it work now for you?

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xiaoweiz May 13, 2015

No, still looking for http://irkernel.github.io/bin/macosx/mavericks/contrib/3.2

No, still looking for http://irkernel.github.io/bin/macosx/mavericks/contrib/3.2

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hmm, that’s OK: i tried to make this URL work, too, but it appears that GH pages doesn’t support symlinks!

so until we figure out a way to fix this, you could try to install the ZMQ headers as described here

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flying-sheep commented May 13, 2015

hmm, that’s OK: i tried to make this URL work, too, but it appears that GH pages doesn’t support symlinks!

so until we figure out a way to fix this, you could try to install the ZMQ headers as described here

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hey, @xiaoweiz, please try

install.packages(c('rzmq','repr','IRkernel','IRdisplay'), repos = 'https://irkernel.github.io/', type = 'mac.binary')
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flying-sheep commented May 13, 2015

hey, @xiaoweiz, please try

install.packages(c('rzmq','repr','IRkernel','IRdisplay'), repos = 'https://irkernel.github.io/', type = 'mac.binary')
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xiaoweiz May 13, 2015

It's OK for rzmq:

install.packages('rzmq', repos = 'http://irkernel.github.io/', type = 'mac.binary')
trying URL 'http://irkernel.github.io/bin/macosx/contrib/3.2/rzmq_0.7.7.tgz'
Content type 'application/octet-stream' length 81898 bytes (79 KB)
==================================================
downloaded 79 KB


The downloaded binary packages are in
    /var/folders/qt/mlwd3rvn26v0ydgk4yvm21jm0000gn/T//RtmpjQTXpd/downloaded_packages

but not for the others:

install.packages(c('repr','IRkernel','IRdisplay'), repos = 'https://irkernel.github.io/', type='mac.binary')
Warning: unable to access index for repository https://irkernel.github.io/src/contrib
Warning: unable to access index for repository https://irkernel.github.io/bin/macosx/mavericks/contrib/3.2
Warning message:
packagesrepr’, ‘IRkernel’, ‘IRdisplayare not available (for R version 3.2.0)

It's OK for rzmq:

install.packages('rzmq', repos = 'http://irkernel.github.io/', type = 'mac.binary')
trying URL 'http://irkernel.github.io/bin/macosx/contrib/3.2/rzmq_0.7.7.tgz'
Content type 'application/octet-stream' length 81898 bytes (79 KB)
==================================================
downloaded 79 KB


The downloaded binary packages are in
    /var/folders/qt/mlwd3rvn26v0ydgk4yvm21jm0000gn/T//RtmpjQTXpd/downloaded_packages

but not for the others:

install.packages(c('repr','IRkernel','IRdisplay'), repos = 'https://irkernel.github.io/', type='mac.binary')
Warning: unable to access index for repository https://irkernel.github.io/src/contrib
Warning: unable to access index for repository https://irkernel.github.io/bin/macosx/mavericks/contrib/3.2
Warning message:
packagesrepr’, ‘IRkernel’, ‘IRdisplayare not available (for R version 3.2.0)
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Damn, this is my fault, I only added one path to drat...

Not sure how to find out where to put binaries: http://cran.r-project.org/doc/manuals/R-admin.html#OS-X-packages and http://cran.r-project.org/doc/manuals/R-admin.html#Setting-up-a-package-repository says that it depends on compilers, so installing these packages on a wrong system will not be good :-(

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jankatins commented May 13, 2015

Damn, this is my fault, I only added one path to drat...

Not sure how to find out where to put binaries: http://cran.r-project.org/doc/manuals/R-admin.html#OS-X-packages and http://cran.r-project.org/doc/manuals/R-admin.html#Setting-up-a-package-repository says that it depends on compilers, so installing these packages on a wrong system will not be good :-(

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well, let’s see if it works for him. if not, we simply need to install packages built for pre-10.9 in macosx/contrib and 10.9+ in macosx/mavericks/contrib

@xiaoweiz you can install those from source, as they don’t need compileage: install.packages(c('repr','IRkernel','IRdisplay'), repos = 'https://irkernel.github.io/', type='source')

if something crashes, you need to install rzmq from source as well by first installing the headers as described under “Homebrew” or “MacPorts” here

