R devel - Apr 2006 - Installation oddity on Fedora Core 5 (PR#8814)

Hello guys:

I recently installed FC 5 linux and installed R from source. It installed
fine, but there was an oddity that I want to report. Although I used

./configure --prefix=/usr/local/R-2.3.0

make

it did not seem to recognize the prefix and went ahead and installed it in
the source directory -- I usually ``tar xzf'' it to my home directory
and run the installation scripts from there (as root) to install to
/usr/local/R-2.3.0


This procedure worked fine on earlier versions of Fedora as well as on
debian and other distros. Wonder if this is a gcc-4.1 or GNU make issue.

Any feedback will be much appreciated.

Tx.

Sudipto.

*****************************************************************
Sudipto Banerjee, PhD,
Assistant Professor,
Div. of Biostatistics,
University of Minnesota,
A460 Mayo Building, MMC 303,
420 Delaware Street, SE,
Minneapolis, MN 55455.

sudiptob at biostat.umn.edu writes:
> Hello guys:
>
> I recently installed FC 5 linux and installed R from source. It installed
> fine, but there was an oddity that I want to report. Although I used
>
> ./configure --prefix=/usr/local/R-2.3.0
>
> make
You need to do 'make install' I think.

On Thu, 2006-04-27 at 18:10 +0200, sudiptob at biostat.umn.edu
wrote:
> Hello guys:
> 
> I recently installed FC 5 linux and installed R from source. It installed
> fine, but there was an oddity that I want to report. Although I used
> 
> ./configure --prefix=/usr/local/R-2.3.0
> 
> make
> 
> it did not seem to recognize the prefix and went ahead and installed it in
> the source directory -- I usually ``tar xzf'' it to my home
directory
> and run the installation scripts from there (as root) to install to
> /usr/local/R-2.3.0
> 
> 
> This procedure worked fine on earlier versions of Fedora as well as on
> debian and other distros. Wonder if this is a gcc-4.1 or GNU make issue.
> 
> Any feedback will be much appreciated.
> 
> Tx.
> 
> Sudipto.
This question may be akin to "Is the computer plugged in?", but did
you
also run:

  make install

?

HTH,

Marc Schwartz

Hi Marc:

Thanks for your reply. Yeah, I did do

make install

and also tried it with simply make (which is, I presume, enough to
produce the executable scripts for R).

Please keep me posted.

Best,

S.

*****************************************************************
Sudipto Banerjee, PhD,
Div. of Biostatistics,
University of Minnesota,
A460 Mayo Building, MMC 303,
420 Delaware Street, SE,
Minneapolis, MN 55455.



On Thu, 27 Apr 2006, Marc Schwartz (via MN) wrote:
> On Thu, 2006-04-27 at 18:10 +0200, sudiptob at biostat.umn.edu wrote:
> > Hello guys:
> >
> > I recently installed FC 5 linux and installed R from source. It
installed
> > fine, but there was an oddity that I want to report. Although I used
> >
> > ./configure --prefix=/usr/local/R-2.3.0
> >
> > make
> >
> > it did not seem to recognize the prefix and went ahead and installed
it in
> > the source directory -- I usually ``tar xzf'' it to my home
directory
> > and run the installation scripts from there (as root) to install to
> > /usr/local/R-2.3.0
> >
> >
> > This procedure worked fine on earlier versions of Fedora as well as on
> > debian and other distros. Wonder if this is a gcc-4.1 or GNU make
issue.
> >
> > Any feedback will be much appreciated.
> >
> > Tx.
> >
> > Sudipto.
>
> This question may be akin to "Is the computer plugged in?", but
did you
> also run:
>
>   make install
>
> ?
>
> HTH,
>
> Marc Schwartz
>
>
>

Guys: Let's hold off on this one for a while. I just tried installing
mplayer and got the same oddity! It might be an FC5 installation issue - I
will get back to you on this one.

Thanks for your help folks.

*****************************************************************
Sudipto Banerjee, PhD,
Assistant Professor,
Div. of Biostatistics,
University of Minnesota,
A460 Mayo Building, MMC 303,
420 Delaware Street, SE,
Minneapolis, MN 55455.



On Thu, 27 Apr 2006, Marc Schwartz (via MN) wrote:
> On Thu, 2006-04-27 at 18:10 +0200, sudiptob at biostat.umn.edu wrote:
> > Hello guys:
> >
> > I recently installed FC 5 linux and installed R from source. It
installed
> > fine, but there was an oddity that I want to report. Although I used
> >
> > ./configure --prefix=/usr/local/R-2.3.0
> >
> > make
> >
> > it did not seem to recognize the prefix and went ahead and installed
it in
> > the source directory -- I usually ``tar xzf'' it to my home
directory
> > and run the installation scripts from there (as root) to install to
> > /usr/local/R-2.3.0
> >
> >
> > This procedure worked fine on earlier versions of Fedora as well as on
> > debian and other distros. Wonder if this is a gcc-4.1 or GNU make
issue.
> >
> > Any feedback will be much appreciated.
> >
> > Tx.
> >
> > Sudipto.
>
> This question may be akin to "Is the computer plugged in?", but
did you
> also run:
>
>   make install
>
> ?
>
> HTH,
>
> Marc Schwartz
>
>
>

Hi Sudipto,

OK. Just for clarification:

'make' will simply do the compilation 'in place' in the source
directory
tree. No installation is performed here.

'make install' will actually do the installation into the target folder.

