[BioC] Error compiling affyio - undefined symbol: egzread

Neil Saunders neil.saunders at csiro.au
Tue May 11 04:33:10 CEST 2010 

> I think it would help to post the entire transcript here; I think you
> have a (non-standard) libz somewhere in your system. The headers are

Thanks for the reply Martin - complete log is posted below.  I ran 
ldconfig, seems that zlib is detected OK, so I'm unsure where the 
problem lies.  Other packages (including several from Bioconductor) 
installed without error.

Neil

--------------------------------------------------
 > source("http://www.bioconductor.org/biocLite.R")
BioC_mirror = http://www.bioconductor.org
Change using chooseBioCmirror().
 > biocLite("affyio")
Using R version 2.11.0, biocinstall version 2.6.7.
Installing Bioconductor version 2.6 packages:
[1] "affyio"
Please wait...

Warning in install.packages(pkgs = pkgs, repos = repos, ...) :
   argument 'lib' is missing: using 
'/home/sau103/R/i486-pc-linux-gnu-library/2.11'
trying URL 
'http://www.bioconductor.org/packages/2.6/bioc/src/contrib/affyio_1.16.0.tar.gz'
Content type 'application/x-gzip' length 107863 bytes (105 Kb)
opened URL
==================================================
downloaded 105 Kb

* installing *source* package ‘affyio’ ...
checking for gcc... gcc-4.4
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc-4.4 accepts -g... yes
checking for gcc-4.4 option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc-4.4 -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking for main in -lz... yes
checking zlib.h usability... yes
checking zlib.h presence... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
checking for pthread_create in -lpthread... yes
checking if we can use pthreads... yes
checking if PTHREAD_STACK_MIN is defined... yes
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/usr/share/R/include -DPACKAGE_NAME=\"\" 
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
-DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 
-DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 
-DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 
-DUSE_PTHREADS=1    -g -O2   -fpic  -g -O2 -c fread_functions.c -o 
fread_functions.o
gcc -std=gnu99 -I/usr/share/R/include -DPACKAGE_NAME=\"\" 
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
-DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 
-DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 
-DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 
-DUSE_PTHREADS=1    -g -O2   -fpic  -g -O2 -c read_abatch.c -o read_abatch.o
gcc -std=gnu99 -I/usr/share/R/include -DPACKAGE_NAME=\"\" 
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
-DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 
-DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 
-DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 
-DUSE_PTHREADS=1    -g -O2   -fpic  -g -O2 -c read_bpmap.c -o read_bpmap.o
gcc -std=gnu99 -I/usr/share/R/include -DPACKAGE_NAME=\"\" 
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
-DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 
-DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 
-DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 
-DUSE_PTHREADS=1    -g -O2   -fpic  -g -O2 -c read_cdf_xda.c -o 
read_cdf_xda.o
gcc -std=gnu99 -I/usr/share/R/include -DPACKAGE_NAME=\"\" 
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
-DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 
-DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 
-DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 
-DUSE_PTHREADS=1    -g -O2   -fpic  -g -O2 -c read_cdffile2.c -o 
read_cdffile2.o
gcc -std=gnu99 -I/usr/share/R/include -DPACKAGE_NAME=\"\" 
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
-DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 
-DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 
-DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 
-DUSE_PTHREADS=1    -g -O2   -fpic  -g -O2 -c read_celfile_generic.c -o 
read_celfile_generic.o
gcc -std=gnu99 -I/usr/share/R/include -DPACKAGE_NAME=\"\" 
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
-DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 
-DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 
-DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 
-DUSE_PTHREADS=1    -g -O2   -fpic  -g -O2 -c read_clf.c -o read_clf.o
gcc -std=gnu99 -I/usr/share/R/include -DPACKAGE_NAME=\"\" 
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
-DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 
-DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 
-DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 
-DUSE_PTHREADS=1    -g -O2   -fpic  -g -O2 -c read_generic.c -o 
read_generic.o
gcc -std=gnu99 -I/usr/share/R/include -DPACKAGE_NAME=\"\" 
-DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" 
-DPACKAGE_BUGREPORT=\"\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 
-DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 
-DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 
-DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DHAVE_ZLIB=1 -DHAVE_LIBPTHREAD=1 
-DUSE_PTHREADS=1    -g -O2   -fpic  -g -O2 -c read_pgf.c -o read_pgf.o
read_pgf.c: In function ‘pgf_count_probeset_types’:
read_pgf.c:1265: warning: assignment from incompatible pointer type
gcc -std=gnu99 -shared -o affyio.so fread_functions.o read_abatch.o 
read_bpmap.o read_cdf_xda.o read_cdffile2.o read_celfile_generic.o 
read_clf.o read_generic.o read_pgf.o -lpthread -lz -lpthread 
-L/usr/lib/R/lib -lR
installing to /home/sau103/R/i486-pc-linux-gnu-library/2.11/affyio/libs
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Error in dyn.load(file, DLLpath = DLLpath, ...) :
   unable to load shared library 
'/home/sau103/R/i486-pc-linux-gnu-library/2.11/affyio/libs/affyio.so':
   /home/sau103/R/i486-pc-linux-gnu-library/2.11/affyio/libs/affyio.so: 
undefined symbol: egzread
ERROR: loading failed
* removing ‘/home/sau103/R/i486-pc-linux-gnu-library/2.11/affyio’

The downloaded packages are in
	‘/tmp/RtmpOj28OT/downloaded_packages’
Warning message:
In install.packages(pkgs = pkgs, repos = repos, ...) :
   installation of package 'affyio' had non-zero exit status

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