Building R-3.2.0 from source.

I am cross-posting this to r-sig-fedora (I hope that's not an egregious sin)
in the hope that doing so might provide some source of insight.

I tried

    sudo yum install zlib

and was told

Package zlib-1.2.5-7.fc17.x86_64 already installed and latest version

Likewise for "zlib-devel".

I also tried

    sudo yum install bzlib

and was told

No package bzlib available.

Likewise for "bzlib-devel".

Finally I sort of got some joy with "lzma" and "lzma-devel" --- both of
those yielded an actual installation.  But it didn't help.

I re-did the configure and then the make and got the same errors/complaints
about undefined references to deflate, inflate, crc32, etc.

Can anyone provide any guidance/suggestions about what else I could try?
I'm getting very frustrated! :-)

cheers,

Rolf Turner

On 11/05/15 00:50, peter dalgaard wrote:

On 10 May 2015, at 14:15 , Rolf Turner <r.turner at auckland.ac.nz> wrote:



I am just now getting around to upgrading from 3.1.2 to 3.2.0 and am
getting hammered by a problem which is beyond my limited capabilities of
handling.

I executed

  ./configure --with-tcltk --with cairo

which seemed to go just fine, and then did:

   make

In fairly short order I started getting  error messages like unto:

connections.o: In function `gzcon_write':
/home/rolf/Desktop/Rinst/R-3.2.0/src/main/connections.c:5469: undefined
reference to `deflate'

There were also complaints about undefined references to inflate, crc32,
deflateEnd, inflateEnd, inflateReset, inflateInit2_, deflateInit2_,
compress, uncompress, and zlibVersion, many of which were issued repeatedly.
It finally gave up, saying:

collect2: error: ld returned 1 exit status

A bit of googling informed me (I think?) that a workaround was to
configure using --without-system-pcre.  This however achieved nothing in my
case.

Can anyone point me at what I need to do to fix this?  Install or update
something?

I am running an (elderly, no-longer-supported) Fedora 17 Linux.

Thanks for any assistance.

PCRE (regular expressions) won't help you with compression algorithms...
If anything, it is  --without-system-xz, -zlib, -bzlib that would come into
play, but it would be a better idea to ensure that you do have the libraries
and headers installed.

I'm not completely up to speed on Fedora, but the order of the day is that
you need to install some variation of lzma/zlib/bzlib and their -dev/-devel
header files etc. Check appendix A.1 and A.2 of the R Installation and
Administration manual.

--
Technical Editor ANZJS
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276
Home phone: +64-9-480-4619

1. R 3.2.0 is packaged for Fedora now; it's in Rawhide and Fedora 22.
I'm running Fedora 22 (late beta) and haven't had any problems with R.
RStudio Desktop Preview (0.99.435) from the RStudio Fedora RPM is also
running fine. You might save yourself some hassles by upgrading to
Fedora 22.

2. I have a bash script to build R from source that works on Fedora
22. It probably also works on Fedora 21 but it's been a while since I
tried it. Note that it installs 'calibre' and makes the ebooks of the
manuals. It also does some packaging things at the end you probably
don't need.

On Sun, May 10, 2015 at 2:52 PM, Rolf Turner <r.turner at auckland.ac.nz> wrote:

I am cross-posting this to r-sig-fedora (I hope that's not an egregious sin)
in the hope that doing so might provide some source of insight.

I tried

     sudo yum install zlib

and was told

Package zlib-1.2.5-7.fc17.x86_64 already installed and latest version

Likewise for "zlib-devel".

I also tried

     sudo yum install bzlib

and was told

No package bzlib available.

Likewise for "bzlib-devel".

Finally I sort of got some joy with "lzma" and "lzma-devel" --- both of
those yielded an actual installation.  But it didn't help.

I re-did the configure and then the make and got the same errors/complaints
about undefined references to deflate, inflate, crc32, etc.

Can anyone provide any guidance/suggestions about what else I could try?
I'm getting very frustrated! :-)

cheers,

Rolf Turner

On 11/05/15 00:50, peter dalgaard wrote:

On 10 May 2015, at 14:15 , Rolf Turner <r.turner at auckland.ac.nz> wrote:



I am just now getting around to upgrading from 3.1.2 to 3.2.0 and am
getting hammered by a problem which is beyond my limited capabilities of
handling.

I executed

   ./configure --with-tcltk --with cairo

which seemed to go just fine, and then did:

    make

In fairly short order I started getting  error messages like unto:

connections.o: In function `gzcon_write':
/home/rolf/Desktop/Rinst/R-3.2.0/src/main/connections.c:5469: undefined
reference to `deflate'

There were also complaints about undefined references to inflate, crc32,
deflateEnd, inflateEnd, inflateReset, inflateInit2_, deflateInit2_,
compress, uncompress, and zlibVersion, many of which were issued repeatedly.
It finally gave up, saying:

collect2: error: ld returned 1 exit status

A bit of googling informed me (I think?) that a workaround was to
configure using --without-system-pcre.  This however achieved nothing in my
case.

