RPM-style install (SLED 10.1)

[Stas Kolenikov]

I am trying to install R on a SLED 10.1 machine.
R-base-2.7.0-7.1-i586.rpm fails with

stas@linux-6b8s:~/RPMs> rpm -Uvh R-base-2.7.0-7.1.i586.rpm
warning: R-base-2.7.0-7.1.i586.rpm: Header V3 DSA signature: NOKEY,
key ID 14ec5930
error: Failed dependencies:
        libgfortran.so.1 is needed by R-base-2.7.0-7.1.i586

I tried to trick it into believing there's the library by setting up the link:

stas@linux-6b8s:~/RPMs> ls -l /usr/lib/libgf*
lrwxrwxrwx 1 root root      29 2008-05-08 17:45
/usr/lib/libgfortran.so.1 -> /usr/lib/libgfortran.so.3.0.0
lrwxrwxrwx 1 root root      20 2008-05-08 17:37
/usr/lib/libgfortran.so.3 -> libgfortran.so.3.0.0
-rwxr-xr-x 1 root root 2251139 2008-05-01 09:43 /usr/lib/libgfortran.so.3.0.0

but that did not work, either. I went on and installed GCC's gfortran,
but it did not provide libgfortran.so.1 either:

stas@linux-6b8s:~/RPMs> ls -l /usr/irun/lib/libgf*
-rw-r--r-- 1 1005 1011 4330512 2008-03-02 02:29 /usr/irun/lib/libgfortran.a
-rwxr-xr-x 1 1005 1011    1009 2008-03-02 02:29 /usr/irun/lib/libgfortran.la
-rwxr-xr-x 1 1005 1011 2509309 2008-03-02 02:29 /usr/irun/lib/libgfortran.so
-rwxr-xr-x 1 1005 1011 2509309 2008-03-02 02:29 /usr/irun/lib/libgfortran.so.3
-rwxr-xr-x 1 1005 1011 2509309 2008-03-02 02:29
/usr/irun/lib/libgfortran.so.3.0.0

Any reason R wants that package instead of the newer one? Of course
rpm --nodeps was an option, but then it fails to load r-stats with the
same message about the missing library:

Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared library '/usr/lib/R/library/stats/libs/stats.so':
  /usr/lib/R/library/stats/libs/stats.so: undefined symbol: _gfortran_pow_r8_i4
During startup - Warning message:
package stats in options("defaultPackages") was not found

I am stuck... I am trying to compile R from 2.6.2 sources in the
meantime, but that's painful for a Linux newbie like me on a brand-new
computer that does not necessarily have all the packages. I almost
want to switch to Ubuntu as R installation back there was a single
click :))

--
Stas Kolenikov, also found at http://stas.kolenikov.name
Small print: Please do not reply to my Gmail address as I don't check
it regularly.

______________________________________________
R-help@... 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.

[Horace Tso]

Stas, this doesn't solve your problem but may shed some light on what might have gone wrong. Just recently I installed R 2.7.0 under openSuse 10.3 in a brand new 64-bit Lenovo ThinkPad. The first install failed because of a dependency error just like yours. It complained it couldn't find BLAS and libgfortran. I then got on the varous repositories and installed a couple flavours (don't remember how many) of fortran and finally it went through. Right now, in my /usr/lib64, i have libgfortran.so.2.0.0.

HTH.

Horace




-----Original Message-----
From: r-help-bounces@... [mailto:r-help-bounces@...] On Behalf Of Stas Kolenikov
Sent: Monday, May 12, 2008 7:33 AM
To: r-help@...
Subject: [R] RPM-style install (SLED 10.1)

I am trying to install R on a SLED 10.1 machine.
R-base-2.7.0-7.1-i586.rpm fails with

stas@linux-6b8s:~/RPMs> rpm -Uvh R-base-2.7.0-7.1.i586.rpm
warning: R-base-2.7.0-7.1.i586.rpm: Header V3 DSA signature: NOKEY,
key ID 14ec5930
error: Failed dependencies:
        libgfortran.so.1 is needed by R-base-2.7.0-7.1.i586

I tried to trick it into believing there's the library by setting up the link:

stas@linux-6b8s:~/RPMs> ls -l /usr/lib/libgf*
lrwxrwxrwx 1 root root      29 2008-05-08 17:45
/usr/lib/libgfortran.so.1 -> /usr/lib/libgfortran.so.3.0.0
lrwxrwxrwx 1 root root      20 2008-05-08 17:37
/usr/lib/libgfortran.so.3 -> libgfortran.so.3.0.0
-rwxr-xr-x 1 root root 2251139 2008-05-01 09:43 /usr/lib/libgfortran.so.3.0.0

but that did not work, either. I went on and installed GCC's gfortran,
but it did not provide libgfortran.so.1 either:

stas@linux-6b8s:~/RPMs> ls -l /usr/irun/lib/libgf*
-rw-r--r-- 1 1005 1011 4330512 2008-03-02 02:29 /usr/irun/lib/libgfortran.a
-rwxr-xr-x 1 1005 1011    1009 2008-03-02 02:29 /usr/irun/lib/libgfortran.la
-rwxr-xr-x 1 1005 1011 2509309 2008-03-02 02:29 /usr/irun/lib/libgfortran.so
-rwxr-xr-x 1 1005 1011 2509309 2008-03-02 02:29 /usr/irun/lib/libgfortran.so.3
-rwxr-xr-x 1 1005 1011 2509309 2008-03-02 02:29
/usr/irun/lib/libgfortran.so.3.0.0

