R linux install: FORTRAN compiling error

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R linux install: FORTRAN compiling error

vaneet
Hello,

I have basic familiarity with Unix but by most standards a novice.  I am trying to install R on a linux machine and am following the instructions in the R install and admin guide in terms of what is required to compile the R source code.  I downloaded R version 2.11.1 and extracted the files into my home directory.  I realize I need a FORTRAN compiler to help with this process and have tried installing a few but still cannot past the configuration step of installing R:

./configure --with-readline=no

Once I run this command after installing GFortran I get the following error:
...
checking whether we can compute C Make dependencies... yes, using gcc -std=gnu99 -MM
checking whether gcc -std=gnu99 supports -c -o FILE.lo... yes
checking how to get verbose linking output from gfortran... configure: WARNING: compilation failed

checking for Fortran 77 libraries of gfortran...
checking how to get verbose linking output from gcc -std=gnu99... -v
checking for C libraries of gcc -std=gnu99...  -L/usr/local/lib64 -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2 -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64 -L/lib/../lib64 -L/usr/lib/../lib64 -lgcc_s
checking for dummy main to link with Fortran 77 libraries... none
checking for Fortran 77 name-mangling scheme... configure: error: in `/home/lotayv01/R-2.11.1':
configure: error: cannot compile a simple Fortran program
See `config.log' for more details.

For more details I can show you the section in the config.log file

...
/data/home/lotayv01/usr/local/gfortran/bin/../libexec/gcc/i686-pc-linux-gnu/4.6.0/f951: error while loading shared libraries: libmpc.so.2: cannot open shared object file: No such file or directory
configure:22471: $? = 1
configure: failed program was:
|       program main
|
|       end
configure:22548: WARNING: compilation failed
configure:22554: result:
configure:22556: checking for Fortran 77 libraries of gfortran
configure:22579: gfortran -o conftest -L/usr/local/lib64 conftest.f
/data/home/lotayv01/usr/local/gfortran/bin/../libexec/gcc/i686-pc-linux-gnu/4.6.0/f951: error while loading shared libraries: libmpc.so.2: cannot open shared object file: No such file or directory
...

When I check the version of Gfortran at the console command line I get this:
GNU Fortran (GCC) 4.6.0 20100407 (experimental) [trunk revision 158083]
Copyright (C) 2010 Free Software Foundation, Inc.

Even before this I tried the g95 fortran compiler and the same thing happened, how can I fix this problem, any help on this matter would be greatly appreciated.

Thanks
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Re: R linux install: FORTRAN compiling error

Matt Shotwell
This is not an issue with R, but with gfortran. See the following:

http://gcc.gnu.org/wiki/GFortran#news (under heading "gfortran 4.5")

http://gcc.gnu.org/ml/fortran/2010-04/msg00061.html

Also, I suspect you are using a precompiled gcc/gfortran, and it assumes
you have libmpc.so.2 <http://www.muliprecision.org> installed. If you
compile all of gcc, you won't see this problem. However, this is
probably not the simplest solution. I'd try the solution in the second
link above. Else, if `gcc --version` <= 4.4, get the compiled gfortran
at that version.

P.S. `grep -R mpc.h R-2.11.1/*` indicates R does not depend on libmpc


Matt Shotwell
Graduate Student
Division of Biostatistics and Epidemiology
Medical University of South Carolina


On Wed, 2010-06-02 at 17:07 -0400, vaneet wrote:

