From jmacdon at med.umich.edu  Fri Sep 29 15:38:52 2006
From: jmacdon at med.umich.edu (James W. MacDonald)
Date: Fri, 29 Sep 2006 09:38:52 -0400
Subject: [Rd] Build error/zlib question
In-Reply-To: <Pine.LNX.4.64.0609291143430.19030@gannet.stats.ox.ac.uk>
References: <451BF61E.47B0.00EE.0@med.umich.edu>
	<451CE715.1090701@statistik.uni-dortmund.de>
	<Pine.LNX.4.64.0609291143430.19030@gannet.stats.ox.ac.uk>
Message-ID: <451D21EC.6090107@med.umich.edu>

Prof Brian Ripley wrote:
> 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.

Thank you for the hint. This does allow the package to build.

> 
> 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.

I made no claim for this package building on an installed version; if 
you read the sentence right after the one you quote, you will notice 
that I state both versions of R were compiled from source.

> 
> 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!

Thanks for the advice. When I get the chance I will look into supplying 
such an animal with the package.

Best,

Jim


> 
>> 
>> 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
>>> 
>>> 
>>> ********************************************************** 
>>> Electronic Mail is not secure, may not be read every day, and
>>> should not be used for urgent or sensitive issues.
>>> 
>>> ______________________________________________ 
>>> R-devel at r-project.org mailing list 
>>> https://stat.ethz.ch/mailman/listinfo/r-devel
>> 
>> 
>> ______________________________________________ 
>> R-devel at r-project.org mailing list 
>> https://stat.ethz.ch/mailman/listinfo/r-devel
>> 
> 


-- 
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


**********************************************************
Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues.




[Rd] Build error/zlib question
James W. MacDonald