install R packages on OS X

[Kirill Vankov]

I was hoping that new release 4.7 will fix the problem, seeing that
the ticket 5634 has been closed. However, I just tried to install a
new package and got an error message:

=====
Detected SAGE64 flag
Building Sage on OS X in 64-bit mode
----------------------------------------------------------------------
| Sage Version 4.7, Release Date: 2011-05-23 |
| Type notebook() for the GUI, and license() for information. |
----------------------------------------------------------------------
sage: r.install_packages('actuar')

R version 2.10.1 (2009-12-14)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> options(repos="http://cran.r-project.org/"); install.packages("actuar")
trying URL 'http://cran.r-project.org/src/contrib/actuar_1.1-2.tar.gz'
Content type 'application/x-gzip' length 1457732 bytes (1.4 Mb)
opened URL
==================================================
downloaded 1.4 Mb

* installing *source* package ‘actuar’ ...
** libs
Warning: R include directory is empty -- perhaps need to install R-
devel.rpm or similar
make: /Users/buildbot/build/sage/bsd-1/bsd_64_binary/build/sage-4.7/
local/lib/R/share/make/shlib.mk: No such file or directory
make: *** No rule to make target `/Users/buildbot/build/sage/bsd-1/
bsd_64_binary/build/sage-4.7/local/lib/R/share/make/shlib.mk'. Stop.
ERROR: compilation failed for package ‘actuar’
* removing ‘/Applications/Sage-4.7-OSX-64bit-10.6.app/Contents/
Resources/sage/local/lib/R/library/actuar’

The downloaded packages are in
‘/private/var/folders/D8/D8+XDdMDEJ4XIybIIPvnt++++TQ/-Tmp-/RtmpZeAJMz/
downloaded_packages’
Updating HTML index of packages in '.Library'
Warning messages:
1: In install.packages("actuar") :
installation of package 'actuar' had non-zero exit status
2: In file.create(f.tg) :
cannot create file '/Users/buildbot/build/sage/bsd-1/bsd_64_binary/
build/sage-4.7/local/lib/R/doc/html/packages.html', reason 'No such
file or directory'
3: In tools:::unix.packages.html(.Library) :
cannot create HTML package index
>

real 0m3.328s
user 0m0.927s
sys 0m0.196s
Please restart Sage in order to use 'actuar'.
sage:
=====

I do not understand, am I missing something on my Mac or the way sage
has been compiled for Mac still does not support R packages
installation?

Regards,
Kirill

[kcrisman]

On Jun 16, 10:44 am, Kirill Vankov <kirill.van...@gmail.com> wrote:
> I was hoping that new release 4.7 will fix the problem, seeing that
> the ticket 5634 has been closed. However, I just tried to install a

The errors reported there were of a different nature, primarily
related to us long ago not having installed the suggested packages in
R.

> new package and got an error message:

That is sad!

> =====
> Detected SAGE64 flag
> Building Sage on OS X in 64-bit mode

Does this happen every time you start Sage? That is odd.

> ----------------------------------------------------------------------
> | Sage Version 4.7, Release Date: 2011-05-23                         |
> | Type notebook() for the GUI, and license() for information.        |
> ----------------------------------------------------------------------
> sage: r.install_packages('actuar')
>

> Warning: R include directory is empty -- perhaps need to install R-
> devel.rpm or similar
> make: /Users/buildbot/build/sage/bsd-1/bsd_64_binary/build/sage-4.7/
> local/lib/R/share/make/shlib.mk: No such file or directory
> make: *** No rule to make target `/Users/buildbot/build/sage/bsd-1/
> bsd_64_binary/build/sage-4.7/local/lib/R/share/make/shlib.mk'.  Stop.
> ERROR: compilation failed for package ‘actuar’

> =====
>
> I do not understand, am I missing something on my Mac or the way sage
> has been compiled for Mac still does not support R packages
> installation?
>

Unfortunately, we still have some hard links that are created during
installation of the R package. These are incredibly tricky to track
down. Presumably you have no directories like the ones in

'/Users/buildbot/build/sage/bsd-1/bsd_64_binary/build/sage-4.7/local/
lib/R/doc/html/packages.html'

There are several open tickets to fix this sort of thing, but no one
has been working on them lately - presumably due to not understanding
enough about the issues. Others may have some comments.