> Hello,
>
> I have basic familiarity with Unix but by most standards a novice.  I am
> trying to install R on a linux machine and am following the instructions in
> the R install and admin guide in terms of what is required to compile the R
> source code.  I downloaded R version 2.11.1 and extracted the files into my
> home directory.  I realize I need a FORTRAN compiler to help with this
> process and have tried installing a few but still cannot past the
> configuration step of installing R:
>
> ./configure --with-readline=no
>
> Once I run this command after installing GFortran I get the following error:
> ...
> checking whether we can compute C Make dependencies... yes, using gcc
> -std=gnu99 -MM
> checking whether gcc -std=gnu99 supports -c -o FILE.lo... yes
> checking how to get verbose linking output from gfortran... configure:
> WARNING: compilation failed
>
> checking for Fortran 77 libraries of gfortran...
> checking how to get verbose linking output from gcc -std=gnu99... -v
> checking for C libraries of gcc -std=gnu99...  -L/usr/local/lib64
> -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2
> -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64 -L/lib/../lib64
> -L/usr/lib/../lib64 -lgcc_s
> checking for dummy main to link with Fortran 77 libraries... none
> checking for Fortran 77 name-mangling scheme... configure: error: in
> `/home/lotayv01/R-2.11.1':
> configure: error: cannot compile a simple Fortran program
> See `config.log' for more details.
>
> For more details I can show you the section in the config.log file
>
> ...
> /data/home/lotayv01/usr/local/gfortran/bin/../libexec/gcc/i686-pc-linux-gnu/4.6.0/f951:
> error while loading shared libraries: libmpc.so.2: cannot open shared object
> file: No such file or directory
> configure:22471: $? = 1
> configure: failed program was:
> |       program main
> |
> |       end
> configure:22548: WARNING: compilation failed
> configure:22554: result:
> configure:22556: checking for Fortran 77 libraries of gfortran
> configure:22579: gfortran -o conftest -L/usr/local/lib64 conftest.f
> /data/home/lotayv01/usr/local/gfortran/bin/../libexec/gcc/i686-pc-linux-gnu/4.6.0/f951:
> error while loading shared libraries: libmpc.so.2: cannot open shared object
> file: No such file or directory
> ...
>
> When I check the version of Gfortran at the console command line I get this:
> GNU Fortran (GCC) 4.6.0 20100407 (experimental) [trunk revision 158083]
> Copyright (C) 2010 Free Software Foundation, Inc.
>
> Even before this I tried the g95 fortran compiler and the same thing
> happened, how can I fix this problem, any help on this matter would be
> greatly appreciated.
>
> Thanks

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Re: R linux install: FORTRAN compiling error

Brian Ripley
On Wed, 2 Jun 2010, Matt Shotwell wrote:

> This is not an issue with R, but with gfortran. See the following:
>
> http://gcc.gnu.org/wiki/GFortran#news (under heading "gfortran 4.5")
>
> http://gcc.gnu.org/ml/fortran/2010-04/msg00061.html
>
> Also, I suspect you are using a precompiled gcc/gfortran, and it assumes
> you have libmpc.so.2 <http://www.muliprecision.org> installed. If you
> compile all of gcc, you won't see this problem. However, this is
> probably not the simplest solution. I'd try the solution in the second
> link above. Else, if `gcc --version` <= 4.4, get the compiled gfortran
> at that version.

And as the output indicates it is 4.1.2.  So this is an ancient Linux
(perhaps RHEL?), and you really need the gfortran (and libgfortran)
from the distribution.

Mixing an unreleased bleeding-edage gfortran with a gcc from early
2007 is not going to work well, most likely not at all.

>
> P.S. `grep -R mpc.h R-2.11.1/*` indicates R does not depend on libmpc
>
>
> Matt Shotwell
> Graduate Student
> Division of Biostatistics and Epidemiology
> Medical University of South Carolina
>
>
> On Wed, 2010-06-02 at 17:07 -0400, vaneet wrote:
>> Hello,
>>
>> I have basic familiarity with Unix but by most standards a novice.  I am
>> trying to install R on a linux machine and am following the instructions in
>> the R install and admin guide in terms of what is required to compile the R
>> source code.  I downloaded R version 2.11.1 and extracted the files into my
>> home directory.  I realize I need a FORTRAN compiler to help with this
>> process and have tried installing a few but still cannot past the
>> configuration step of installing R:
>>
>> ./configure --with-readline=no
>>
>> Once I run this command after installing GFortran I get the following error:
>> ...
>> checking whether we can compute C Make dependencies... yes, using gcc
>> -std=gnu99 -MM
>> checking whether gcc -std=gnu99 supports -c -o FILE.lo... yes
>> checking how to get verbose linking output from gfortran... configure:
>> WARNING: compilation failed
>>
>> checking for Fortran 77 libraries of gfortran...
>> checking how to get verbose linking output from gcc -std=gnu99... -v
>> checking for C libraries of gcc -std=gnu99...  -L/usr/local/lib64
>> -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2
>> -L/usr/lib/gcc/x86_64-redhat-linux/4.1.2/../../../../lib64 -L/lib/../lib64
>> -L/usr/lib/../lib64 -lgcc_s
>> checking for dummy main to link with Fortran 77 libraries... none
>> checking for Fortran 77 name-mangling scheme... configure: error: in
>> `/home/lotayv01/R-2.11.1':
>> configure: error: cannot compile a simple Fortran program
>> See `config.log' for more details.
>>
>> For more details I can show you the section in the config.log file
>>
>> ...
>> /data/home/lotayv01/usr/local/gfortran/bin/../libexec/gcc/i686-pc-linux-gnu/4.6.0/f951:
>> error while loading shared libraries: libmpc.so.2: cannot open shared object
>> file: No such file or directory
>> configure:22471: $? = 1
>> configure: failed program was:
>> |       program main
>> |
>> |       end
>> configure:22548: WARNING: compilation failed
>> configure:22554: result:
>> configure:22556: checking for Fortran 77 libraries of gfortran
>> configure:22579: gfortran -o conftest -L/usr/local/lib64 conftest.f
>> /data/home/lotayv01/usr/local/gfortran/bin/../libexec/gcc/i686-pc-linux-gnu/4.6.0/f951:
>> error while loading shared libraries: libmpc.so.2: cannot open shared object
>> file: No such file or directory
>> ...
>>
>> When I check the version of Gfortran at the console command line I get this:
>> GNU Fortran (GCC) 4.6.0 20100407 (experimental) [trunk revision 158083]
>> Copyright (C) 2010 Free Software Foundation, Inc.
>>
>> Even before this I tried the g95 fortran compiler and the same thing
>> happened, how can I fix this problem, any help on this matter would be
>> greatly appreciated.
>>
>> Thanks
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-help
> PLEASE do read the posting guide http://www.R-project.org/posting-guide.html
> and provide commented, minimal, self-contained, reproducible code.
>