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flying-sheep commented May 13, 2015

well, let’s see if it works for him. if not, we simply need to install packages built for pre-10.9 in macosx/contrib and 10.9+ in macosx/mavericks/contrib

@xiaoweiz you can install those from source, as they don’t need compileage: install.packages(c('repr','IRkernel','IRdisplay'), repos = 'https://irkernel.github.io/', type='source')

if something crashes, you need to install rzmq from source as well by first installing the headers as described under “Homebrew” or “MacPorts” here

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@xiaoweiz can you give me the output of

> .Platform$pkgType
[1] "win.binary"
> getOption("pkgType")
[1] "both"
> getOption("repos")
                                CRAN                            CRANextra 
          "http://cran.rstudio.com/" "http://www.stats.ox.ac.uk/pub/RWin" 
attr(,"RStudio")
[1] TRUE
> contrib.url(getOption("repos"), getOption("pkgType"))
[1] "http://cran.rstudio.com/src/contrib"            "http://www.stats.ox.ac.uk/pub/RWin/src/contrib"
> contrib.url(getOption("repos"), .Platform$pkgType)
[1] "http://cran.rstudio.com/bin/windows/contrib/3.2"            "http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.2"

And can you do it for 3.2 and 3.1? I'm wondering why we didn't get this error before (could also be that noone on mac installed the package :-))

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jankatins commented May 13, 2015

@xiaoweiz can you give me the output of

> .Platform$pkgType
[1] "win.binary"
> getOption("pkgType")
[1] "both"
> getOption("repos")
                                CRAN                            CRANextra 
          "http://cran.rstudio.com/" "http://www.stats.ox.ac.uk/pub/RWin" 
attr(,"RStudio")
[1] TRUE
> contrib.url(getOption("repos"), getOption("pkgType"))
[1] "http://cran.rstudio.com/src/contrib"            "http://www.stats.ox.ac.uk/pub/RWin/src/contrib"
> contrib.url(getOption("repos"), .Platform$pkgType)
[1] "http://cran.rstudio.com/bin/windows/contrib/3.2"            "http://www.stats.ox.ac.uk/pub/RWin/bin/windows/contrib/3.2"

And can you do it for 3.2 and 3.1? I'm wondering why we didn't get this error before (could also be that noone on mac installed the package :-))

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@flying-sheep I think it should work as I think our packages are build on the maverics+ macosx system, but this should be fixed in drat, so I have to put in a check/switch there...

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jankatins commented May 13, 2015

@flying-sheep I think it should work as I think our packages are build on the maverics+ macosx system, but this should be fixed in drat, so I have to put in a check/switch there...

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so remove support for OSX 10.8 and smaller by simply moving the files?

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flying-sheep commented May 13, 2015

so remove support for OSX 10.8 and smaller by simply moving the files?

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@JanSchulz like this? (IRkernel/irkernel.github.io#8)

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flying-sheep commented May 13, 2015

@JanSchulz like this? (IRkernel/irkernel.github.io#8)

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@JanSchulz

> .Platform$pkgType
[1] "mac.binary.mavericks"
> getOption("pkgType")
[1] "both"
> getOption("repos")
                     CRAN 
"http://cran.rstudio.com" 
attr(,"RStudio")
[1] TRUE
> contrib.url(getOption("repos"), getOption("pkgType"))
[1] "http://cran.rstudio.com/src/contrib"
> contrib.url(getOption("repos"), .Platform$pkgType)
[1] "http://cran.rstudio.com/bin/macosx/mavericks/contrib/3.2"

@JanSchulz

> .Platform$pkgType
[1] "mac.binary.mavericks"
> getOption("pkgType")
[1] "both"
> getOption("repos")
                     CRAN 
"http://cran.rstudio.com" 
attr(,"RStudio")
[1] TRUE
> contrib.url(getOption("repos"), getOption("pkgType"))
[1] "http://cran.rstudio.com/src/contrib"
> contrib.url(getOption("repos"), .Platform$pkgType)
[1] "http://cran.rstudio.com/bin/macosx/mavericks/contrib/3.2"
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@JanSchulz yeah, drat doesn’t handle mac.binary.mavericks: eddelbuettel/drat#20

@xiaoweiz i moved the packages, so it should work now.

