Problems to install a package

On Jul 28, 2015, at 3:13 PM, Jos? Carlos Guerrero Ant?nez <jcgantunez at gmail.com> wrote:

Hi,

First, thank you for your answers, and I have to admit that don't prepare
to do a bit more work, because I'm a user that I have no programming
skills, and therefore, I depend on people like you, to use these programs.

According to the easier instruction, and I downloaded
gfortran-4.8.2-darwin13.tar.bz2

You'll want to unpack it in the root folder at `/` (or move it there after
unpacking); the directory structure is such that the necessary
pieces are dumped into `/usr/local/` and R will by default be able to discover
everything needed.

It will not let me move the item "usr" to the root folder "/"

Now I have this error message,

install.packages("~/Desktop/RMacoqui_1.0.tar.gz", repos = NULL, type =

"source",
lib="/Library/Frameworks/R.framework/Versions/3.2/Resources/library")
* installing *source* package ?RMacoqui? ...
** libs
gfortran-4.8   -fPIC  -g -O2  -c RMacoqui.f -o RMacoqui.o
gfortran-4.8: warning: couldn?t understand kern.osversion ?14.4.0
f951: internal compiler error: Illegal instruction: 4

f951: internal compiler error: Abort trap: 6
gfortran-4.8: internal compiler error: Abort trap: 6 (program f951)
make: *** [RMacoqui.o] Abort trap: 6
ERROR: compilation failed for package ?RMacoqui?
* removing
?/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RMacoqui?
Warning in install.packages :
 installation of package ?/Users/joseca_IMac/Desktop/RMacoqui_1.0.tar.gz?
had non-zero exit status

Many thanks again,


Best regards,




2015-07-27 23:49 GMT-03:00 Kevin Ushey <kevinushey at gmail.com>:

There error here is, as it says:

make: gfortran-4.8: No such file or directory

In other words, `make` is attempting to call `gfortran-4.8` to compile
FORTRAN code in your package, but is unable to find it -- likely
because it's not installed.

Since 'gfortran' is no longer distributed as part of Apple's command
line tools, you'll need to install it from another source -- Simon
Urbanek hosts a version of 'gfortran' at http://r.research.att.com/
(more specifically, in the `libs` directory at
http://r.research.att.com/libs/gfortran-4.8.2-darwin13.tar.bz2).
You'll want to unpack it in the root folder at `/` (or move it there
after unpacking); the directory structure is such that the necessary
pieces are dumped into `/usr/local/` and R will by default be able to
discover everything needed.

Alternatively (if you're prepared to do a bit more work), you can use
the OS X package manager homebrew to install 'gcc' and hence
'gfortran'. Install homebrew following the instructions here:

   http://brew.sh/

and then, from the command line, call

   brew install gcc

This will install an up-to-date version of both 'gcc' and 'gfortran'.
Since it won't be installed into a directory that's 'visible' to R by
default, you'll need to tell R how to find it -- you can check the
StackOverflow questions + responses here for ideas on how to
accomplish that.


http://stackoverflow.com/questions/29992066/rcpp-warning-directory-not-found-for-option-l-usr-local-cellar-gfortran-4-8

http://stackoverflow.com/questions/19920281/rcpparmadillo-compile-errors-on-os-x-mavericks/19920761#19920761

As an aside -- I am not sure why make is attempting to call
`gfortran-4.8` rather than `gfortran`. You might have to check
`~/.R/Makevars` or other package configuration variables. (Do you
_really_ need to be compiling with `gfortran-4.8` specifically?)

Hope this helps,
Kevin


On Mon, Jul 27, 2015 at 7:19 PM, David Winsemius <dwinsemius at comcast.net>
wrote:

On Jul 27, 2015, at 6:49 PM, Jos? Carlos Guerrero Ant?nez wrote:

Hi,

I have this problem when I try to install a package, I'm working with

OSX

Yosemite 10.10.4.

Best regards,

install.packages("~/Downloads/RMacoqui_1.0.tar.gz", repos = NULL, type

=

"source",
lib="/Library/Frameworks/R.framework/Versions/3.2/Resources/library")
* installing *source* package ?RMacoqui? ...
** libs
gfortran-4.8   -fPIC  -g -O2  -c RMacoqui.f -o RMacoqui.o
make: gfortran-4.8: No such file or directory

I suspect that you have not obtained Xcode and installed Command line

tools and perhaps not installed XQuartz (although that is not the cause of
any error that I see here.)

Apple has pretty much always made XCode available for free. You need to

register with Apple as a developer and then get the XCode version that is
mated to your version of OSX.

--
David

make: *** [RMacoqui.o] Error 1
ERROR: compilation failed for package ?RMacoqui?
* removing

?/Library/Frameworks/R.framework/Versions/3.2/Resources/library/RMacoqui?

Warning in install.packages :
installation of package ?/Users/joseca/Downloads/RMacoqui_1.0.tar.gz?

had

non-zero exit status




--
################################################################
Dr. Jos? Carlos Guerrero
Laboratorio de Desarrollo Sustentable y Gesti?n Ambiental del Territorio
(LDSGAT)
Instituto de Ecolog?a y Ciencias Ambientales (IECA)
Facultad de Ciencias
Universidad de la Rep?blica
Montevideo-URUGUAY
################################################################

     [[alternative HTML version deleted]]

David Winsemius
Alameda, CA, USA

-- 
################################################################
Dr. Jos? Carlos Guerrero
Laboratorio de Desarrollo Sustentable y Gesti?n Ambiental del Territorio
(LDSGAT)
Instituto de Ecolog?a y Ciencias Ambientales (IECA)
Facultad de Ciencias
Universidad de la Rep?blica
Montevideo-URUGUAY
################################################################

	[[alternative HTML version deleted]]