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 'E:/biocbld/bbs-2.3-bioc/meat/affyio.Rcheck'
* using R version 2.8.1 (2008-12-22)
* using session charset: ISO8859-1
* 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'
WARNING: found \itemize inside \value in file 'check.cdf.type.Rd'
See 'E:/biocbld/bbs-2.3-bioc/meat/affyio.Rcheck/00install.out' for details.
* 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 using pdflatex ... OK
WARNING: There was 1 warning, see
E:/biocbld/bbs-2.3-bioc/meat/affyio.Rcheck/00check.log
for details
installing R.css in E:/biocbld/bbs-2.3-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_clf.d from read_clf.c
making read_generic.d from read_generic.c
making read_pgf.d from read_pgf.c
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-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 -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c read_abatch.c -o read_abatch.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -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 -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -Wall -c read_cdf_xda.c -o read_cdf_xda.o
gcc -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-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 -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-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: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 -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -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 -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -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 -std=gnu99 -DHAVE_ZLIB -Ie:/biocbld/bbs-2.3-bioc/R/include -O3 -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
windres --preprocessor="gcc -E -xc -DRC_INVOKED" -I e:/biocbld/bbs-2.3-bioc/R/include -i affyio_res.rc -o affyio_res.o
gcc -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_clf.o read_generic.o read_pgf.o affyio_res.o -Le:/biocbld/bbs-2.3-bioc/R/bin -lRzlib -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
WARNING: found \itemize inside \value in file 'check.cdf.type.Rd'
WARNING: found \itemize inside \value in file 'check.cdf.type.Rd'
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
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\bbs-2.3-bioc\meat\affyio.Rcheck\00_pkg_src\affyio\chm\affyio.chm
Compile time: 0 minutes, 0 seconds
6 Topics
11 Local links
0 Internet links
1 Graphic
Created e:\biocbld\bbs-2.3-bioc\meat\affyio.Rcheck\00_pkg_src\affyio\chm\affyio.chm, 19,627 bytes
Compression increased file by 1,961 bytes.
adding MD5 sums
* DONE (affyio)