Any reason R wants that package instead of the newer one? Of course
rpm --nodeps was an option, but then it fails to load r-stats with the
same message about the missing library:

Error in dyn.load(file, DLLpath = DLLpath, ...) :
  unable to load shared library '/usr/lib/R/library/stats/libs/stats.so':
  /usr/lib/R/library/stats/libs/stats.so: undefined symbol: _gfortran_pow_r8_i4
During startup - Warning message:
package stats in options("defaultPackages") was not found

I am stuck... I am trying to compile R from 2.6.2 sources in the
meantime, but that's painful for a Linux newbie like me on a brand-new
computer that does not necessarily have all the packages. I almost
want to switch to Ubuntu as R installation back there was a single
click :))

--
Stas Kolenikov, also found at http://stas.kolenikov.name
Small print: Please do not reply to my Gmail address as I don't check
it regularly.

______________________________________________
R-help@... 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.

______________________________________________
R-help@... 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.

[Stas Kolenikov]

That's what I ended up doing. I've had complaints about blas, too, but
I rpm-ed them out with --nodeps. I've compiled R from the sources (I
had to add some -devel- packages, too), and then copied over the
stats.*.so library from my fully successful 2.6.2 compilation to
semi-successful 2.7.0 installation. So I cannot actually tell if I
have 2.7.0 or 2.6.2 on this computer... and I don't know if any other
problems may appear later.

And yes I have a ThinkPad although it is 32 bit.

On 5/12/08, Horace Tso <Horace.Tso@...> wrote:

> Stas, this doesn't solve your problem but may shed some light on what might have gone wrong. Just recently I installed R 2.7.0 under openSuse 10.3 in a brand new 64-bit Lenovo ThinkPad. The first install failed because of a dependency error just like yours. It complained it couldn't find BLAS and libgfortran. I then got on the varous repositories and installed a couple flavours (don't remember how many) of fortran and finally it went through. Right now, in my /usr/lib64, i have libgfortran.so.2.0.0.
>
>
>  -----Original Message-----
>  From: r-help-bounces@... [mailto:r-help-bounces@...] On Behalf Of Stas Kolenikov
>  Sent: Monday, May 12, 2008 7:33 AM
>  To: r-help@...
>  Subject: [R] RPM-style install (SLED 10.1)
>
>  I am trying to install R on a SLED 10.1 machine.
>  R-base-2.7.0-7.1-i586.rpm fails with
>
>  stas@linux-6b8s:~/RPMs> rpm -Uvh R-base-2.7.0-7.1.i586.rpm
>  warning: R-base-2.7.0-7.1.i586.rpm: Header V3 DSA signature: NOKEY,
>  key ID 14ec5930
>  error: Failed dependencies:
>         libgfortran.so.1 is needed by R-base-2.7.0-7.1.i586
>
>  I tried to trick it into believing there's the library by setting up the link:
>
>  stas@linux-6b8s:~/RPMs> ls -l /usr/lib/libgf*
>  lrwxrwxrwx 1 root root      29 2008-05-08 17:45
>  /usr/lib/libgfortran.so.1 -> /usr/lib/libgfortran.so.3.0.0
>  lrwxrwxrwx 1 root root      20 2008-05-08 17:37
>  /usr/lib/libgfortran.so.3 -> libgfortran.so.3.0.0
>  -rwxr-xr-x 1 root root 2251139 2008-05-01 09:43 /usr/lib/libgfortran.so.3.0.0
>
>  but that did not work, either. I went on and installed GCC's gfortran,
>  but it did not provide libgfortran.so.1 either:
>
>  stas@linux-6b8s:~/RPMs> ls -l /usr/irun/lib/libgf*
>  -rw-r--r-- 1 1005 1011 4330512 2008-03-02 02:29 /usr/irun/lib/libgfortran.a
>  -rwxr-xr-x 1 1005 1011    1009 2008-03-02 02:29 /usr/irun/lib/libgfortran.la
>  -rwxr-xr-x 1 1005 1011 2509309 2008-03-02 02:29 /usr/irun/lib/libgfortran.so
>  -rwxr-xr-x 1 1005 1011 2509309 2008-03-02 02:29 /usr/irun/lib/libgfortran.so.3
>  -rwxr-xr-x 1 1005 1011 2509309 2008-03-02 02:29
>  /usr/irun/lib/libgfortran.so.3.0.0
>
>  Any reason R wants that package instead of the newer one? Of course
>  rpm --nodeps was an option, but then it fails to load r-stats with the
>  same message about the missing library:
>
>  Error in dyn.load(file, DLLpath = DLLpath, ...) :
>   unable to load shared library '/usr/lib/R/library/stats/libs/stats.so':
>   /usr/lib/R/library/stats/libs/stats.so: undefined symbol: _gfortran_pow_r8_i4
>  During startup - Warning message:
>  package stats in options("defaultPackages") was not found
>
>  I am stuck... I am trying to compile R from 2.6.2 sources in the
>  meantime, but that's painful for a Linux newbie like me on a brand-new
>  computer that does not necessarily have all the packages. I almost
>  want to switch to Ubuntu as R installation back there was a single
>  click :))
>
>  --
>  Stas Kolenikov, also found at http://stas.kolenikov.name
>  Small print: Please do not reply to my Gmail address as I don't check
>  it regularly.
>
>
> ______________________________________________
>  R-help@... 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.
>

--
Stas Kolenikov, also found at http://stas.kolenikov.name

Small print: Please do not reply to my Gmail address as I don't check
it regularly.

______________________________________________
R-help@... 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.