Trouble building R 3.5.0 under Ubuntu 18.04

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Trouble building R 3.5.0 under Ubuntu 18.04

Steve Gutreuter
I would love to hear from anyone who has successfully built 3.5.0 under
 Ubuntu 18.04 (Bionic Beaver).  My attempts have failed, including:

export LDFLAGS="$LDFLAGS -fPIC"
export CXXFLAGS="$CXXFLAGS -fPIC"
export CFLAGS="$CFLAGS -fPIC"
./configure --enable-R-shlib --prefix=/usr/lib/R/3.5.0

#### Configure completes normally without errors or warnings

make

#### make fails, always with lines like:
/usr/bin/x86_64-linux-gnu-ld: ../appl/dtrsl.o: relocation R_X86_64_32
against `.rodata' can not be used when making a shared object;
recompile with -fPIC
/usr/bin/x86_64-linux-gnu-ld: attrib.o: relocation R_X86_64_PC32
against symbol `R_NilValue' can not be used when making a shared
object; recompile with -fPIC
/usr/bin/x86_64-linux-gnu-ld: final link failed: Bad value
collect2: error: ld returned 1 exit status
Makefile:177: recipe for target 'libR.so' failed
make[3]: *** [libR.so] Error 1
make[3]: Leaving directory '/home/steve/src/R/R-3.5.0/src/main'
Makefile:135: recipe for target 'R' failed

How does one set the -fPIC flag?

I have never had trouble compiling under Mint, which is based on
Ubuntu.

Thanks!
Steve

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Re: Trouble building R 3.5.0 under Ubuntu 18.04

Bert Gunter-2
Seems O/T for this list, which is about R programming.

Have you tried an internet search on "Install R on ubuntu" or similar.

I found  this:
https://www.linode.com/docs/development/r/how-to-install-r-on-ubuntu-and-debian/

There are also r-sig-debian and r-sig-fedora mailing lists, in case that
might help.

Cheers,
Bert






Bert Gunter

"The trouble with having an open mind is that people keep coming along and
sticking things into it."
-- Opus (aka Berkeley Breathed in his "Bloom County" comic strip )

On Tue, May 22, 2018 at 3:47 PM, Steve Gutreuter <[hidden email]>
wrote:

> I would love to hear from anyone who has successfully built 3.5.0 under
>  Ubuntu 18.04 (Bionic Beaver).  My attempts have failed, including:
>
> export LDFLAGS="$LDFLAGS -fPIC"
> export CXXFLAGS="$CXXFLAGS -fPIC"
> export CFLAGS="$CFLAGS -fPIC"
> ./configure --enable-R-shlib --prefix=/usr/lib/R/3.5.0
>
> #### Configure completes normally without errors or warnings
>
> make
>
> #### make fails, always with lines like:
> /usr/bin/x86_64-linux-gnu-ld: ../appl/dtrsl.o: relocation R_X86_64_32
> against `.rodata' can not be used when making a shared object;
> recompile with -fPIC
> /usr/bin/x86_64-linux-gnu-ld: attrib.o: relocation R_X86_64_PC32
> against symbol `R_NilValue' can not be used when making a shared
> object; recompile with -fPIC
> /usr/bin/x86_64-linux-gnu-ld: final link failed: Bad value
> collect2: error: ld returned 1 exit status
> Makefile:177: recipe for target 'libR.so' failed
> make[3]: *** [libR.so] Error 1
> make[3]: Leaving directory '/home/steve/src/R/R-3.5.0/src/main'
> Makefile:135: recipe for target 'R' failed
>
> How does one set the -fPIC flag?
>
> I have never had trouble compiling under Mint, which is based on
> Ubuntu.
>
> Thanks!
> Steve
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> 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.
>

        [[alternative HTML version deleted]]

______________________________________________
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Re: Trouble building R 3.5.0 under Ubuntu 18.04

Ista Zahn
In reply to this post by Steve Gutreuter
On Tue, May 22, 2018 at 6:47 PM, Steve Gutreuter <[hidden email]> wrote:
> I would love to hear from anyone who has successfully built 3.5.0 under
>  Ubuntu 18.04 (Bionic Beaver).