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flying-sheep commented May 13, 2015

@JanSchulz yeah, drat doesn’t handle mac.binary.mavericks: eddelbuettel/drat#20

@xiaoweiz i moved the packages, so it should work now.

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xiaoweiz May 13, 2015

@flying-sheep I had a successful installation from source with Homebrew before. I just thought I gave the binary installation a shot, which is obviously more convenient.

@flying-sheep I had a successful installation from source with Homebrew before. I just thought I gave the binary installation a shot, which is obviously more convenient.

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as said: binary should work now :)

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flying-sheep commented May 13, 2015

as said: binary should work now :)

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@xiaoweiz if you have multiple R versions installed, could you send the output of the last line from these as well?

contrib.url(getOption("repos"), .Platform$pkgType)

I'm wondering if we don't have any mac users which download the package or if something changed between 3.1 and 3.2...

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jankatins commented May 13, 2015

@xiaoweiz if you have multiple R versions installed, could you send the output of the last line from these as well?

contrib.url(getOption("repos"), .Platform$pkgType)

I'm wondering if we don't have any mac users which download the package or if something changed between 3.1 and 3.2...

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xiaoweiz May 13, 2015

@JanSchulz I have only one R version installed, which is 3.2.
@flying-sheep Sorry to inform you that the binary installation still fails....

install.packages('rzmq', repos = 'http://irkernel.github.io/', type = 'mac.binary')
Warning in install.packages :
  cannot open: HTTP status was '404 Not Found'
Warning in install.packages :
  cannot open: HTTP status was '404 Not Found'
Warning in install.packages :
  unable to access index for repository http://irkernel.github.io/bin/macosx/contrib/3.2

   packagerzmqis available as a source package but not as a binary

Warning in install.packages :
  packagerzmqis not available (as a binary package for R version 3.2.0)

@JanSchulz I have only one R version installed, which is 3.2.
@flying-sheep Sorry to inform you that the binary installation still fails....

install.packages('rzmq', repos = 'http://irkernel.github.io/', type = 'mac.binary')
Warning in install.packages :
  cannot open: HTTP status was '404 Not Found'
Warning in install.packages :
  cannot open: HTTP status was '404 Not Found'
Warning in install.packages :
  unable to access index for repository http://irkernel.github.io/bin/macosx/contrib/3.2

   packagerzmqis available as a source package but not as a binary

Warning in install.packages :
  packagerzmqis not available (as a binary package for R version 3.2.0)
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Ok...

Can you do that once without any type parameter (ok, that's above and only looks in the mavericks subdir) and once with type=Platform$pkgType or type="mac.binary.mavericks"?

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jankatins commented May 13, 2015

Ok...

Can you do that once without any type parameter (ok, that's above and only looks in the mavericks subdir) and once with type=Platform$pkgType or type="mac.binary.mavericks"?

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xiaoweiz May 13, 2015

Both give the same error message as above.

Both give the same error message as above.

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Just to make sure because I didn't expect that: This:

install.packages('rzmq', repos = 'http://irkernel.github.io/', type = 'mac.binary.mavericks')

warns about

Warning in install.packages :
  unable to access index for repository http://irkernel.github.io/bin/macosx/contrib/3.2

[path without mavericks in it?]

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jankatins commented May 13, 2015

Just to make sure because I didn't expect that: This:

install.packages('rzmq', repos = 'http://irkernel.github.io/', type = 'mac.binary.mavericks')

warns about

Warning in install.packages :
  unable to access index for repository http://irkernel.github.io/bin/macosx/contrib/3.2

[path without mavericks in it?]

