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affyio 1.6.0
Benjamin Milo Bolstad
Last Changed Date: 2007-10-02 17:41:09 -0700
Last Changed Rev: 27709
lamb1 Linux (SUSE 10.1) x86_64  OK  OK 
wellington Linux (SUSE 9.2) i686  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) x64  OK  OK  OK 
pitt Mac OS X (10.4.10) i386  OK  OK [ OK ]
Package: affyio
Version: 1.6.0
Command: /Users/biocbuild/BBS/utils/build-universal.sh affyio_1.6.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R affyio.buildbin-libdir
RetCode: 0
Time: 20.4 seconds
Status: OK
PackageFile: affyio_1.6.0.tgz

Command output

                    INSTALLATION WITH 'R CMD INSTALL affyio_1.6.0.tar.gz'

* Installing to library 'affyio.buildbin-libdir'
* Installing *source* package 'affyio' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
** arch - i386
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DHAVE_ZLIB=1  -msse3    -fPIC  -g -O2 -Wall -march=nocona -c fread_functions.c -o fread_functions.o
fread_functions.c:301: warning: 'swap_uint_32' defined but not used
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DHAVE_ZLIB=1  -msse3    -fPIC  -g -O2 -Wall -march=nocona -c read_abatch.c -o read_abatch.o
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DHAVE_ZLIB=1  -msse3    -fPIC  -g -O2 -Wall -march=nocona -c read_bpmap.c -o read_bpmap.o
read_bpmap.c: In function 'ReadBPMAPHeader':
read_bpmap.c:76: warning: unused variable 'version_number_int'
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DHAVE_ZLIB=1  -msse3    -fPIC  -g -O2 -Wall -march=nocona -c read_cdf_xda.c -o read_cdf_xda.o
read_cdf_xda.c: In function 'isPM':
read_cdf_xda.c:614: warning: implicit declaration of function 'toupper'
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DHAVE_ZLIB=1  -msse3    -fPIC  -g -O2 -Wall -march=nocona -c read_cdffile2.c -o read_cdffile2.o
read_cdffile2.c:363: warning: 'token_ends_with' defined but not used
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DHAVE_ZLIB=1  -msse3    -fPIC  -g -O2 -Wall -march=nocona -c read_celfile_generic.c -o read_celfile_generic.o
read_celfile_generic.c: In function 'read_genericcel_file_intensities':
read_celfile_generic.c:591: warning: unused variable 'fread_err'
read_celfile_generic.c:589: warning: unused variable 'cur_index'
read_celfile_generic.c:588: warning: unused variable 'j'
read_celfile_generic.c: In function 'read_genericcel_file_stddev':
read_celfile_generic.c:641: warning: unused variable 'fread_err'
read_celfile_generic.c:639: warning: unused variable 'cur_index'
read_celfile_generic.c:638: warning: unused variable 'j'
read_celfile_generic.c: In function 'read_genericcel_file_npixels':
read_celfile_generic.c:695: warning: unused variable 'fread_err'
read_celfile_generic.c:693: warning: unused variable 'cur_index'
read_celfile_generic.c:692: warning: unused variable 'j'
read_celfile_generic.c: In function 'generic_get_masks_outliers':
read_celfile_generic.c:757: warning: unused variable 'fread_err'
read_celfile_generic.c:755: warning: unused variable 'cur_index'
read_celfile_generic.c:754: warning: unused variable 'j'
read_celfile_generic.c: In function 'generic_apply_masks':
read_celfile_generic.c:849: warning: unused variable 'fread_err'
read_celfile_generic.c:843: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzread_genericcel_file_intensities':
read_celfile_generic.c:1488: warning: unused variable 'fread_err'
read_celfile_generic.c:1486: warning: unused variable 'cur_index'
read_celfile_generic.c:1485: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzread_genericcel_file_stddev':
read_celfile_generic.c:1539: warning: unused variable 'fread_err'
read_celfile_generic.c:1537: warning: unused variable 'cur_index'
read_celfile_generic.c:1536: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzread_genericcel_file_npixels':
read_celfile_generic.c:1593: warning: unused variable 'fread_err'
read_celfile_generic.c:1591: warning: unused variable 'cur_index'
read_celfile_generic.c:1590: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzgeneric_get_masks_outliers':
read_celfile_generic.c:1658: warning: unused variable 'fread_err'
read_celfile_generic.c:1656: warning: unused variable 'cur_index'
read_celfile_generic.c:1655: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzgeneric_apply_masks':
read_celfile_generic.c:1750: warning: unused variable 'fread_err'
read_celfile_generic.c:1744: warning: unused variable 'j'
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DHAVE_ZLIB=1  -msse3    -fPIC  -g -O2 -Wall -march=nocona -c read_generic.c -o read_generic.o
read_generic.c: In function 'determine_MIMETYPE':
read_generic.c:389: warning: control reaches end of non-void function
gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o affyio.so fread_functions.o read_abatch.o read_bpmap.o read_cdf_xda.o read_cdffile2.o read_celfile_generic.o read_generic.o -lz   -F/Library/Frameworks/R.framework/.. -framework R 
** R
** preparing package for lazy loading
** help
 >>> Building/Updating help pages for package 'affyio'
     Formats: text html latex example 
  check.cdf.type                    text    html    latex
  read.cdffile.list                 text    html    latex
  read.celfile                      text    html    latex
  read.celfile.header               text    html    latex
  read.celfile.probeintensity.matri text    html    latex
** building package indices ...
* DONE (affyio)