--
Brian D. Ripley,                  [hidden email]
Professor of Applied Statistics,  http://www.stats.ox.ac.uk/~ripley/
University of Oxford,             Tel:  +44 1865 272861 (self)
1 South Parks Road,                     +44 1865 272866 (PA)
Oxford OX1 3TG, UK                Fax:  +44 1865 272595

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Re: R linux install: FORTRAN compiling error

vaneet
Thanks for your replies.

I understand you think the best solution is to find the gfortran and possibly libgfortran packages from the version of my Linux and gcc distribution which according to a quick check is the following (also this is a 64 bit linux machine):

gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-48)
Copyright (C) 2006 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

The question is do you know where I can find a free gfortran package from this distribution and would I need to completely reinstall the gcc package from that version that includes gfortran and other compilers or can I simply add gfortran to my existing packages?

Thanks
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Re: R linux install: FORTRAN compiling error

vaneet
P.S.  My linux machine has the following info:

Red Hat Enterprise Linux Server release 5.5 (Tikanga)
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Re: R linux install: FORTRAN compiling error

Marc Schwartz-3
In reply to this post by vaneet
On Jun 3, 2010, at 9:17 AM, vaneet wrote:

>
> Thanks for your replies.
>
> I understand you think the best solution is to find the gfortran and
> possibly libgfortran packages from the version of my Linux and gcc
> distribution which according to a quick check is the following (also this is
> a 64 bit linux machine):
>
> gcc (GCC) 4.1.2 20080704 (Red Hat 4.1.2-48)
> Copyright (C) 2006 Free Software Foundation, Inc.
> This is free software; see the source for copying conditions.  There is NO
> warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
>
> The question is do you know where I can find a free gfortran package from
> this distribution and would I need to completely reinstall the gcc package
> from that version that includes gfortran and other compilers or can I simply
> add gfortran to my existing packages?
>
> Thanks


Sorry that I am coming to this late, but is there a reason that you did not install R using already available RPMs other than perhaps not being aware that they exist?

For RHEL 4 and 5 there is the EPEL:

  https://fedoraproject.org/wiki/EPEL

which provides pre-built binaries of many add-on packages, including R. R 2.11.0 is available there and Tom Callaway posted on the Fedora SIG list this morning that 2.11.1 is in the updates testing repo.

If you do need a FORTRAN compiler, which you may yet for add-on CRAN packages, one should be available via the regular RHEL repos, for which you would have already paid for access (not to mention direct telephone support from RH).

For RHEL 5 (based upon your followup), follow the instructions here:

  https://fedoraproject.org/wiki/EPEL/FAQ#howtouse

to gain access to the EPEL.

Then, as root, you can use:

  yum install R-core R-devel

to install R.

By staying with RPMs specifically built for your release, you tend to obviate version incompatibility issues, as Prof. Ripley has noted.