The workaround for you is pretty simple, though it will take a few
hours of sleep for it to happen.

1) Download the *source* to Sage, e.g. at http://www.sagemath.org/download-source.html

2) Follow the instructions to build Sage from source. It consists of
going into a certain directory in Terminal and typing "make".

3) Wait a few hours.

4) Now try to install your package!

http://trac.sagemath.org/sage_trac/ticket/8274 is probably where this
should get fixed. I'll put something about this there.


Good luck! I use R optional packages all the time, so I hope it
should work for you if you build from source.

- kcrisman

[amaseam]

On 2011-06-16 kcrisman wrote:

>
> On Jun 16, 10:44 am, Kirill Vankov wrote:
>> Detected SAGE64 flag
>> Building Sage on OS X in 64-bit mode
>
> Does this happen every time you start Sage?  That is odd.

About that, see trac tickets 10303, 11077, 9960:
http://trac.sagemath.org/sage_trac/ticket/10303
http://trac.sagemath.org/sage_trac/ticket/11077
http://trac.sagemath.org/sage_trac/ticket/9960

[Kirill Vankov]

> > Detected SAGE64 flag
> > Building Sage on OS X in 64-bit mode
>
> Does this happen every time you start Sage?  That is odd.

Yes, it does. But I really had never noticed, since usually I start
sage not from terminal

> down.  Presumably you have no directories like the ones in
>
> '/Users/buildbot/build/sage/bsd-1/bsd_64_binary/build/sage-4.7/local/
> lib/R/doc/html/packages.html'

Indeed I have no this type of directories. Moreover, I tried to make
one, but it did not help.

> The workaround for you is pretty simple, though it will take a few
> hours of sleep for it to happen.
>

> 1) Download the *source* to Sage, e.g. athttp://www.sagemath.org/download-source.html

> 2) Follow the instructions to build Sage from source.  It consists of
> going into a certain directory in Terminal and typing "make".
> 3) Wait a few hours.
> 4) Now try to install your package!

I'll try. Thank you for your suggestions.

Kirill

[George]

On 17 June, 06:07, Kirill Vankov <kirill.van...@gmail.com> wrote:
> > > Detected SAGE64 flag
> > > Building Sage on OS X in 64-bit mode
>
> > Does this happen every time you start Sage?  That is odd.
>
> Yes, it does.  But I really had never noticed, since usually I start
> sage not from terminal
>
> > down.  Presumably you have no directories like the ones in
>
> > '/Users/buildbot/build/sage/bsd-1/bsd_64_binary/build/sage-4.7/local/
> > lib/R/doc/html/packages.html'

I also ran into the problem of incorrect directories in R using
sage-4.6.2-linux-64bit-ubuntu_10.04.1_lts-x86_64-Linux. R
stores these settings in the following text files:

sage/local/lib/R/bin/R
sage/local/lib/R/bin/libtool
sage/local/lib/R/etc/Makeconf
sage/local/lib/R/etc/ldpath
sage/local/lib/R/etc/Renviron
sage/local/bin/R

so simply replacing the bad paths with the ones that match your
installation worked for me.

The R documentation mentions other ways to override the default
settings of the variables on a per-user basis.

> Indeed I have no this type of directories.  Moreover, I tried to make
> one, but it did not help.
>
> > The workaround for you is pretty simple, though it will take a few
> > hours of sleep for it to happen.
>
> > 1) Download the *source* to Sage, e.g. athttp://www.sagemath.org/download-source.html
> > 2) Follow the instructions to build Sage from source.  It consists of
> > going into a certain directory in Terminal and typing "make".
> > 3) Wait a few hours.
> > 4) Now try to install your package!