This is the wrong list, see R-sig-debian. That said,

apt-get update
apt-get build-dep r-base
wget https://cran.r-project.org/src/base/R-3/R-3.5.0.tar.gz
tar -xvf R-3.5.0.tar.gz
cd R-3.5.0
./configure
make
./bin/R

works for me.

--Ista
 My attempts have failed, including:

>
> export LDFLAGS="$LDFLAGS -fPIC"
> export CXXFLAGS="$CXXFLAGS -fPIC"
> export CFLAGS="$CFLAGS -fPIC"
> ./configure --enable-R-shlib --prefix=/usr/lib/R/3.5.0
>
> #### Configure completes normally without errors or warnings
>
> make
>
> #### make fails, always with lines like:
> /usr/bin/x86_64-linux-gnu-ld: ../appl/dtrsl.o: relocation R_X86_64_32
> against `.rodata' can not be used when making a shared object;
> recompile with -fPIC
> /usr/bin/x86_64-linux-gnu-ld: attrib.o: relocation R_X86_64_PC32
> against symbol `R_NilValue' can not be used when making a shared
> object; recompile with -fPIC
> /usr/bin/x86_64-linux-gnu-ld: final link failed: Bad value
> collect2: error: ld returned 1 exit status
> Makefile:177: recipe for target 'libR.so' failed
> make[3]: *** [libR.so] Error 1
> make[3]: Leaving directory '/home/steve/src/R/R-3.5.0/src/main'
> Makefile:135: recipe for target 'R' failed
>
> How does one set the -fPIC flag?
>
> I have never had trouble compiling under Mint, which is based on
> Ubuntu.
>
> Thanks!
> Steve
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> 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.

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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.
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Re: Trouble building R 3.5.0 under Ubuntu 18.04

Kevin E. Thorpe
I suspect the main difficulty the OP is having is building R with shlib
support.

Steve, can you build from source without the --enable-R-shlib flag on
configure?

Kevin

On 05/23/2018 01:58 PM, Ista Zahn wrote:

> On Tue, May 22, 2018 at 6:47 PM, Steve Gutreuter <[hidden email]> wrote:
>> I would love to hear from anyone who has successfully built 3.5.0 under
>>   Ubuntu 18.04 (Bionic Beaver).
>
> This is the wrong list, see R-sig-debian. That said,
>
> apt-get update
> apt-get build-dep r-base
> wget https://cran.r-project.org/src/base/R-3/R-3.5.0.tar.gz
> tar -xvf R-3.5.0.tar.gz
> cd R-3.5.0
> ./configure
> make
> ./bin/R
>
> works for me.
>
> --Ista
>   My attempts have failed, including:
>>
>> export LDFLAGS="$LDFLAGS -fPIC"
>> export CXXFLAGS="$CXXFLAGS -fPIC"
>> export CFLAGS="$CFLAGS -fPIC"
>> ./configure --enable-R-shlib --prefix=/usr/lib/R/3.5.0
>>
>> #### Configure completes normally without errors or warnings
>>
>> make
>>
>> #### make fails, always with lines like:
>> /usr/bin/x86_64-linux-gnu-ld: ../appl/dtrsl.o: relocation R_X86_64_32
>> against `.rodata' can not be used when making a shared object;
>> recompile with -fPIC
>> /usr/bin/x86_64-linux-gnu-ld: attrib.o: relocation R_X86_64_PC32
>> against symbol `R_NilValue' can not be used when making a shared
>> object; recompile with -fPIC
>> /usr/bin/x86_64-linux-gnu-ld: final link failed: Bad value
>> collect2: error: ld returned 1 exit status
>> Makefile:177: recipe for target 'libR.so' failed
>> make[3]: *** [libR.so] Error 1
>> make[3]: Leaving directory '/home/steve/src/R/R-3.5.0/src/main'
>> Makefile:135: recipe for target 'R' failed
>>
>> How does one set the -fPIC flag?
>>
>> I have never had trouble compiling under Mint, which is based on
>> Ubuntu.
>>
>> Thanks!
>> Steve
>>


