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| Package 1/28 | Hostname | OS | Arch | BUILD | CHECK | BUILD BIN |
affy1.14.0Rafael A. IrizarryLast Changed Date: 2007-04-24 11:21:48 -0700 Last Changed Rev: 24214 | lamb1 | Linux (SUSE 10.1) | x86_64 | OK | OK | |
| liverpool | Windows Server 2003 R2 (32-bit) | x64 | OK | [ OK ] | OK |
| Package: affy |
| Version: 1.14.0 |
| Command: E:\biocbld\bbs-2.0-bioc\R\bin\R.exe CMD check affy_1.14.0.tar.gz |
| RetCode: 0 |
| Time: 161.2 seconds |
| Status: OK |
| CheckDir: affy.Rcheck |
| Warnings: 0 |
* checking for working latex ... OK * using log directory 'E:/biocbld/bbs-2.0-biocLite/meat/affy.Rcheck' * using R version 2.5.0 (2007-04-23) * checking for file 'affy/DESCRIPTION' ... OK * this is package 'affy' version '1.14.0' * checking package dependencies ... OK * checking if this is a source package ... OK * checking whether package 'affy' 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 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 data for non-ASCII characters ... OK * checking for CRLF line endings in C/C++/Fortran sources/headers ... OK * checking for portable compilation flags in Makevars ... OK * checking for portable use of $BLAS_LIBS ... OK * creating affy-Ex.R ... OK * checking examples ... OK * checking tests ... make[1]: Entering directory `/cygdrive/e/biocbld/bbs-2.0-biocLite/meat/affy.Rcheck/tests' Running 'affybatch.R' Running 'bg.correct.R' Running 'expression.values.R' Running 'normalize.methods.R' make[1]: Leaving directory `/cygdrive/e/biocbld/bbs-2.0-biocLite/meat/affy.Rcheck/tests' OK * checking package vignettes in 'inst/doc' ... OK * creating affy-manual.tex ... OK * checking affy-manual.tex ... OK
affy.Rcheck/00install.out:
installing R.css in E:/biocbld/bbs-2.0-biocLite/meat/affy.Rcheck
---------- Making package affy ------------
**********************************************
WARNING: this package has a configure script
It probably needs manual configuration
**********************************************
adding build stamp to DESCRIPTION
making DLL ...
making chipbackground.d from chipbackground.c
making getall_locations.d from getall_locations.c
making mas5calls.d from mas5calls.c
making qnorm.d from qnorm.c
making rma2.d from rma2.c
making rma_background2.d from rma_background2.c
making rma_common.d from rma_common.c
gcc -Ie:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.0-bioc/R/include -Wall -O3 -std=gnu99 -c chipbackground.c -o chipbackground.o
gcc -Ie:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.0-bioc/R/include -Wall -O3 -std=gnu99 -c getall_locations.c -o getall_locations.o
gcc -Ie:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.0-bioc/R/include -Wall -O3 -std=gnu99 -c mas5calls.c -o mas5calls.o
gcc -Ie:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.0-bioc/R/include -Wall -O3 -std=gnu99 -c qnorm.c -o qnorm.o
qnorm.c: In function `qnorm_c_determine_target':
qnorm.c:1489: warning: unused variable `ind'
qnorm.c:1490: warning: unused variable `dimat'
qnorm.c:1494: warning: unused variable `ranks'
qnorm.c:1564: warning: no return statement in function returning non-void
qnorm.c: In function `R_qnorm_using_target':
qnorm.c:1572: warning: unused variable `dim2'
qnorm.c: In function `qnorm_c_determine_target':
qnorm.c:1564: warning: control reaches end of non-void function
qnorm.c: At top level:
qnorm.c:118: warning: 'min' defined but not used
qnorm.c:357: warning: 'qnorm_c_old' defined but not used
qnorm.c:431: warning: 'qnorm_robust_c_old' defined but not used
gcc -Ie:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.0-bioc/R/include -Wall -O3 -std=gnu99 -c rma2.c -o rma2.o
rma2.c: In function `get_col_median':
rma2.c:183: warning: unused variable `i'
gcc -Ie:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.0-bioc/R/include -Wall -O3 -std=gnu99 -c rma_background2.c -o rma_background2.o
gcc -Ie:/biocbld/bbs-2.0-bioc/R/src/extra/zlib -DHAVE_ZLIB -Ie:/biocbld/bbs-2.0-bioc/R/include -Wall -O3 -std=gnu99 -c rma_common.c -o rma_common.o
rma_common.c: In function `median':
rma_common.c:60: warning: unused variable `i'
rma_common.c: In function `median_nocopy':
rma_common.c:103: warning: unused variable `i'
windres -I e:/biocbld/bbs-2.0-bioc/R/include -i affy_res.rc -o affy_res.o
gcc -shared -s -o affy.dll affy.def chipbackground.o getall_locations.o mas5calls.o qnorm.o rma2.o rma_background2.o rma_common.o affy_res.o -Le:/biocbld/bbs-2.0-bioc/R/bin -lR
