affyio 1.6.1
Benjamin Milo Bolstad
| Snapshot Date: 2008-04-02 12:12:36 -0700 (Wed, 02 Apr 2008) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_1/madman/Rpacks/affyio | | Last Changed Rev: 27950 / Revision: 30807 | | 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 'D:/biocbld/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 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 R.css in D:/biocbld/bbs-2.1-bioc/meat/affyio.Rcheck
---------- Making package affyio ------------
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
adding build stamp to DESCRIPTION
installing NAMESPACE file and metadata
making DLL ...
making fread_functions.d from fread_functions.c
making read_abatch.d from read_abatch.c
making read_bpmap.d from read_bpmap.c
making read_cdf_xda.d from read_cdf_xda.c
making read_cdffile2.d from read_cdffile2.c
making read_celfile_generic.d from read_celfile_generic.c
making read_generic.d from read_generic.c
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c fread_functions.c -o fread_functions.o
fread_functions.c:301: warning: 'swap_uint_32' defined but not used
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c read_abatch.c -o read_abatch.o
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -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-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -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-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -Wall -c read_cdffile2.c -o read_cdffile2.o
read_cdffile2.c:363: warning: 'token_ends_with' defined but not used
gcc-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -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-sjlj -std=gnu99 -Id:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -DHAVE_ZLIB -Id:/biocbld/bbs-2.1-bioc/R/include -O3 -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
windres --preprocessor="gcc-sjlj -E -xc -DRC_INVOKED" -I d:/biocbld/bbs-2.1-bioc/R/include -i affyio_res.rc -o affyio_res.o
gcc-sjlj -std=gnu99 -shared -s -o affyio.dll affyio.def fread_functions.o read_abatch.o read_bpmap.o read_cdf_xda.o read_cdffile2.o read_celfile_generic.o read_generic.o affyio_res.o -Ld:/biocbld/bbs-2.1-bioc/R/bin -Ld:/biocbld/bbs-2.1-bioc/R/src/extra/zlib -lz -lR
... DLL made
installing DLL
installing R files
preparing package affyio for lazy loading
installing man source files
installing indices
installing help
>>> Building/Updating help pages for package 'affyio'
Formats: text html latex example chm
check.cdf.type text html latex chm
read.cdffile.list text html latex chm
read.celfile text html latex chm
read.celfile.header text html latex chm
read.celfile.probeintensity.matri text html latex chm
HHC5012: Error: Cannot create a temporary file in your TEMP path.
HHC4016: Warning: Cannot open "\Affymetrix\GDAC NetAffx;c:\gs\gs8.51\bin;c:\Program Files\Java\jdk1.5.0_06\bin;c:\program files\imagemagick-6.3.2-q16;c:\Program Files\MySQL\MySQL Server 5.0\bin;c:\Program Files\ggobi".
Microsoft HTML Help Compiler 4.74.8702
Compiling d:\biocbld\bbs-2.1-bioc\meat\affyio.Rcheck\00_pkg_src\affyio\chm\affyio.chm
HHC4016: Warning: Cannot open "\Affymetrix\GDAC NetAffx;c:\gs\gs8.51\bin;c:\Program Files\Java\jdk1.5.0_06\bin;c:\program files\imagemagick-6.3.2-q16;c:\Program Files\MySQL\MySQL Server 5.0\bin;c:\Program Files\ggobi".
The following files were not compiled:
adding MD5 sums
* DONE (affyio)