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xiaoweiz May 13, 2015

Ah, I didn't notice the minor difference.

install.packages('rzmq', repos = 'http://irkernel.github.io/', type = 'mac.binary.mavericks')
Warning: unable to access index for repository http://irkernel.github.io/bin/macosx/mavericks/contrib/3.2
install.packages('rzmq', repos = 'http://irkernel.github.io/', type = 'mac.binary')
Warning: unable to access index for repository http://irkernel.github.io/bin/macosx/contrib/3.2

Ah, I didn't notice the minor difference.

install.packages('rzmq', repos = 'http://irkernel.github.io/', type = 'mac.binary.mavericks')
Warning: unable to access index for repository http://irkernel.github.io/bin/macosx/mavericks/contrib/3.2
install.packages('rzmq', repos = 'http://irkernel.github.io/', type = 'mac.binary')
Warning: unable to access index for repository http://irkernel.github.io/bin/macosx/contrib/3.2
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igozali Apr 7, 2016

Hi, I was wondering why this issue is closed, as running the R commands to install IRkernel still results in the missing header error. If we still need rzmq or any zmq-related stuff, it would be nice if this was written in the requirements section of the README.md.

I'm on Mac OS X 10.11.3 if that's useful.

> install.packages(c('rzmq','repr','IRkernel','IRdisplay'), 
    repos = c('http://irkernel.github.io/', getOption('repos')))
Installing packages into ‘/usr/local/lib/R/3.2/site-library’
(as ‘lib’ is unspecified)
trying URL 'http://irkernel.github.io/src/contrib/rzmq_0.7.7.tar.gz'
Content type 'application/octet-stream' length 897372 bytes (876 KB)
==================================================
downloaded 876 KB

trying URL 'http://irkernel.github.io/src/contrib/repr_0.4.tar.gz'
Content type 'application/octet-stream' length 11355 bytes (11 KB)
==================================================
downloaded 11 KB

trying URL 'http://irkernel.github.io/src/contrib/IRkernel_0.5.tar.gz'
Content type 'application/octet-stream' length 17951 bytes (17 KB)
==================================================
downloaded 17 KB

trying URL 'http://irkernel.github.io/src/contrib/IRdisplay_0.3.tar.gz'
Content type 'application/octet-stream' length 3385 bytes
==================================================
downloaded 3385 bytes

* installing *source* package ‘rzmq’ ...
** libs
clang++ -std=c++11 -I/usr/local/Cellar/r/3.2.3/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I../inst/cppzmq -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include  -I/usr/local/include   -fPIC  -g -O2 -c interface.cpp -o interface.o
interface.cpp:22:10: fatal error: 'zmq.h' file not found
#include <zmq.h>
         ^
1 error generated.
make: *** [interface.o] Error 1
ERROR: compilation failed for package ‘rzmq’
* removing ‘/usr/local/lib/R/3.2/site-library/rzmq’
* installing *source* package ‘repr’ ...
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (repr)
* installing *source* package ‘IRdisplay’ ...
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (IRdisplay)
ERROR: dependency ‘rzmq’ is not available for package ‘IRkernel’
* removing ‘/usr/local/lib/R/3.2/site-library/IRkernel’

The downloaded source packages are in
    ‘/private/var/folders/s2/c_t0x85x0w9ffm8d001ppb0m0000gn/T/RtmpBPb3b5/downloaded_packages’
Warning messages:
1: In install.packages(c("rzmq", "repr", "IRkernel", "IRdisplay"),  :
  installation of package ‘rzmq’ had non-zero exit status
2: In install.packages(c("rzmq", "repr", "IRkernel", "IRdisplay"),  :
  installation of package ‘IRkernel’ had non-zero exit status

igozali commented Apr 7, 2016

Hi, I was wondering why this issue is closed, as running the R commands to install IRkernel still results in the missing header error. If we still need rzmq or any zmq-related stuff, it would be nice if this was written in the requirements section of the README.md.

I'm on Mac OS X 10.11.3 if that's useful.

> install.packages(c('rzmq','repr','IRkernel','IRdisplay'), 
    repos = c('http://irkernel.github.io/', getOption('repos')))
Installing packages into ‘/usr/local/lib/R/3.2/site-library’
(as ‘lib’ is unspecified)
trying URL 'http://irkernel.github.io/src/contrib/rzmq_0.7.7.tar.gz'
Content type 'application/octet-stream' length 897372 bytes (876 KB)
==================================================
downloaded 876 KB

trying URL 'http://irkernel.github.io/src/contrib/repr_0.4.tar.gz'
Content type 'application/octet-stream' length 11355 bytes (11 KB)
==================================================
downloaded 11 KB

trying URL 'http://irkernel.github.io/src/contrib/IRkernel_0.5.tar.gz'
Content type 'application/octet-stream' length 17951 bytes (17 KB)
==================================================
downloaded 17 KB

trying URL 'http://irkernel.github.io/src/contrib/IRdisplay_0.3.tar.gz'
Content type 'application/octet-stream' length 3385 bytes
==================================================
downloaded 3385 bytes

