> 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 ------------------------------------------------------------ Statistical Bioinformatics - Health CSIRO Mathematics, Informatics and Statistics Locked Bag 17, North Ryde, NSW 1670, Australia http://friendfeed.com/neilfws

Thanks to Martin for helping solve this problem. There was a "rogue" zlib.h in /usr/local/include on my system, in addition to the "correct" zlib.h in /usr/include. I think the former may be a result of installing the EMBOSS package. I moved the rogue copy and installation now works as normal. Neil Saunders -- Statistical Bioinformatics - Health CSIRO Mathematics, Informatics and Statistics Locked Bag 17, North Ryde, NSW 1670, Australia