Back to the "Multiple platform build/check report"
| Package 25/208 | OS | Arch | BUILD | CHECK | BUILD BIN |
beadarray1.3.0Mark Dunning | Linux (SUSE 9.2) | x86_64 | OK | WARNINGS | |
| Linux (SUSE 10.1) | x86_64 | OK | WARNINGS | ||
| Linux (SUSE 9.2) | i686 | OK | WARNINGS | ||
| Solaris 2.9 | sparc | OK | ERROR | ||
| Windows Server 2003 | x86_64 | OK | WARNINGS | OK | |
| Windows Server 2003 | NA | OK | [ ERROR ] | OK | |
| Mac OS X (10.4.6) | i686 | OK | WARNINGS |
| Package: beadarray |
| Version: 1.3.0 |
| Command: E:\biocbld\2.0d\R\bin\R.exe CMD check beadarray_1.3.0.tar.gz |
| RetCode: 1 |
| Time: 145.5 seconds |
| Status: ERROR |
| CheckDir: beadarray.Rcheck |
| Warnings: NA |
* checking for working latex ... OK
* using log directory 'E:/biocbld/2.0d/Rpacks/beadarray.Rcheck'
* using R version 2.5.0 Under development (unstable) (2006-12-05 r40126)
* checking for file 'beadarray/DESCRIPTION' ... OK
* this is package 'beadarray' version '1.3.0'
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'beadarray' can be installed ... WARNING
Found the following significant warnings:
Warning: '\.' is an unrecognized escape in a character string
Warning: unrecognized escape removed from "AVG_Signal.(\.+)"
See 'E:/biocbld/2.0d/Rpacks/beadarray.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 syntax errors ... WARNING
Warning: '\.' is an unrecognized escape in a character string
Warning: unrecognized escape removed from "AVG_Signal.(\.+)"
* checking R files for non-ASCII characters ... 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 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 ... WARNING
Undocumented S4 methods:
generic 'show' and siglist 'BeadLevelList'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See the chapter 'Writing R documentation files' in manual 'Writing R
Extensions'.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'backgroundCorrect':
backgroundCorrect
Code: function(object, method = "subtract", offset = 0, verbose =
FALSE)
Docs: function(object, method = "subtract", offset = 0)
Argument names in code not in docs:
verbose
Codoc mismatches from documentation object 'readQC':
plotQC
Code: function(QC, ...)
Docs: function(object, ...)
Argument names in code not in docs:
QC
Argument names in docs not in code:
object
Mismatches in argument names:
Position: 1 Code: QC Docs: object
* checking Rd \usage sections ... OK
* checking for CRLF line endings in C/C++/Fortran sources/headers ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating beadarray-Ex.R ... OK
* checking examples ... OK
* creating beadarray-manual.tex ... OK
* checking beadarray-manual.tex ... ERROR
LaTeX errors when creating DVI version.
This typically indicates Rd problems.
beadarray.Rcheck/00install.out:
installing R.css in E:/biocbld/2.0d/Rpacks/beadarray.Rcheck
---------- Making package beadarray ------------
adding build stamp to DESCRIPTION
installing NAMESPACE file and metadata
making DLL ...
