[Rd] Build error/zlib question

From: James MacDonald <jmacdon_at_med.umich.edu>
Date: Thu 28 Sep 2006 - 20:21:41 GMT


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.

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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