affyio 1.10.1
Benjamin Milo Bolstad
| Bioconductor Changelog | | Snapshot Date: 2009-04-18 11:27:48 -0700 (Sat, 18 Apr 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_3/madman/Rpacks/affyio | | Last Changed Rev: 34993 / Revision: 38965 | | Last Changed Date: 2008-10-30 10:29:17 -0700 (Thu, 30 Oct 2008) |
| wilson2 | Linux (openSUSE 11.1) / x86_64 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | WARNINGS | OK |
| pelham | Mac OS X Leopard (10.5.6) / i386 | OK | [ WARNINGS ] | OK |
* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.3-bioc/meat/affyio.Rcheck'
* using R version 2.8.1 Patched (2009-03-18 r48200)
* using session charset: ASCII
* checking for file 'affyio/DESCRIPTION' ... OK
* this is package 'affyio' version '1.10.1'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'affyio' can be installed ... WARNING
Found the following significant warnings:
WARNING: found \itemize inside \value in file 'check.cdf.type.Rd'
See '/Users/biocbuild/bbs-2.3-bioc/meat/affyio.Rcheck/00install.out' for details.
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable compilation flags in Makevars ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating affyio-Ex.R ... OK
* checking examples ... OK
* creating affyio-manual.tex ... OK
* checking affyio-manual.tex using pdflatex ... OK
WARNING: There was 1 warning, see
/Users/biocbuild/bbs-2.3-bioc/meat/affyio.Rcheck/00check.log
for details
* 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/bin/grep
checking for egrep... /usr/bin/grep -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
** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -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 -g -O2 -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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -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 -g -O2 -fPIC -g -O2 -Wall -c read_abatch.c -o read_abatch.o
read_abatch.c: In function 'readfile_group':
read_abatch.c:4338: warning: unused variable 'Current_intensity'
read_abatch.c: In function 'checkFileCDF_group':
read_abatch.c:4356: warning: control reaches end of non-void function
read_abatch.c: In function 'readfile_group':
read_abatch.c:4347: warning: control reaches end of non-void function
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -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 -g -O2 -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 'version_number_int'
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -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 -g -O2 -fPIC -g -O2 -Wall -c read_cdf_xda.c -o read_cdf_xda.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -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 -g -O2 -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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -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 -g -O2 -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:697: warning: unused variable 'fread_err'
read_celfile_generic.c:695: warning: unused variable 'cur_index'
read_celfile_generic.c:694: warning: unused variable 'j'
read_celfile_generic.c: In function 'read_genericcel_file_stddev':
read_celfile_generic.c:747: warning: unused variable 'fread_err'
read_celfile_generic.c:745: warning: unused variable 'cur_index'
read_celfile_generic.c:744: warning: unused variable 'j'
read_celfile_generic.c: In function 'read_genericcel_file_npixels':
read_celfile_generic.c:801: warning: unused variable 'fread_err'
read_celfile_generic.c:799: warning: unused variable 'cur_index'
read_celfile_generic.c:798: warning: unused variable 'j'
read_celfile_generic.c: In function 'generic_get_masks_outliers':
read_celfile_generic.c:863: warning: unused variable 'fread_err'
read_celfile_generic.c:861: warning: unused variable 'cur_index'
read_celfile_generic.c:860: warning: unused variable 'j'
read_celfile_generic.c: In function 'generic_apply_masks':
read_celfile_generic.c:955: warning: unused variable 'fread_err'
read_celfile_generic.c:949: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzread_genericcel_file_intensities':
read_celfile_generic.c:1689: warning: unused variable 'fread_err'
read_celfile_generic.c:1687: warning: unused variable 'cur_index'
read_celfile_generic.c:1686: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzread_genericcel_file_stddev':
read_celfile_generic.c:1740: warning: unused variable 'fread_err'
read_celfile_generic.c:1738: warning: unused variable 'cur_index'
read_celfile_generic.c:1737: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzread_genericcel_file_npixels':
read_celfile_generic.c:1794: warning: unused variable 'fread_err'
read_celfile_generic.c:1792: warning: unused variable 'cur_index'
read_celfile_generic.c:1791: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzgeneric_get_masks_outliers':
read_celfile_generic.c:1859: warning: unused variable 'fread_err'
read_celfile_generic.c:1857: warning: unused variable 'cur_index'
read_celfile_generic.c:1856: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzgeneric_apply_masks':
read_celfile_generic.c:1951: warning: unused variable 'fread_err'
read_celfile_generic.c:1945: warning: unused variable 'j'
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -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 -g -O2 -fPIC -g -O2 -Wall -c read_clf.c -o read_clf.o
read_clf.c: In function 'read_clf_header':
read_clf.c:557: warning: unused variable 'i'
read_clf.c: At top level:
read_clf.c:292: warning: 'token_ends_with' defined but not used
read_clf.c:389: warning: 'IsCommentLine' defined but not used
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -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 -g -O2 -fPIC -g -O2 -Wall -c read_generic.c -o read_generic.o
read_generic.c: In function 'determine_MIMETYPE':
read_generic.c:398: warning: control reaches end of non-void function
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include -I/Library/Frameworks/R.framework/Versions/2.8/Resources/include/i386 -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 -g -O2 -fPIC -g -O2 -Wall -c read_pgf.c -o read_pgf.o
read_pgf.c: In function 'read_pgf_header':
read_pgf.c:901: warning: unused variable 'i'
read_pgf.c: In function 'insert_level0':
read_pgf.c:1167: warning: unused variable 'temp_ptr'
read_pgf.c: In function 'pgf_count_probeset_types':
read_pgf.c:1265: warning: assignment from incompatible pointer type
read_pgf.c: At top level:
read_pgf.c:363: warning: 'token_ends_with' defined but not used
gcc-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -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_clf.o read_generic.o read_pgf.o -lpthread -lz -lpthread -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** R
** preparing package for lazy loading
** help
>>> Building/Updating help pages for package 'affyio'
Formats: text html latex example
WARNING: found \itemize inside \value in file 'check.cdf.type.Rd'
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)