[BioC] Failure to install specific packages from Bioconductor on a Linux machine running R 2.3.1

[Michael Oldham]

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.tar.
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,
--