--
Kevin E. Thorpe
Head of Biostatistics,  Applied Health Research Centre (AHRC)
Li Ka Shing Knowledge Institute of St. Michael's Hospital
Assistant Professor, Dalla Lana School of Public Health
University of Toronto
email: [hidden email]  Tel: 416.864.5776  Fax: 416.864.3016

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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.
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Re: Trouble building R 3.5.0 under Ubuntu 18.04

Ista Zahn
On Wed, May 23, 2018 at 2:27 PM, Kevin E. Thorpe
<[hidden email]> wrote:
> I suspect the main difficulty the OP is having is building R with shlib
> support.

apt-get update
apt-get build-dep r-base
wget https://cran.r-project.org/src/base/R-3/R-3.5.0.tar.gz
tar -xvf R-3.5.0.tar.gz
cd R-3.5.0
./configure --enable-R-shlib
make

also works fine here. FWIW, I'm starting with the ubuntu:latest docker
image and going from there.

Best,
Ista

>
> Steve, can you build from source without the --enable-R-shlib flag on
> configure?
>
> Kevin
>
>
> On 05/23/2018 01:58 PM, Ista Zahn wrote:
>>
>> On Tue, May 22, 2018 at 6:47 PM, Steve Gutreuter <[hidden email]>
>> wrote:
>>>
>>> I would love to hear from anyone who has successfully built 3.5.0 under
>>>   Ubuntu 18.04 (Bionic Beaver).
>>
>>
>> This is the wrong list, see R-sig-debian. That said,
>>
>> apt-get update
>> apt-get build-dep r-base
>> wget https://cran.r-project.org/src/base/R-3/R-3.5.0.tar.gz
>> tar -xvf R-3.5.0.tar.gz
>> cd R-3.5.0
>> ./configure
>> make
>> ./bin/R
>>
>> works for me.
>>
>> --Ista
>>   My attempts have failed, including:
>>>
>>>
>>> export LDFLAGS="$LDFLAGS -fPIC"
>>> export CXXFLAGS="$CXXFLAGS -fPIC"
>>> export CFLAGS="$CFLAGS -fPIC"
>>> ./configure --enable-R-shlib --prefix=/usr/lib/R/3.5.0
>>>
>>> #### Configure completes normally without errors or warnings
>>>
>>> make
>>>
>>> #### make fails, always with lines like:
>>> /usr/bin/x86_64-linux-gnu-ld: ../appl/dtrsl.o: relocation R_X86_64_32
>>> against `.rodata' can not be used when making a shared object;
>>> recompile with -fPIC
>>> /usr/bin/x86_64-linux-gnu-ld: attrib.o: relocation R_X86_64_PC32
>>> against symbol `R_NilValue' can not be used when making a shared
>>> object; recompile with -fPIC
>>> /usr/bin/x86_64-linux-gnu-ld: final link failed: Bad value
>>> collect2: error: ld returned 1 exit status
>>> Makefile:177: recipe for target 'libR.so' failed
>>> make[3]: *** [libR.so] Error 1
>>> make[3]: Leaving directory '/home/steve/src/R/R-3.5.0/src/main'
>>> Makefile:135: recipe for target 'R' failed
>>>
>>> How does one set the -fPIC flag?
>>>
>>> I have never had trouble compiling under Mint, which is based on
>>> Ubuntu.
>>>
>>> Thanks!
>>> Steve
>>>
>
>
> --
> Kevin E. Thorpe
> Head of Biostatistics,  Applied Health Research Centre (AHRC)
> Li Ka Shing Knowledge Institute of St. Michael's Hospital
> Assistant Professor, Dalla Lana School of Public Health
> University of Toronto
> email: [hidden email]  Tel: 416.864.5776  Fax: 416.864.3016
>
>
> ______________________________________________
> [hidden email] mailing list -- To UNSUBSCRIBE and more, see
> 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.

______________________________________________
[hidden email] mailing list -- To UNSUBSCRIBE and more, see
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.