affy 1.32.1
Rafael A. Irizarry
| Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/affy | | Last Changed Rev: 62374 / Revision: 64395 | | Last Changed Date: 2012-01-30 06:50:45 -0800 (Mon, 30 Jan 2012) |
| wilson2 | Linux (openSUSE 11.4) / x86_64 | OK | [ OK ] | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/affy.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘affy/DESCRIPTION’ ... OK
* this is package ‘affy’ version ‘1.32.1’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package ‘affy’ can be installed ... OK
* checking installed package size ... 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 package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... 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 ... NOTE
File ‘affy/R/zzz.R’:
.onLoad calls:
require(Biobase)
Package startup functions should not change the search path.
See section ‘Good practice’ in ?.onAttach.
cleancdfname: no visible binding for global variable ‘mapCdfName’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... NOTE
‘library’ or ‘require’ call not declared from: ‘widgetTools’
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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) and $(LAPACK_LIBS) ... OK
* checking compiled code ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK
* installing *source* package ‘affy’ ...
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-2.9-bioc/R/include -DHAVE_ZLIB=1 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c chipbackground.c -o chipbackground.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -DHAVE_ZLIB=1 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c getall_locations.c -o getall_locations.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -DHAVE_ZLIB=1 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c mas5calls.c -o mas5calls.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -DHAVE_ZLIB=1 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c rma2.c -o rma2.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.9-bioc/R/include -DHAVE_ZLIB=1 -I/usr/local/include -I"/loc/home/biocbuild/bbs-2.9-bioc/R/library/preprocessCore/include" -fpic -g -O2 -c rma_common.c -o rma_common.o
gcc -std=gnu99 -shared -L/usr/local/lib64 -o affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lz -L/home/biocbuild/bbs-2.9-bioc/R/lib -lR
installing to /loc/home/biocbuild/bbs-2.9-bioc/meat/affy.Rcheck/affy/libs
** R
** data
** demo
** inst
** preparing package for lazy loading
Creating a generic function for ‘open’ from package ‘base’ in package ‘affy’
Creating a generic function for ‘close’ from package ‘base’ in package ‘affy’
Creating a generic function for ‘colnames’ from package ‘base’ in package ‘affy’
Creating a generic function for ‘barplot’ from package ‘graphics’ in package ‘affy’
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
‘affy.Rnw’
‘builtinMethods.Rnw’
‘customMethods.Rnw’
‘vim.Rnw’
** testing if installed package can be loaded
* DONE (affy)