                    INSTALLATION OF ppc LIBS WITH 'R_ARCH=/ppc R CMD INSTALL --libs-only affyio_1.6.0.tar.gz'

* Installing to library 'affyio.buildbin-libdir'
* Installing *source* package 'affyio' ...
creating cache ./config.cache
checking how to run the C preprocessor... cc -E
checking for main in -lz... yes
checking for zlib.h... yes
checking if zlib version >= 1.1.3... yes
updating cache ./config.cache
creating ./config.status
creating src/Makevars
** libs
** arch - ppc
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -DHAVE_ZLIB=1  -I/usr/local/include    -fPIC  -g -O2 -Wall -c fread_functions.c -o fread_functions.o
fread_functions.c:301: warning: 'swap_uint_32' defined but not used
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -DHAVE_ZLIB=1  -I/usr/local/include    -fPIC  -g -O2 -Wall -c read_abatch.c -o read_abatch.o
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -DHAVE_ZLIB=1  -I/usr/local/include    -fPIC  -g -O2 -Wall -c read_bpmap.c -o read_bpmap.o
read_bpmap.c: In function 'ReadBPMAPHeader':
read_bpmap.c:77: warning: unused variable 'unsigned_version_number_int'
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -DHAVE_ZLIB=1  -I/usr/local/include    -fPIC  -g -O2 -Wall -c read_cdf_xda.c -o read_cdf_xda.o
read_cdf_xda.c: In function 'isPM':
read_cdf_xda.c:614: warning: implicit declaration of function 'toupper'
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -DHAVE_ZLIB=1  -I/usr/local/include    -fPIC  -g -O2 -Wall -c read_cdffile2.c -o read_cdffile2.o
read_cdffile2.c:363: warning: 'token_ends_with' defined but not used
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -DHAVE_ZLIB=1  -I/usr/local/include    -fPIC  -g -O2 -Wall -c read_celfile_generic.c -o read_celfile_generic.o
read_celfile_generic.c: In function 'read_genericcel_file_intensities':
read_celfile_generic.c:591: warning: unused variable 'fread_err'
read_celfile_generic.c:589: warning: unused variable 'cur_index'
read_celfile_generic.c:588: warning: unused variable 'j'
read_celfile_generic.c: In function 'read_genericcel_file_stddev':
read_celfile_generic.c:641: warning: unused variable 'fread_err'
read_celfile_generic.c:639: warning: unused variable 'cur_index'
read_celfile_generic.c:638: warning: unused variable 'j'
read_celfile_generic.c: In function 'read_genericcel_file_npixels':
read_celfile_generic.c:695: warning: unused variable 'fread_err'
read_celfile_generic.c:693: warning: unused variable 'cur_index'
read_celfile_generic.c:692: warning: unused variable 'j'
read_celfile_generic.c: In function 'generic_get_masks_outliers':
read_celfile_generic.c:757: warning: unused variable 'fread_err'
read_celfile_generic.c:755: warning: unused variable 'cur_index'
read_celfile_generic.c:754: warning: unused variable 'j'
read_celfile_generic.c: In function 'generic_apply_masks':
read_celfile_generic.c:849: warning: unused variable 'fread_err'
read_celfile_generic.c:843: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzread_genericcel_file_intensities':
read_celfile_generic.c:1488: warning: unused variable 'fread_err'
read_celfile_generic.c:1486: warning: unused variable 'cur_index'
read_celfile_generic.c:1485: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzread_genericcel_file_stddev':
read_celfile_generic.c:1539: warning: unused variable 'fread_err'
read_celfile_generic.c:1537: warning: unused variable 'cur_index'
read_celfile_generic.c:1536: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzread_genericcel_file_npixels':
read_celfile_generic.c:1593: warning: unused variable 'fread_err'
read_celfile_generic.c:1591: warning: unused variable 'cur_index'
read_celfile_generic.c:1590: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzgeneric_get_masks_outliers':
read_celfile_generic.c:1658: warning: unused variable 'fread_err'
read_celfile_generic.c:1656: warning: unused variable 'cur_index'
read_celfile_generic.c:1655: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzgeneric_apply_masks':
read_celfile_generic.c:1750: warning: unused variable 'fread_err'
read_celfile_generic.c:1744: warning: unused variable 'j'
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -DHAVE_ZLIB=1  -I/usr/local/include    -fPIC  -g -O2 -Wall -c read_generic.c -o read_generic.o
read_generic.c: In function 'determine_MIMETYPE':
read_generic.c:389: warning: control reaches end of non-void function
gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o affyio.so fread_functions.o read_abatch.o read_bpmap.o read_cdf_xda.o read_cdffile2.o read_celfile_generic.o read_generic.o -lz   -F/Library/Frameworks/R.framework/.. -framework R 
* DONE (affyio)