HTH,

Marc Schwartz

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Re: R linux install: FORTRAN compiling error

vaneet
I tried downloading the pre-built binaries of R from this website and then installing the rpms but is seems they depend on so many other packages to be installed first.  I tried simply the R package first:

warning: R-2.11.0-1.el5.x86_64.rpm: Header V3 DSA signature: NOKEY, key ID 217521f6
error: Failed dependencies:
        R-devel = 2.11.0-1.el5 is needed by R-2.11.0-1.el5.x86_64
        libRmath-devel = 2.11.0-1.el5 is needed by R-2.11.0-1.el5.x86_64

Then when I tried to install those packages there were more dependencies:

warning: R-devel-2.11.0-1.el5.x86_64.rpm: Header V3 DSA signature: NOKEY, key ID 217521f6
error: Failed dependencies:
        R-core = 2.11.0-1.el5 is needed by R-devel-2.11.0-1.el5.x86_64
        bzip2-devel is needed by R-devel-2.11.0-1.el5.x86_64
        gcc-gfortran is needed by R-devel-2.11.0-1.el5.x86_64
        libX11-devel is needed by R-devel-2.11.0-1.el5.x86_64
        pcre-devel is needed by R-devel-2.11.0-1.el5.x86_64
        pkgconfig is needed by R-devel-2.11.0-1.el5.x86_64
        tcl-devel is needed by R-devel-2.11.0-1.el5.x86_64
        tetex-latex is needed by R-devel-2.11.0-1.el5.x86_64
        tk-devel is needed by R-devel-2.11.0-1.el5.x86_64

So I thought perhaps R-core would have everything needed to install and run R but still:

warning: R-core-2.11.0-1.el5.x86_64.rpm: Header V3 DSA signature: NOKEY, key ID 217521f6
error: Failed dependencies:
        libgfortran.so.1()(64bit) is needed by R-core-2.11.0-1.el5.x86_64
        perl(File::Copy::Recursive) is needed by R-core-2.11.0-1.el5.x86_64
        tetex-latex is needed by R-core-2.11.0-1.el5.x86_64
        xdg-utils is needed by R-core-2.11.0-1.el5.x86_64

Is there any way I can get an RPM that has all the necessary packages built in to install and run R? Or do I have to find all these packages that are needed to install these 'R' rpms for which many are not found on the FedoraProject website (libgfortran, gcc-fortran....).  Also which 'R' rpm would I use to simply run R on the linux machine, would it be R-core?

Thanks

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Re: R linux install: FORTRAN compiling error

vaneet
Also would I need to install the R package as root in order for all users to use it? I'm assuming I would have to, I don't have root access now but I could possibly obtain it.  For now this is simply a test install so if there is a way to install the R package simply under my user name please let me know how.

Thanks
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Re: R linux install: FORTRAN compiling error

Marc Schwartz-3
In reply to this post by vaneet
On Jun 3, 2010, at 10:38 AM, vaneet wrote:

>
> I tried downloading the pre-built binaries of R from this website and then
> installing the rpms but is seems they depend on so many other packages to be
> installed first.  I tried simply the R package first:
>
> warning: R-2.11.0-1.el5.x86_64.rpm: Header V3 DSA signature: NOKEY, key ID
> 217521f6
> error: Failed dependencies:
>        R-devel = 2.11.0-1.el5 is needed by R-2.11.0-1.el5.x86_64
>        libRmath-devel = 2.11.0-1.el5 is needed by R-2.11.0-1.el5.x86_64
>
> Then when I tried to install those packages there were more dependencies:
>
> warning: R-devel-2.11.0-1.el5.x86_64.rpm: Header V3 DSA signature: NOKEY,
> key ID 217521f6
> error: Failed dependencies:
>        R-core = 2.11.0-1.el5 is needed by R-devel-2.11.0-1.el5.x86_64
>        bzip2-devel is needed by R-devel-2.11.0-1.el5.x86_64
>        gcc-gfortran is needed by R-devel-2.11.0-1.el5.x86_64
>        libX11-devel is needed by R-devel-2.11.0-1.el5.x86_64
>        pcre-devel is needed by R-devel-2.11.0-1.el5.x86_64
>        pkgconfig is needed by R-devel-2.11.0-1.el5.x86_64
>        tcl-devel is needed by R-devel-2.11.0-1.el5.x86_64
>        tetex-latex is needed by R-devel-2.11.0-1.el5.x86_64
>        tk-devel is needed by R-devel-2.11.0-1.el5.x86_64
>
> So I thought perhaps R-core would have everything needed to install and run
> R but still:
>
> warning: R-core-2.11.0-1.el5.x86_64.rpm: Header V3 DSA signature: NOKEY, key
> ID 217521f6
> error: Failed dependencies:
>        libgfortran.so.1()(64bit) is needed by R-core-2.11.0-1.el5.x86_64
>        perl(File::Copy::Recursive) is needed by R-core-2.11.0-1.el5.x86_64
>        tetex-latex is needed by R-core-2.11.0-1.el5.x86_64
>        xdg-utils is needed by R-core-2.11.0-1.el5.x86_64
>
> Is there any way I can get an RPM that has all the necessary packages built
> in to install and run R? Or do I have to find all these packages that are
> needed to install these 'R' rpms for which many are not found on the
> FedoraProject website (libgfortran, gcc-fortran....).  Also which 'R' rpm
> would I use to simply run R on the linux machine, would it be R-core?
>
> Thanks


The whole point of using 'yum' from the CLI to install RPMs, rather then downloading them separately and using 'rpm' from the CLI, is that yum will reconcile the dependencies of any packages required to install the RPMs that you actually want. Unless the RPM packagers goofed and messed up the dependency specifications (which happens now and then), yum should be pretty straightforward.