You can do 'make install' without 'make' first, but I suspect a
lot of
folks, myself included, will run 'make' first and then run 'make
check-all' before installing, to be sure that the compilation is intact
and passes all checks. 

In fact, I keep the output of 'make check-all' as part of my
installation validation documentation.

That being said, were there any error messages output during 'make
install' that might suggest a problem such as access permission issues
to the target directory or the like?

You might also want to run (I think this is correct):

 dmesg

in a console to look for any 'avc' error messages in the error log. This
would be related to FC5's use of SELinux and there have been very
significant SELinux related policy changes in FC5 that could feasibly be
involved here also.

HTH,

Marc


On Thu, 2006-04-27 at 11:25 -0500, Sudipto Banerjee
wrote:
> Hi Marc:
> 
> Thanks for your reply. Yeah, I did do
> 
> make install
> 
> and also tried it with simply make (which is, I presume, enough to
> produce the executable scripts for R).
> 
> Please keep me posted.
> 
> Best,
> 
> S.
> 
> On Thu, 27 Apr 2006, Marc Schwartz (via MN) wrote:
> 
> > On Thu, 2006-04-27 at 18:10 +0200, sudiptob at biostat.umn.edu wrote:
> > > Hello guys:
> > >
> > > I recently installed FC 5 linux and installed R from source. It
installed
> > > fine, but there was an oddity that I want to report. Although I
used
> > >
> > > ./configure --prefix=/usr/local/R-2.3.0
> > >
> > > make
> > >
> > > it did not seem to recognize the prefix and went ahead and
installed it in
> > > the source directory -- I usually ``tar xzf'' it to my
home directory
> > > and run the installation scripts from there (as root) to install
to
> > > /usr/local/R-2.3.0
> > >
> > >
> > > This procedure worked fine on earlier versions of Fedora as well
as on
> > > debian and other distros. Wonder if this is a gcc-4.1 or GNU make
issue.
> > >
> > > Any feedback will be much appreciated.
> > >
> > > Tx.
> > >
> > > Sudipto.
> >
> > This question may be akin to "Is the computer plugged in?",
but did you
> > also run:
> >
> >   make install
> >
> > ?
> >
> > HTH,
> >
> > Marc Schwartz
> >

Hi Marc:

Thanks so much for the input. You are right that I do not do the make
check-all (bad habit!) and usually just go:

./configure --prefixmake
make install

route. Yes, I realized I had forgotten to mention make install in my
original mail, but I did try with that. I am simply reinstalling FC5
*disabling* the SElinux and see what happens. I will keep you posted.

Best,

S.

*****************************************************************
Sudipto Banerjee, PhD,
Div. of Biostatistics,
University of Minnesota,
A460 Mayo Building, MMC 303,
420 Delaware Street, SE,
Minneapolis, MN 55455.



On Thu, 27 Apr 2006, Marc Schwartz (via MN) wrote:
> Hi Sudipto,
>
> OK. Just for clarification:
>
> 'make' will simply do the compilation 'in place' in the
source directory
> tree. No installation is performed here.
>
> 'make install' will actually do the installation into the target
folder.
>
> You can do 'make install' without 'make' first, but I
suspect a lot of
> folks, myself included, will run 'make' first and then run
'make
> check-all' before installing, to be sure that the compilation is intact
> and passes all checks.
>
> In fact, I keep the output of 'make check-all' as part of my
> installation validation documentation.
>
> That being said, were there any error messages output during 'make
> install' that might suggest a problem such as access permission issues
> to the target directory or the like?
>
> You might also want to run (I think this is correct):
>
>  dmesg
>
> in a console to look for any 'avc' error messages in the error log.
This
> would be related to FC5's use of SELinux and there have been very
> significant SELinux related policy changes in FC5 that could feasibly be
> involved here also.
>
> HTH,
>
> Marc
>
>
> On Thu, 2006-04-27 at 11:25 -0500, Sudipto Banerjee wrote:
> > Hi Marc:
> >
> > Thanks for your reply. Yeah, I did do
> >
> > make install
> >
> > and also tried it with simply make (which is, I presume, enough to
> > produce the executable scripts for R).
> >
> > Please keep me posted.
> >
> > Best,
> >
> > S.
>
> >
> > On Thu, 27 Apr 2006, Marc Schwartz (via MN) wrote:
> >
> > > On Thu, 2006-04-27 at 18:10 +0200, sudiptob at biostat.umn.edu
wrote:
> > > > Hello guys:
> > > >
> > > > I recently installed FC 5 linux and installed R from source.
It installed
> > > > fine, but there was an oddity that I want to report.
Although I used
> > > >
> > > > ./configure --prefix=/usr/local/R-2.3.0
> > > >
> > > > make
> > > >
> > > > it did not seem to recognize the prefix and went ahead and
installed it in
> > > > the source directory -- I usually ``tar xzf'' it to
my home directory
> > > > and run the installation scripts from there (as root) to
install to
> > > > /usr/local/R-2.3.0
> > > >
> > > >
> > > > This procedure worked fine on earlier versions of Fedora as
well as on
> > > > debian and other distros. Wonder if this is a gcc-4.1 or GNU
make issue.
> > > >
> > > > Any feedback will be much appreciated.
> > > >
> > > > Tx.
> > > >
> > > > Sudipto.
> > >
> > > This question may be akin to "Is the computer plugged
in?", but did you
> > > also run:
> > >
> > >   make install
> > >
> > > ?
> > >
> > > HTH,
> > >
> > > Marc Schwartz
> > >
>
>