[BioC] Problems compiling lumi on Solaris Sparc and R 2.9.0

[ngrundma]

Hello,

I am new to R and bioconductor and only want to compile some 
bioconductor packages on a Solaris 10 Sparc system.  I am using gcc 3.4.6.
I searched for a solution, but have not found something that really 
helps.  Packages like beadarray work, but compiling lumi gave me 
following output:

-- snip --
R version 2.9.0 (2009-04-17)
Copyright (C) 2009 The R Foundation for Statistical Computing
ISBN 3-900051-07-0

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

 > source("http://bioconductor.org/biocLite.R")
 > biocLite("lumi")
Using R version 2.9.0, biocinstall version 2.4.13.
Installing Bioconductor version 2.4 packages:
[1] "lumi"
Please wait...

also installing the dependencies âaffyioâ, âaffyâ, âpreprocessCoreâ

trying URL 
'http://bioconductor.org/packages/2.4/bioc/src/contrib/affyio_1.12.0.tar.gz'
Content type 'application/x-gzip' length 106183 bytes (103 Kb)
opened URL
==================================================

...

* Installing *source* package 'affyio' ...
checking for gcc... gcc
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 accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /usr/sfw/bin/ggrep
checking for egrep... /usr/sfw/bin/ggrep -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
configure: creating ./config.status
config.status: creating src/Makevars
** libs
gcc -std=gnu99 -I/usr/local/lib/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 -I/usr/local/include -I/usr/local/ssl/include 
-I/usr/local/pgsql/include -I/usr/local/include/ncurses 
-I/usr/openwin/include -I/usr/local/rrdtool-1.2.19/include   -g -O2 
-fPIC  -O2 -L/usr/local/pgsql/lib -R/usr/local/pgsql/lib 
-L/usr/local/lib -R/usr/local/lib -L/usr/local/ssl/lib 
-R/usr/local/ssl/lib -L/usr/openwin/lib -R/usr/openwin/lib 
-I/usr/local/rrdtool-1.2.19/include -c fread_functions.c -o 
fread_functions.o
gcc -std=gnu99 -I/usr/local/lib/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 -I/usr/local/include -I/usr/local/ssl/include 
-I/usr/local/pgsql/include -I/usr/local/include/ncurses 
-I/usr/openwin/include -I/usr/local/rrdtool-1.2.19/include   -g -O2 
-fPIC  -O2 -L/usr/local/pgsql/lib -R/usr/local/pgsql/lib 
-L/usr/local/lib -R/usr/local/lib -L/usr/local/ssl/lib 
-R/usr/local/ssl/lib -L/usr/openwin/lib -R/usr/openwin/lib 
-I/usr/local/rrdtool-1.2.19/include -c read_abatch.c -o read_abatch.o
read_abatch.c: In function `read_probeintensities':
read_abatch.c:4421: error: `PTHREAD_STACK_MIN' undeclared (first use in 
this function)
read_abatch.c:4421: error: (Each undeclared identifier is reported only once
read_abatch.c:4421: error: for each function it appears in.)
*** Error code 1
make: Fatal error: Command failed for target `read_abatch.o'
ERROR: compilation failed for package 'affyio'
* Removing '/local/usr/local/lib/R/library/affyio'

...

  Vignettes contain introductory material. To view, type
  'openVignette()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation(pkgname)'.

Warning in library(pkg, character.only = TRUE, logical.return = TRUE, 
lib.loc = lib.loc) :
  there is no package called 'affy'
Error : package 'affy' could not be loaded
ERROR: lazy loading failed for package 'lumi'
* Removing '/local/usr/local/lib/R/library/lumi'

The downloaded packages are in
        â/tmp/RtmpGxu6pv/downloaded_packagesâ
Updating HTML index of packages in '.Library'
Warning messages:
1: In install.packages(pkgs = pkgs, repos = repos, dependencies = 
dependencies,  :
  installation of package 'affyio' had non-zero exit status
2: In install.packages(pkgs = pkgs, repos = repos, dependencies = 
dependencies,  :
  installation of package 'preprocessCore' had non-zero exit status
3: In install.packages(pkgs = pkgs, repos = repos, dependencies = 
dependencies,  :
  installation of package 'affy' had non-zero exit status
4: In install.packages(pkgs = pkgs, repos = repos, dependencies = 
dependencies,  :
  installation of package 'lumi' had non-zero exit status
-- snip --

Is there anyone who had the same (or similar) problem and has a hint how 
to avoid it?

Many thanks, Norbert

-- 
Institute of Bioinformatics
Faculty of Medicine
University of Muenster, Germany
fax: +49-251-8353005
phone: +49-251-8353007

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