undefined symbol: cholmod_factorize_p

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undefined symbol: cholmod_factorize_p

Göran Broström-3
I am installing R_3.5.1 from source on ubuntu 18.04, and 'config' +
'make' gives me (at the end)

Loading required package: Matrix
Error: package or namespace load failed for ‘Matrix’ in dyn.load(file,
DLLpath = DLLpath, ...):
  unable to load shared object
'/home/goran/src/R-3.5.1/library/Matrix/libs/Matrix.so':
   /home/goran/src/R-3.5.1/library/Matrix/libs/Matrix.so: undefined
symbol: cholmod_factorize_p
Error in eval(exprs[i], envir) : require(Matrix) is not TRUE
ERROR: installing package indices failed
* removing ‘/home/goran/src/R-3.5.1/library/Matrix’
Makefile:51: recipe for target 'Matrix.ts' failed
make[2]: *** [Matrix.ts] Error 1
make[2]: Leaving directory '/home/goran/src/R-3.5.1/src/library/Recommended'
Makefile:39: recipe for target 'recommended-packages' failed
make[1]: *** [recommended-packages] Error 2
make[1]: Leaving directory '/home/goran/src/R-3.5.1/src/library/Recommended'
Makefile:77: recipe for target 'stamp-recommended' failed
make: *** [stamp-recommended] Error 2

What am I missing?

Göran

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Re: undefined symbol: cholmod_factorize_p

Jeroen Ooms
On Fri, Jul 6, 2018 at 11:57 PM, Göran Broström <[hidden email]> wrote:
> I am installing R_3.5.1 from source on ubuntu 18.04, and 'config' + 'make'
> gives me (at the end)

Probably something went wrong earlier in the build when compiling the
Matrix package. However it's much easier to install R form the
binaries:

  sudo add-apt-repository -y ppa:marutter/rrutter3.5
  sudo apt-get update
  sudo apt-get install r-base

If you really want to build from source, have a look at which flags
and dependencies are used in the r-base source package on
Debian/Ubuntu.

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Re: undefined symbol: cholmod_factorize_p

Göran Broström-3


On 2018-07-07 13:08, Jeroen Ooms wrote:

> On Fri, Jul 6, 2018 at 11:57 PM, Göran Broström
> <[hidden email]> wrote:
>> I am installing R_3.5.1 from source on ubuntu 18.04, and 'config' +
>> 'make' gives me (at the end)
>
> Probably something went wrong earlier in the build when compiling
> the Matrix package. However it's much easier to install R form the
> binaries:
>
> sudo add-apt-repository -y ppa:marutter/rrutter3.5 sudo apt-get
> update sudo apt-get install r-base

Thanks, after a discussion with Dirk on r-sig-debian I did just that.
The reason I compiled R from source was that I had some problems with
the binary install but without the ppa:marutter. With it everything works.

>
> If you really want to build from source, have a look at which flags
> and dependencies are used in the r-base source package on
> Debian/Ubuntu.
>
I certainly will be able to do that (it has "always" worked seamlessly
for me, don't understand what happened this time. Maybe the upgrade to
18.04), so I will have a look.

Many thanks, Göran

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Re: undefined symbol: cholmod_factorize_p (solved)

Göran Broström-3


On 2018-07-07 13:41, Göran Broström wrote:

>
>
> On 2018-07-07 13:08, Jeroen Ooms wrote:
>> On Fri, Jul 6, 2018 at 11:57 PM, Göran Broström
>> <[hidden email]> wrote:
>>> I am installing R_3.5.1 from source on ubuntu 18.04, and 'config' +
>>> 'make' gives me (at the end)
>>
>> Probably something went wrong earlier in the build when compiling
>> the Matrix package. However it's much easier to install R form the
>> binaries:
>>
>> sudo add-apt-repository -y ppa:marutter/rrutter3.5 sudo apt-get
>> update sudo apt-get install r-base
>
> Thanks, after a discussion with Dirk on r-sig-debian I did just that.
> The reason I compiled R from source was that I had some problems with
> the binary install but without the ppa:marutter. With it everything works.
>
>>
>> If you really want to build from source, have a look at which flags
>> and dependencies are used in the r-base source package on Debian/Ubuntu.
>>
> I certainly will be able to do that (it has "always" worked seamlessly
> for me, don't understand what happened this time. Maybe the upgrade to
> 18.04), so I will have a look.

I had a look in ~/.R and there I found a file 'Makevars' containing:

PKG_LIBS = $(LAPACK_LIBS) $(BLAS_LIBS) $(FLIBS)

Removing it removed the problem! Its existence was a result of a
discussion on r-pkg-devel, which I now will take up again (but after the
game).

Göran

> Many thanks, Göran
>
> ______________________________________________
> [hidden email] mailing list
> https://stat.ethz.ch/mailman/listinfo/r-devel

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