affy 1.36.1
Rafael A. Irizarry
| Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/affy | | Last Changed Rev: 72927 / Revision: 74773 | | Last Changed Date: 2013-01-25 09:54:50 -0800 (Fri, 25 Jan 2013) |
| lamb1 | Linux (openSUSE 12.1) / x86_64 | OK | WARNINGS | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | WARNINGS | OK |
| perceval | Mac OS X Leopard (10.5.8) / i386 | OK | [ WARNINGS ] | OK |
* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/affy.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'affy/DESCRIPTION' ... OK
* this is package 'affy' version '1.36.1'
* 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 for left-over 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 ... WARNING
Foreign function calls with 'PACKAGE' argument in a base package:
.C("loess_raw", ..., PACKAGE = "stats")
.Fortran("lowesp", ..., PACKAGE = "stats")
.Fortran("lowesw", ..., PACKAGE = "stats")
Foreign function calls with 'PACKAGE' argument in a different package:
.Call("read_abatch", ..., PACKAGE = "affyio")
.Call("read_abatch_stddev", ..., PACKAGE = "affyio")
Packages should not make .C/.Call/.Fortran calls to base packages. They
are not part of the API, for use only by R itself and subject to change
without notice.
* checking R code for possible problems ... NOTE
featureNames,AffyBatch: warning in ls(env = cdf.envir): partial
argument match of 'env' to 'envir'
geneNames,AffyBatch: warning in ls(env = cdf.envir): partial argument
match of 'env' to 'envir'
show,AffyBatch: warning in ls(env = cdf.env): partial argument match of
'env' to 'envir'
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 ... OK
* 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 sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
user system elapsed
mas5 43.238 0.602 45.588
MAplot 24.345 1.791 26.707
expresso 20.954 1.352 22.625
bgc 6.073 0.697 6.978
AffyBatch-class 6.431 0.275 6.833
AffyRNAdeg 5.254 0.207 5.533
ProgressBarText-class 1.027 0.050 16.575
* 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
WARNING: There was 1 warning.
NOTE: There was 1 note.
See
'/Users/biocbuild/bbs-2.11-bioc/meat/affy.Rcheck/00check.log'
for details.
* 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
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -DHAVE_ZLIB=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c chipbackground.c -o chipbackground.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -DHAVE_ZLIB=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c getall_locations.c -o getall_locations.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -DHAVE_ZLIB=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c mas5calls.c -o mas5calls.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -DHAVE_ZLIB=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c rma2.c -o rma2.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -DNDEBUG -DHAVE_ZLIB=1 -I/usr/local/include -I"/Library/Frameworks/R.framework/Versions/2.15/Resources/library/preprocessCore/include" -fPIC -g -O2 -Wall -pedantic -c rma_common.c -o rma_common.o
gcc -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o affy.so chipbackground.o getall_locations.o mas5calls.o rma2.o rma_common.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.11-bioc/meat/affy.Rcheck/affy/libs/i386
** 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 'barplot' from package 'graphics' in package 'affy'
** help
*** installing help indices
** building package indices
** installing vignettes
'affy.Rnw'
'builtinMethods.Rnw'
'customMethods.Rnw'
'vim.Rnw'
** testing if installed package can be loaded
* DONE (affy)