Dear all, I have run into difficulty installing Bioconductor on a Linux machine running Fedora Core 5 (2.6.16-1.2133_FC5SMP). I have R version 2.3.1 installed and am trying to install version 1.8 of Bionconductor. After I type the following commands at the R prompt: >source("http://www.bioconductor.org/biocLite.R") >biocLite() I am told: Running getBioC version 0.1.6 with R version 2.3.1 Running biocinstall version 1.8.4 with R version 2.3.1 Your version of R requires version 1.8 of Bioconductor. Will install the following packages: (etc.........) Installation proceeds and all packages install successfully except for affyio, affy, matchprobes, gcrma, and affyPLM. It seems that all of these packages ultimately depend on affyio, so I tried installing that package by itself. I have pasted the errors resulting from that attempt below. Does anyone have any idea what might be causing this problem? Thanks very much for your help. ~ Mike O. > source("http://www.bioconductor.org/biocLite.R") > biocLite(c("affyio")) Running getBioC version 0.1.6 with R version 2.3.1 Running biocinstall version 1.8.4 with R version 2.3.1 Your version of R requires version 1.8 of Bioconductor. trying URL 'http://bioconductor.org/packages/1.8/bioc/src/contrib/affyio_1.0.0.ta r. gz' Content type 'application/x-gzip' length 55558 bytes opened URL ================================================== downloaded 54Kb * Installing *source* package 'affyio' ... creating cache ./config.cache checking how to run the C preprocessor... cc -E checking for main in -lz... no updating cache ./config.cache creating ./config.status creating src/Makevars ** libs gcc -I/usr/lib/R/include -I/usr/lib/R/include -I/usr/local/include -f pic -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack- pro tector --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic -fasync hronous-unwind-tables -c read_abatch.c -o read_abatch.o read_abatch.c:146:18: error: zlib.h: No such file or directory read_abatch.c: In function ?get_masks_outliers?: read_abatch.c:864: warning: unused variable ?cur_index? read_abatch.c: At top level: read_abatch.c:1169: error: expected declaration specifiers or ?...? before ?gzFile? read_abatch.c: In function ?ReadgzFileLine?: read_abatch.c:1170: warning: implicit declaration of function ?gzgets? read_abatch.c:1170: error: ?currentFile? undeclared (first use in this function)read_abatch.c:1170: error: (Each undeclared identifier is reported only once read_abatch.c:1170: error: for each function it appears in.) read_abatch.c:1170: warning: comparison between pointer and integer read_abatch.c: At top level: read_abatch.c:1190: error: expected ?=?, ?,?, ?;?, ?asm? or ?__attribute__? before ?open_gz_cel_file? read_abatch.c:1231: error: expected ?)? before ?my_file? read_abatch.c:1254: error: expected ?)? before ?my_file? read_abatch.c: In function ?check_gzcel_file?: read_abatch.c:1285: error: ?gzFile? undeclared (first use in this function) read_abatch.c:1285: error: expected ?;? before ?currentFile? read_abatch.c:1289: error: ?currentFile? undeclared (first use in this function)read_abatch.c:1289: warning: implicit declaration of function ?open_gz_cel_file?read_abatch.c:1292: warning: implicit declaration of function ?gzAdvanceToSection? read_abatch.c:1293: warning: implicit declaration of function ?gzfindStartsWith?read_abatch.c:1318: warning: implicit declaration of function ?gzclose? read_abatch.c: In function ?read_gzcel_file_intensities?: read_abatch.c:1346: error: ?gzFile? undeclared (first use in this function) read_abatch.c:1346: error: expected ?;? before ?currentFile? read_abatch.c:1351: error: ?currentFile? undeclared (first use in this function)read_abatch.c:1357: error: too many arguments to function ?ReadgzFileLine? read_abatch.c: In function ?read_gzcel_file_stddev?: read_abatch.c:1401: error: ?gzFile? undeclared (first use in this function) read_abatch.c:1401: error: expected ?;? before ?currentFile? read_abatch.c:1406: error: ?currentFile? undeclared (first use in this function)read_abatch.c:1412: error: too many arguments to function ?ReadgzFileLine? read_abatch.c: In function ?read_gzcel_file_npixels?: read_abatch.c:1460: error: ?gzFile? undeclared (first use in this function) read_abatch.c:1460: error: expected ?;? before ?currentFile? read_abatch.c:1465: error: ?currentFile? undeclared (first use in this function)read_abatch.c:1471: error: too many arguments to function ?ReadgzFileLine? read_abatch.c: In function ?gz_apply_masks?: read_abatch.c:1526: error: ?gzFile? undeclared (first use in this function) read_abatch.c:1526: error: expected ?;? before ?currentFile? read_abatch.c:1535: error: ?currentFile? undeclared (first use in this function)read_abatch.c:1548: error: too many arguments to function ?ReadgzFileLine? read_abatch.c:1572: error: too many arguments to function ?ReadgzFileLine? read_abatch.c: In function ?gz_get_header_info?: read_abatch.c:1606: error: ?gzFile? undeclared (first use in this function) read_abatch.c:1606: error: expected ?;? before ?currentFile? read_abatch.c:1610: error: ?currentFile? undeclared (first use in this function)read_abatch.c: In function ?gz_get_detailed_header_info?: read_abatch.c:1664: error: ?gzFile? undeclared (first use in this function) read_abatch.c:1664: error: ?currentFile? undeclared (first use in this function)read_abatch.c: In function ?gz_get_masks_outliers?: read_abatch.c:1773: error: ?gzFile? undeclared (first use in this function) read_abatch.c:1773: error: ?currentFile? undeclared (first use in this function)read_abatch.c:1798: error: too many arguments to function ?ReadgzFileLine? read_abatch.c:1826: error: too many arguments to function ?ReadgzFileLine? read_abatch.c:1775: warning: unused variable ?cur_index? read_abatch.c: In function ?isgzTextCelFile?: read_abatch.c:1869: error: ?gzFile? undeclared (first use in this function) read_abatch.c:1869: error: expected ?;? before ?currentFile? read_abatch.c:1871: error: ?currentFile? undeclared (first use in this function)read_abatch.c:1871: warning: implicit declaration of function ?gzopen? read_abatch.c:1876: error: too many arguments to function ?ReadgzFileLine? read_abatch.c: In function ?fread_char?: read_abatch.c:2104: warning: unused variable ?i? read_abatch.c: In function ?binary_get_detailed_header_info?: read_abatch.c:2384: warning: unused variable ?cdfName? read_abatch.c: In function ?binary_get_masks_outliers?: read_abatch.c:2781: warning: unused variable ?cur_index? read_abatch.c: In function ?ReadHeader?: read_abatch.c:3027: warning: unused variable ?cel_dimensions_names? read_abatch.c: In function ?R_read_cel_file?: read_abatch.c:3872: warning: unused variable ?myCEL? read_abatch.c:3877: warning: control reaches end of non-void function read_abatch.c: In function ?read_cel_file?: read_abatch.c:3854: warning: control reaches end of non-void function make: *** [read_abatch.o] Error 1 chmod: cannot access `/usr/lib/R/library/affyio/libs/*': No such file or directory ERROR: compilation failed for package 'affyio' ** Removing '/usr/lib/R/library/affyio' The downloaded packages are in /tmp/RtmptiX4zb/downloaded_packages Warning message: installation of package 'affyio' had non-zero exit status in: install.packages(pkgs = pkgs, repos = repos, dependencies = dependencies, --

On Tue, 13 Jun 2006, Michael Oldham wrote: ... > checking for main in -lz... no ... > read_abatch.c:146:18: error: zlib.h: No such file or directory Try to install zlib rpm first and see what happens next. Regards, Zong-Pei