affyio 1.6.1
Benjamin Milo Bolstad
| Snapshot Date: 2008-04-09 12:13:20 -0700 (Wed, 09 Apr 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_1/madman/Rpacks/affyio | | Last Changed Rev: 27950 / Revision: 30966 | | Last Changed Date: 2007-10-11 19:26:19 -0700 (Thu, 11 Oct 2007) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | OK | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | OK | OK | |
| wellington | Linux (openSUSE 10.3) / i686 | OK | [ OK ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| lemming | Windows Server 2003 (32-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
* checking for working latex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.1-bioc/meat/affyio.Rcheck'
* using R version 2.6.2 (2008-02-08)
* checking for file 'affyio/DESCRIPTION' ... OK
* this is package 'affyio' version '1.6.1'
* 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 ... OK
* 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 ... OK
* 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
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include -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 -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include -DHAVE_ZLIB=1 -I/usr/local/include -fpic -g -O2 -Wall -c read_abatch.c -o read_abatch.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include -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:76: warning: unused variable 'version_number_int'
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include -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 -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include -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 -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include -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:599: warning: unused variable 'fread_err'
read_celfile_generic.c:597: warning: unused variable 'cur_index'
read_celfile_generic.c:596: warning: unused variable 'j'
read_celfile_generic.c: In function 'read_genericcel_file_stddev':
read_celfile_generic.c:649: warning: unused variable 'fread_err'
read_celfile_generic.c:647: warning: unused variable 'cur_index'
read_celfile_generic.c:646: warning: unused variable 'j'
read_celfile_generic.c: In function 'read_genericcel_file_npixels':
read_celfile_generic.c:703: warning: unused variable 'fread_err'
read_celfile_generic.c:701: warning: unused variable 'cur_index'
read_celfile_generic.c:700: warning: unused variable 'j'
read_celfile_generic.c: In function 'generic_get_masks_outliers':
read_celfile_generic.c:765: warning: unused variable 'fread_err'
read_celfile_generic.c:763: warning: unused variable 'cur_index'
read_celfile_generic.c:762: warning: unused variable 'j'
read_celfile_generic.c: In function 'generic_apply_masks':
read_celfile_generic.c:857: warning: unused variable 'fread_err'
read_celfile_generic.c:851: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzread_genericcel_file_intensities':
read_celfile_generic.c:1496: warning: unused variable 'fread_err'
read_celfile_generic.c:1494: warning: unused variable 'cur_index'
read_celfile_generic.c:1493: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzread_genericcel_file_stddev':
read_celfile_generic.c:1547: warning: unused variable 'fread_err'
read_celfile_generic.c:1545: warning: unused variable 'cur_index'
read_celfile_generic.c:1544: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzread_genericcel_file_npixels':
read_celfile_generic.c:1601: warning: unused variable 'fread_err'
read_celfile_generic.c:1599: warning: unused variable 'cur_index'
read_celfile_generic.c:1598: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzgeneric_get_masks_outliers':
read_celfile_generic.c:1666: warning: unused variable 'fread_err'
read_celfile_generic.c:1664: warning: unused variable 'cur_index'
read_celfile_generic.c:1663: warning: unused variable 'j'
read_celfile_generic.c: In function 'gzgeneric_apply_masks':
read_celfile_generic.c:1758: warning: unused variable 'fread_err'
read_celfile_generic.c:1752: warning: unused variable 'j'
gcc -std=gnu99 -I/home/biocbuild/bbs-2.1-bioc/R/include -I/home/biocbuild/bbs-2.1-bioc/R/include -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 -std=gnu99 -shared -L/usr/local/lib -o affyio.so fread_functions.o read_abatch.o read_bpmap.o read_cdffile2.o read_cdf_xda.o read_celfile_generic.o read_generic.o -lz -L/home/biocbuild/bbs-2.1-bioc/R/lib -lR
** 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)