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 ?affyio?, ?affy?, ?preprocessCore? trying URL 'http://bioconductor.org/packages/2.4/bioc/src/contrib/affyio_1.12.0.t ar.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 ?/tmp/RtmpGxu6pv/downloaded_packages? 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 Use *BSD because Linux is a patch for Linux

Hi Norbert, [I've cc'd the maintainer of affyio] On 1/14/10 1:57 AM, ngrundma wrote: > 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 Some suggestions below, but note that you are using rather old versions of gcc and R. Our build server uses gcc 4.3.2. The current release of R is 2.10.1. If you can, I would recommend upgrading R and then trying the installation again. But more below... > * Installing *source* package 'affyio' ... This is actually the package that you are having problems with, not lumi. > 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' > It looks like the problem is that Solaris is missing PTHREAD_STACK_MIN. Some digging suggests that there is a way to access this macro on Solaris with an appropriate compile time flag, perhaps __EXTENSIONS__, but perhaps one of _POSIX* defines would also work. This page has some details: http://wikis.sun.com/display/SolAppPro/Home I would try: Find you platform string: R --slave -e "R.version"|grep platform Create ~/.R/Makevars-R_PLATFORM, replacing R_PLATFORM with the value obtained above. I have: ~/.R/Makevars-i386-apple-darwin10.2.0 Inside this file add: CFLAGS=-D__EXTENSIONS__ Then try starting R and doing biocLite("affyio"). Let us know how it goes. There may be a way to make this less painful for the next Solaris user. + seth -- Seth Falcon Bioconductor Core Team | FHCRC