Re: [Rd] Build error/zlib question

From: Prof Brian Ripley <ripley_at_stats.ox.ac.uk>
Date: Fri 29 Sep 2006 - 10:48:46 GMT

On Fri, 29 Sep 2006, Uwe Ligges wrote:

>
>
> James MacDonald wrote:
>> Hi,
>>
>> I am unable to build a package I maintain using a relatively current
>> build of R-2.4.0 alpha, whereas the package builds just fine on R-2.3.1.
>> Both versions of R were built from source. I'm hoping a guRu might be
>> able to give some help.

>
> The entry points are no longer exported, you probably have to specify
> the zlib header files (which reside in R/src/extra/zlib).

I think Uwe meant to say '-L$(RHOME)/src/extra/zlib -lz' is needed in PKG_LIBS. Note that this package would not build in an installed version of R, so it did not 'builds just fine on R-2.3.1' as claimed.

However, this is all against the advice of 'Writing R Extensions', and the change is documented in the CHANGES file. What you should really do is to supply your own zlib compiled to your own requirements. If you make use of private entry points, expect self-imposed trouble!

>
> Uwe Ligges
>
>
>> Some snippets from the build process:
>>
>> R-2.3.1
>>
>> making DLL ...
>> gcc -Ic:/R-2.3.1/src/extra/zlib -DHAVE_ZLIB -Ic:/R-2.3.1/include -Wall
>> -O2 -c read_cdffile.c -o read_cdffile.o
>> read_cdffile.c: In function `readQC':
>> read_cdffile.c:565: warning: unused variable `param_unit'
>> windres --include-dir c:/R-2.3.1/include -i makecdfenv_res.rc -o
>> makecdfenv_res.o
>> gcc -shared -s -o makecdfenv.dll makecdfenv.def read_cdffile.o
>> makecdfenv_res.o -Lc:/R-2.3.1/bin -lR
>> ... DLL made
>>
>> R-2.4.0 beta
>>
>> making DLL ...
>> gcc -Ic:/rw2040dev/src/extra/zlib -DHAVE_ZLIB -Ic:/rw2040dev/include
>> -Wall -O2 -std=gnu99 -c read_cdffile.c -o read_cdffile.o
>> read_cdffile.c: In function `readQC':
>> read_cdffile.c:565: warning: unused variable `param_unit'
>> windres --include-dir c:/rw2040dev/include -i makecdfenv_res.rc -o
>> makecdfenv_res.o
>> gcc -shared -s -o makecdfenv.dll makecdfenv.def read_cdffile.o
>> makecdfenv_res.o -Lc:/rw2040dev/bin -lR
>> read_cdffile.o:read_cdffile.c:(.text+0x42): undefined reference to
>> `gzgets'
>> read_cdffile.o:read_cdffile.c:(.text+0xf3): undefined reference to
>> `gzopen'
>> read_cdffile.o:read_cdffile.c:(.text+0x10f): undefined reference to
>> `gzgets'
>> read_cdffile.o:read_cdffile.c:(.text+0x140): undefined reference to
>> `gzrewind'
>> read_cdffile.o:read_cdffile.c:(.text+0x177): undefined reference to
>> `gzclose'
>> collect2: ld returned 1 exit status
>> make[3]: *** [makecdfenv.dll] Error 1
>> make[2]: *** [srcDynlib] Error 2
>> make[1]: *** [all] Error 2
>> make: *** [pkg-makecdfenv] Error 2
>>
>>> version
>> _
>> platform i386-pc-mingw32
>> arch i386
>> os mingw32
>> system i386, mingw32
>> status alpha
>> major 2
>> minor 4.0
>> year 2006
>> month 09
>> day 10
>> svn rev 39242
>> language R
>> version.string R version 2.4.0 alpha (2006-09-10 r39242)
>>
>> TIA,
>>
>> Jim
>>
>> James W. MacDonald, M.S.
>> Biostatistician
>> Affymetrix and cDNA Microarray Core
>> University of Michigan Cancer Center
>> 1500 E. Medical Center Drive
>> 7410 CCGC
>> Ann Arbor MI 48109
>> 734-647-5623
>>
>>
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>
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-- 
Brian D. Ripley,                  ripley@stats.ox.ac.uk
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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Received on Fri Sep 29 20:51:37 2006

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