Can anyone point me at what I need to do to fix this?  Install or update
something?

I am running an (elderly, no-longer-supported) Fedora 17 Linux.

Thanks for any assistance.

PCRE (regular expressions) won't help you with compression algorithms...
If anything, it is  --without-system-xz, -zlib, -bzlib that would come into
play, but it would be a better idea to ensure that you do have the libraries
and headers installed.

I'm not completely up to speed on Fedora, but the order of the day is that
you need to install some variation of lzma/zlib/bzlib and their -dev/-devel
header files etc. Check appendix A.1 and A.2 of the R Installation and
Administration manual.

--
Technical Editor ANZJS
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276
Home phone: +64-9-480-4619

On 11/05/15 12:06, M. Edward (Ed) Borasky wrote:

1. R 3.2.0 is packaged for Fedora now; it's in Rawhide and Fedora 22.
I'm running Fedora 22 (late beta) and haven't had any problems with R.
RStudio Desktop Preview (0.99.435) from the RStudio Fedora RPM is also
running fine. You might save yourself some hassles by upgrading to
Fedora 22.

I'm sure I would, but I don't dare.  Everything I see on the Fedora
mailing list fills me with terror in respect of the disasters that can
occur.  I don't have the skills to cope with such disasters and I have no
access to support in respect of Fedora.

 2. I have a bash script to build R from source that works on Fedora

22. It probably also works on Fedora 21 but it's been a while since I
tried it. Note that it installs 'calibre' and makes the ebooks of the
manuals. It also does some packaging things at the end you probably
don't need.

Thanks, but I don't think it's any help in my situation.

I had no problem at all building R 3.1.2 from source.  What changed from
3.1.2 to 3.2.0 that would cause those undefined reference problems?

cheers,

Rolf Turner

On Sun, May 10, 2015 at 2:52 PM, Rolf Turner <r.turner at auckland.ac.nz>
wrote:

I am cross-posting this to r-sig-fedora (I hope that's not an egregious
sin)
in the hope that doing so might provide some source of insight.

I tried

     sudo yum install zlib

and was told

 Package zlib-1.2.5-7.fc17.x86_64 already installed and latest version

Likewise for "zlib-devel".

I also tried

     sudo yum install bzlib

and was told

 No package bzlib available.

Likewise for "bzlib-devel".

Finally I sort of got some joy with "lzma" and "lzma-devel" --- both of
those yielded an actual installation.  But it didn't help.

I re-did the configure and then the make and got the same
errors/complaints
about undefined references to deflate, inflate, crc32, etc.

Can anyone provide any guidance/suggestions about what else I could try?
I'm getting very frustrated! :-)

cheers,

Rolf Turner

On 11/05/15 00:50, peter dalgaard wrote:

 On 10 May 2015, at 14:15 , Rolf Turner <r.turner at auckland.ac.nz>

wrote:



I am just now getting around to upgrading from 3.1.2 to 3.2.0 and am
getting hammered by a problem which is beyond my limited capabilities
of
handling.

I executed

   ./configure --with-tcltk --with cairo

which seemed to go just fine, and then did:

    make

In fairly short order I started getting  error messages like unto:

 connections.o: In function `gzcon_write':

/home/rolf/Desktop/Rinst/R-3.2.0/src/main/connections.c:5469:
undefined
reference to `deflate'

There were also complaints about undefined references to inflate,
crc32,
deflateEnd, inflateEnd, inflateReset, inflateInit2_, deflateInit2_,
compress, uncompress, and zlibVersion, many of which were issued
repeatedly.
It finally gave up, saying:

 collect2: error: ld returned 1 exit status

A bit of googling informed me (I think?) that a workaround was to
configure using --without-system-pcre.  This however achieved nothing
in my
case.

Can anyone point me at what I need to do to fix this?  Install or
update
something?

I am running an (elderly, no-longer-supported) Fedora 17 Linux.

Thanks for any assistance.

PCRE (regular expressions) won't help you with compression algorithms...
If anything, it is  --without-system-xz, -zlib, -bzlib that would come
into
play, but it would be a better idea to ensure that you do have the
libraries
and headers installed.

I'm not completely up to speed on Fedora, but the order of the day is
that
you need to install some variation of lzma/zlib/bzlib and their
-dev/-devel
header files etc. Check appendix A.1 and A.2 of the R Installation and
Administration manual.

--
Technical Editor ANZJS
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276
Home phone: +64-9-480-4619

--
Technical Editor ANZJS
Department of Statistics
University of Auckland
Phone: +64-9-373-7599 ext. 88276
Home phone: +64-9-480-4619