What you have above, is what is colloquially known as "RPM Dependency Hell", which is what yum was designed to avoid.  :-)

If you install the EPEL configuration RPM (as root), as is noted on the 'How To Use EPEL' page that I linked to, then all you should need to do is use the yum command (as root) that I provided to install R. Any required dependencies will be installed during that process. yum will get any needed RPMS from either the EPEL or the RHEL repos as may be required, to satisfy them.

And to answer your follow up question, yes, you will need to be root to engage in a system-wide R installation (and for the other missing system wide components). I don't know that the required RPMs are 'relocatable' to enable a local user install. For that, you might very well need to compile R from source, with appropriate configure/install time location options defined.

However, as noted, you are missing required system wide components, for which you will need to be root anyway. So you may as well get root access and move forward from there.

HTH,

Marc

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R linux install: FORTRAN compiling error

R P Herrold
In reply to this post by vaneet
On Thu, 3 Jun 2010, vaneet wrote:

> Is there any way I can get an RPM that has all the necessary packages built
> in to install and run R? Or do I have to find all these packages that are
> needed to install these 'R' rpms for which many are not found on the
> FedoraProject website (libgfortran, gcc-fortran....).  Also which 'R' rpm
> would I use to simply run R on the linux machine, would it be R-core?

This is really a usage issue of Fedora and its package
dependency solving and retrieval tool 'yum' and of the
author's unfamiliarity with the tools

> error: Failed dependencies:
>        R-core = 2.11.0-1.el5 is needed by R-devel-2.11.0-1.el5.x86_64
>        bzip2-devel is needed by R-devel-2.11.0-1.el5.x86_64
>        gcc-gfortran is needed by R-devel-2.11.0-1.el5.x86_64
>        libX11-devel is needed by R-devel-2.11.0-1.el5.x86_64
>        pcre-devel is needed by R-devel-2.11.0-1.el5.x86_64
>        pkgconfig is needed by R-devel-2.11.0-1.el5.x86_64
>        tcl-devel is needed by R-devel-2.11.0-1.el5.x86_64
>        tetex-latex is needed by R-devel-2.11.0-1.el5.x86_64
>        tk-devel is needed by R-devel-2.11.0-1.el5.x86_64

All of these except 'R-core' are present to a base Fedora or
RHEL system through use of that 'yum' tool (which is somewhat
like 'apt-get' for those from a Debian background; the R-core
pachage is almost certainly adjacent to the R package you are
trying to install

The suggestions of others about ancient versions and so forth
are speculation, and not accurate, and acting to take
'curative steps' upon such speculation will almost certainly
damage the integrity of a RHEL installation

I build, and 'spot' of Red Hat build R packages that install
without issue on Fedora, and for me, for CentOS [a community
rebuild of RHEL]   While I have not had occasion to build the
latest release over the weekend, I am certain I shall without
a need for the invasive changes noted

There is a support list for just this in the R list heirarchy,
to which such questons might properly be taken
  r-sig-fedora.r-project.org
which is not limited solely to the Fedora users of the RPM
packaging system

-- Russ herrold

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Re: R linux install: FORTRAN compiling error

vaneet
Thanks for your help,

I was able to get someone with root access to execute the yum command for me and install R on the linux machine and it work!!
mnr
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Re: R linux install: FORTRAN compiling error

mnr
This post has NOT been accepted by the mailing list yet.
In reply to this post by vaneet
What's wrong with this package with FORTRAN code?
When I write R CMD check package name
I have a note.
Here's the error:
* checking compiled code ... NOTE
File 'C:/Users/Utente/Desktop/Prova/package_name.Rcheck/ package_name /libs/i386/ package_name.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Object: ' package_name.o'
File 'C:/Users/Utente/Desktop/Prova/ package_name.Rcheck/ package_name /libs/x64/ package_name.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Object: ' package_name.o'

Compiled code should not call functions which might terminate R nor write to stdout/stderr instead of to the console.
Could you help me?
Regards
Marta