making BLImagePlot.d from BLImagePlot.c
making createBeadSummaryData.d from createBeadSummaryData.c
making findProbeIndices.d from findProbeIndices.c
making readBeadImages.d from readBeadImages.c
making returnTIFF.d from returnTIFF.c
gcc -Ie:/biocbld/2.0d/R/include -Wall -O2 -std=gnu99 -c BLImagePlot.c -o BLImagePlot.o
gcc -Ie:/biocbld/2.0d/R/include -Wall -O2 -std=gnu99 -c createBeadSummaryData.c -o createBeadSummaryData.o
createBeadSummaryData.c: In function `findAllOutliers':
createBeadSummaryData.c:243: warning: 'status' might be used uninitialized in this function
gcc -Ie:/biocbld/2.0d/R/include -Wall -O2 -std=gnu99 -c findProbeIndices.c -o findProbeIndices.o
gcc -Ie:/biocbld/2.0d/R/include -Wall -O2 -std=gnu99 -c readBeadImages.c -o readBeadImages.o
readBeadImages.c: In function `readBeadImage':
readBeadImages.c:554: warning: 'BeginData' might be used uninitialized in this function
readBeadImages.c:554: warning: 'ImageWidth' might be used uninitialized in this function
readBeadImages.c:554: warning: 'ImageHeight' might be used uninitialized in this function
readBeadImages.c:554: warning: 'StripOffset' might be used uninitialized in this function
readBeadImages.c:555: warning: 'offset' might be used uninitialized in this function
readBeadImages.c:555: warning: 'records' might be used uninitialized in this function
gcc -Ie:/biocbld/2.0d/R/include -Wall -O2 -std=gnu99 -c returnTIFF.c -o returnTIFF.o
returnTIFF.c: In function `readTIFF':
returnTIFF.c:101: warning: implicit declaration of function `getPixelIntensities'
returnTIFF.c:17: warning: 'BeginData' might be used uninitialized in this function
returnTIFF.c:17: warning: 'ImageWidth' might be used uninitialized in this function
returnTIFF.c:17: warning: 'ImageHeight' might be used uninitialized in this function
returnTIFF.c:17: warning: 'StripOffset' might be used uninitialized in this function
returnTIFF.c:18: warning: 'offset' might be used uninitialized in this function
returnTIFF.c:18: warning: 'records' might be used uninitialized in this function
windres --include-dir e:/biocbld/2.0d/R/include -i beadarray_res.rc -o beadarray_res.o
gcc -shared -s -o beadarray.dll beadarray.def BLImagePlot.o createBeadSummaryData.o findProbeIndices.o readBeadImages.o returnTIFF.o beadarray_res.o -Le:/biocbld/2.0d/R/bin -lR
... DLL made
installing DLL
installing R files
installing inst files
installing data files
installing man source files
installing indices
not zipping data
installing help
>>> Building/Updating help pages for package 'beadarray'
Formats: text html latex example chm
BLData text html latex chm
BSData text html latex chm
BeadLevelNormalise text html latex chm
DiffScore text html latex chm
LargeDataObject text html latex example chm
QC text html latex chm
backgroundCorrect text html latex example chm
backgroundNormalise text html latex example chm
cbind text html latex chm
class-BeadLevelList text html latex chm
class.ExpressionSetIllumina text html latex chm
createBeadSummaryData text html latex example chm
dim text html latex chm
dimnames text html latex chm
displayTIFFImage text html latex example chm
findAllOutliers text html latex example chm
findBeadStatus text html latex example chm
imageplot text html latex chm
interactivePlots text html latex chm
medianNormalise text html latex example chm
plotBeadIntensities text html latex example chm
plotBeadLocations text html latex example chm
plotMA text html latex chm
plotMAXY text html latex example chm
plotOnSAM text html latex chm
plotXY text html latex chm
rankInvariantNormalise text html latex example chm
readBeadLevelData text html latex example chm
readBeadSummaryData text html latex example chm
readBeadSummaryTargets text html latex example chm
readBeadTargets text html latex example chm
readQC text html latex example chm
Microsoft HTML Help Compiler 4.74.8702
Compiling e:\biocbld\2.0d\Rpacks\beadarray.Rcheck\00_pkg_src\beadarray\chm\beadarray.chm
Compile time: 0 minutes, 0 seconds
33 Topics
120 Local links
0 Internet links
1 Graphic
Created e:\biocbld\2.0d\Rpacks\beadarray.Rcheck\00_pkg_src\beadarray\chm\beadarray.chm, 61,014 bytes
Compression decreased file by 72,723 bytes.
preparing package beadarray for lazy loading
Loading required package: limma
Loading required package: Biobase
Loading required package: tools
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()' or start with 'help(Biobase)'. For details
on reading vignettes, see the openVignette help page.
Loading required package: affy
Loading required package: affyio
Warning: '\.' is an unrecognized escape in a character string
Warning: unrecognized escape removed from "AVG_Signal.(\.+)"
adding MD5 sums
* DONE (beadarray)