Seems like overkill if R is the only package that stores paths a build
time.

[kcrisman]

> > > The workaround for you is pretty simple, though it will take a few
> > > hours of sleep for it to happen.
>
> > > 1) Download the *source* to Sage, e.g. athttp://www.sagemath.org/download-source.html
> > > 2) Follow the instructions to build Sage from source.  It consists of
> > > going into a certain directory in Terminal and typing "make".
> > > 3) Wait a few hours.
> > > 4) Now try to install your package!
>
> Seems like overkill if R is the only package that stores paths a build
> time.
>

You're right, but not everyone understands what 'replacing bad paths'
is - it's a tricky business, at least for me. These are instructions
that don't require a lot of background.

The real problem is that "R's spkg-install is a mess", as one Trac
ticket says. Probably somewhere in there lies the answer to not hard-
coding these things. But it will take a lot of work by someone who
knows R and Sage's build process to fix that. Please feel free to
try! We'd love the help; R is a very important part of Sage which is
underutilized right now.

- kcrisman

[Kirill Vankov]

After four and a half hours of compillation my sage looks good,
even though I received one warning message
"dvipng command 'dvipng' cannot be run (needed for math display),
check the pngmath_dvipng setting"

The R-package installation option works.
Starting sage in terminal do not produce

Detected SAGE64 flag
Building Sage on OS X in 64-bit mode

messages as before.

I still did not kill the sage.app installation and I will try to fix
"bad" paths as well as suggested by George.

Regards,
Kirill

[Kirill Vankov]

Once I moved the compiled sage into /usr/local/ I cannot install
additional R-packages anymore. Have to move it back.

It is better to instruct whoever is going to compile sage on Mac to do
so at the final destination folder.

K.

[kcrisman]

On Jun 20, 11:49 am, Kirill Vankov <kirill.van...@gmail.com> wrote:
> Once I moved the compiled sage into /usr/local/ I cannot install
> additional R-packages anymore.  Have to move it back.

You shouldn't have to move it anywhere; Sage doesn't have to live
anyplace in particular. Is it only after you move it that you
encounter problems? Maybe you have permission issues there?

At any rate, I install new packages fairly frequently in R on my Mac,
so it's important to clarify exactly what makes this break when you
compile Sage from source. Thanks for any additional details you can
provide.

> It is better to instruct whoever is going to compile sage on Mac to do
> so at the final destination folder.

No, because there is no such folder by default - I doubt that many Mac
users would even know what /usr/local is, for instance.
Unfortunately, we will have to actually fix this hardcoding, which is
often a very subtle and difficult thing to track down :(

- kcrisman

[Kirill Vankov]

> You shouldn't have to move it anywhere; Sage doesn't have to live
> anyplace in particular.  Is it only after you move it that you
> encounter problems?    Maybe you have permission issues there?

Yes, the problems were only with R packages and only after I moved
entire sage folder. I did not want it into my temporary downloads
location... The problem was with hard-coded paths, not the
permissions. Anyway, the fix was easy. I opened all the files listed
above by George:

sage/local/lib/R/bin/R
sage/local/lib/R/bin/libtool
sage/local/lib/R/etc/Makeconf
sage/local/lib/R/etc/ldpath
sage/local/lib/R/etc/Renviron
sage/local/bin/R

and edited obvious lines containing hardcoded paths (using find-
replace-all at once). I think it is relatively easy for general
distribution of Sage compiled for Mac write a post-installation script
fixing these lines, in assumption that final destination will be of /
Applications/Sage.app type.

> No, because there is no such folder by default - I doubt that many Mac
> users would even know what /usr/local is, for instance.

Agree, but I have more Linux experience, than Mac. I just started to
work with Mac and do not know how to convert compiled program into
proper .app application, therefore /usr/local/ was a prefered option
for me.

K.