From ligges at statistik.uni-dortmund.de  Fri Sep 29 11:27:49 2006
From: ligges at statistik.uni-dortmund.de (Uwe Ligges)
Date: Fri, 29 Sep 2006 11:27:49 +0200
Subject: [Rd] Build error/zlib question
In-Reply-To: <451BF61E.47B0.00EE.0@med.umich.edu>
References: <451BF61E.47B0.00EE.0@med.umich.edu>
Message-ID: <451CE715.1090701@statistik.uni-dortmund.de>



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).

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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[Rd] Build error/zlib question
Uwe Ligges