* installing *source* package ‘rzmq’ ...
** libs
clang++ -std=c++11 -I/usr/local/Cellar/r/3.2.3/R.framework/Resources/include -DNDEBUG -I/usr/local/include -I../inst/cppzmq -I/usr/local/opt/gettext/include -I/usr/local/opt/readline/include -I/usr/local/opt/openssl/include -I/usr/local/include  -I/usr/local/include   -fPIC  -g -O2 -c interface.cpp -o interface.o
interface.cpp:22:10: fatal error: 'zmq.h' file not found
#include <zmq.h>
         ^
1 error generated.
make: *** [interface.o] Error 1
ERROR: compilation failed for package ‘rzmq’
* removing ‘/usr/local/lib/R/3.2/site-library/rzmq’
* installing *source* package ‘repr’ ...
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (repr)
* installing *source* package ‘IRdisplay’ ...
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (IRdisplay)
ERROR: dependency ‘rzmq’ is not available for package ‘IRkernel’
* removing ‘/usr/local/lib/R/3.2/site-library/IRkernel’

The downloaded source packages are in
    ‘/private/var/folders/s2/c_t0x85x0w9ffm8d001ppb0m0000gn/T/RtmpBPb3b5/downloaded_packages’
Warning messages:
1: In install.packages(c("rzmq", "repr", "IRkernel", "IRdisplay"),  :
  installation of package ‘rzmq’ had non-zero exit status
2: In install.packages(c("rzmq", "repr", "IRkernel", "IRdisplay"),  :
  installation of package ‘IRkernel’ had non-zero exit status
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irkernel master does not depend on rzmq anymore but on a zmw package which is on cran.

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jankatins commented Apr 8, 2016

irkernel master does not depend on rzmq anymore but on a zmw package which is on cran.

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Specifically, that package is pbdZMQ.

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takluyver commented Apr 8, 2016

Specifically, that package is pbdZMQ.

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igozali Apr 8, 2016

Thanks for your replies! I'm still not sure what that means, since I'm very new to R. Does this mean I can just change "rzmq" to "zmw" in the list of packages that I'm installing?

igozali commented Apr 8, 2016

Thanks for your replies! I'm still not sure what that means, since I'm very new to R. Does this mean I can just change "rzmq" to "zmw" in the list of packages that I'm installing?

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zmw was (I think) a typo for zmq. The library we're moving to is called pbdZMQ. But to use IRkernel with that, you need to install the development version from Github (the last release still uses rzmq, and this is what the instructions on the website get you to install).

There's an R package devtools which can install a package from Github, but if you're new to R, it might be jumping in the deep end a bit.

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takluyver commented Apr 8, 2016

zmw was (I think) a typo for zmq. The library we're moving to is called pbdZMQ. But to use IRkernel with that, you need to install the development version from Github (the last release still uses rzmq, and this is what the instructions on the website get you to install).

There's an R package devtools which can install a package from Github, but if you're new to R, it might be jumping in the deep end a bit.

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igozali Apr 8, 2016

Thanks! For regular or casual users of IRkernel, what would you recommend us to use? Naturally we would prefer stable releases, in which case, should we be aware to install zmq headers in our system?

igozali commented Apr 8, 2016

Thanks! For regular or casual users of IRkernel, what would you recommend us to use? Naturally we would prefer stable releases, in which case, should we be aware to install zmq headers in our system?

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In general, yes, we would advise you to prefer stable releases. However, we're not really sure how to fix all the problems people have installing rzmq - that's why we're switching to pbdzmq, which will hopefully make things better. We need to get a new release out with that.

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takluyver commented Apr 8, 2016

In general, yes, we would advise you to prefer stable releases. However, we're not really sure how to fix all the problems people have installing rzmq - that's why we're switching to pbdzmq, which will hopefully make things better. We need to get a new release out with that.

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