... DLL made
installing DLL
installing R files
save image
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Loading required package: affyio
[1] "ProgressBarText"
[1] "initialize"
Creating a new generic function for "open" in "affy"
[1] "open"
Creating a new generic function for "update" in "affy"
[1] "update"
Creating a new generic function for "close" in "affy"
[1] "close"
[1] "AffyBatch"
[1] "initialize"
[1] "updateObject"
[1] "exprs"
[1] "exprs<-"
[1] "se.exprs"
[1] "se.exprs<-"
[1] "cdfName"
[1] "cdfName"
[1] "intensity"
[1] "intensity"
[1] "intensity<-"
[1] "intensity<-"
[1] "length"
[1] "dim"
[1] "geneNames"
[1] "geneNames<-"
[1] "show"
[1] "indexProbes"
[1] "indexProbes"
[1] "indexProbes"
[1] "pmindex"
[1] "pmindex"
[1] "mmindex"
[1] "mmindex"
[1] "probeNames"
[1] "probeNames"
[1] "probes"
[1] "probes"
[1] "pm"
[1] "pm"
[1] "pm<-"
[1] "pm<-"
[1] "mm"
[1] "mm"
[1] "mm<-"
[1] "mm<-"
[1] "probeset"
[1] "probeset"
[1] "["
[1] "[<-"
[1] "bg.correct"
[1] "bg.correct"
[1] "normalize.methods"
[1] "normalize.methods"
[1] "normalize"
[1] "normalize"
[1] "computeExprSet"
[1] "computeExprSet"
[1] "image"
[1] "image"
[1] "boxplot"
[1] "boxplot"
[1] "hist"
[1] "hist"
[1] "mas5calls"
[1] "mas5calls"
[1] "Mbox"
[1] "Mbox"
[1] "MAplot"
[1] "MAplot"
[1] "ProbeSet"
[1] "show"
[1] "colnames"
[1] "sampleNames"
[1] "colnames"
[1] "pm"
[1] "pm<-"
[1] "mm"
[1] "mm<-"
[1] "express.summary.stat"
[1] "express.summary.stat"
[1] "barplot"
[1] "barplot"
[1] "mas5calls"
installing demos
installing inst files
installing data files
installing man source files
installing indices
not zipping data
installing help
>>> Building/Updating help pages for package 'affy'
Formats: text html latex example chm
AffyBatch-class text html latex example chm
AffyRNAdeg text html latex example chm
MAplot text html latex example chm
ProbeSet-class text html latex example chm
ProgressBarText-class text html latex example chm
SpikeIn text html latex chm
affy-options text html latex example chm
affy.scalevalue.exprSet text html latex chm
affybatch.example text html latex chm
barplot.ProbeSet text html latex example chm
bg.adjust text html latex chm
bgc text html latex example chm
cdfFromBioC text html latex example chm
cdfenv.example text html latex chm
cleancdfname text html latex example chm
debug.affy123 text html latex chm
expresso text html latex example chm
expressoWidget text html latex example chm
fit.li.wong text html latex example chm
generateExprSet-methods text html latex example chm
generateExprVal-methods text html latex example chm
generateExprVal.method.avgdiff text html latex example chm
generateExprVal.method.playerout text html latex chm
hlog text html latex chm
justrma text html latex example chm
list.celfiles text html latex example chm
loess.normalize text html latex chm
maffy.normalise text html latex example chm
maffy.subset text html latex example chm
mas5 text html latex example chm
mas5calls text html latex example chm
merge.AffyBatch text html latex example chm
multiloess text html latex chm
mva.pairs text html latex example chm
normalize-methods text html latex example chm
normalize text html latex chm
normalize.constant text html latex chm
normalize.contrast text html latex example chm
normalize.invariantset text html latex chm
normalize.loess text html latex example chm
normalize.qspline text html latex chm
normalize.quantiles text html latex chm
normalize.quantiles.robust text html latex chm
pairs.AffyBatch text html latex example chm
plot.ProbeSet text html latex example chm
plot.density text html latex example chm
plotLocation text html latex example chm
pmcorrect text html latex example chm
ppsetApply text html latex example chm
probeMatch-methods text html latex chm
probeNames-methods text html latex chm
read.affybatch text html latex example chm
read.probematrix text html latex example chm
rma text html latex example chm
setAffyOptions text html latex example chm
simplemultiLoess text html latex chm
summary text html latex chm
tukey.biweight text html latex chm
whatcdf text html latex chm
xy2indices text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\bbs-2.0-biocLite\meat\affy.Rcheck\00_pkg_src\affy\chm\affy.chm
Compile time: 0 minutes, 1 second
61 Topics
353 Local links
9 Internet links
1 Graphic
Created e:\biocbld\bbs-2.0-biocLite\meat\affy.Rcheck\00_pkg_src\affy\chm\affy.chm, 98,433 bytes
Compression decreased file by 160,087 bytes.
adding MD5 sums
* DONE (affy)