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| 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: /Library/Frameworks/R.framework/Resources/bin/R CMD check beadarray_1.3.0.tar.gz |
| RetCode: 0 |
| Time: 106.1 seconds |
| Status: WARNINGS |
| CheckDir: beadarray.Rcheck |
| Warnings: 4 |
* checking for working latex ... OK
* using log directory '/Users/biocbuild/2.0d/Rpacks/beadarray.Rcheck'
* using R version 2.5.0 Under development (unstable) (2006-10-21 r39702)
* 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
See '/Users/biocbuild/2.0d/Rpacks/beadarray.Rcheck/00install.out' for details.
* 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 syntax errors ... WARNING
Warning: '\.' is an unrecognized escape in a character string
* 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 ... OK
WARNING: There were 4 warnings, see
/Users/biocbuild/2.0d/Rpacks/beadarray.Rcheck/00check.log
for details
beadarray.Rcheck/00install.out:
* Installing *source* package 'beadarray' ...
** libs
** arch - i386
gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c BLImagePlot.c -o BLImagePlot.o
/var/tmp//ccJnmIqx.s:168:indirect jmp without `*'
/var/tmp//ccJnmIqx.s:183:indirect jmp without `*'
gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c createBeadSummaryData.c -o createBeadSummaryData.o
/var/tmp//ccaK0R2Y.s:1255:indirect jmp without `*'
/var/tmp//ccaK0R2Y.s:1270:indirect jmp without `*'
/var/tmp//ccaK0R2Y.s:1285:indirect jmp without `*'
/var/tmp//ccaK0R2Y.s:1300:indirect jmp without `*'
/var/tmp//ccaK0R2Y.s:1315:indirect jmp without `*'
/var/tmp//ccaK0R2Y.s:1330:indirect jmp without `*'
gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c findProbeIndices.c -o findProbeIndices.o
gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c readBeadImages.c -o readBeadImages.o
/var/tmp//ccHMwDeE.s:4080:indirect jmp without `*'
/var/tmp//ccHMwDeE.s:4095:indirect jmp without `*'
/var/tmp//ccHMwDeE.s:4110:indirect jmp without `*'
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/var/tmp//ccHMwDeE.s:4140:indirect jmp without `*'
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/var/tmp//ccHMwDeE.s:4215:indirect jmp without `*'
/var/tmp//ccHMwDeE.s:4230:indirect jmp without `*'
gcc-4.0 -arch i386 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -std=gnu99 -march=pentium-m -mtune=prescott -c returnTIFF.c -o returnTIFF.o
returnTIFF.c: In function 'readTIFF':
returnTIFF.c:101: warning: implicit declaration of function 'getPixelIntensities'
/var/tmp//ccc9l3Tv.s:458:indirect jmp without `*'
/var/tmp//ccc9l3Tv.s:473:indirect jmp without `*'
/var/tmp//ccc9l3Tv.s:488:indirect jmp without `*'
/var/tmp//ccc9l3Tv.s:503:indirect jmp without `*'
/var/tmp//ccc9l3Tv.s:518:indirect jmp without `*'
/var/tmp//ccc9l3Tv.s:533:indirect jmp without `*'
/var/tmp//ccc9l3Tv.s:548:indirect jmp without `*'
/var/tmp//ccc9l3Tv.s:563:indirect jmp without `*'
/var/tmp//ccc9l3Tv.s:578:indirect jmp without `*'
/var/tmp//ccc9l3Tv.s:593:indirect jmp without `*'
/var/tmp//ccc9l3Tv.s:608:indirect jmp without `*'
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/var/tmp//ccc9l3Tv.s:638:indirect jmp without `*'
/var/tmp//ccc9l3Tv.s:653:indirect jmp without `*'
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/var/tmp//ccc9l3Tv.s:683:indirect jmp without `*'
/var/tmp//ccc9l3Tv.s:698:indirect jmp without `*'
/var/tmp//ccc9l3Tv.s:713:indirect jmp without `*'
/var/tmp//ccc9l3Tv.s:728:indirect jmp without `*'
/var/tmp//ccc9l3Tv.s:743:indirect jmp without `*'
gcc-4.0 -arch i386 -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o beadarray.so BLImagePlot.o createBeadSummaryData.o findProbeIndices.o readBeadImages.o returnTIFF.o -F/Library/Frameworks/R.framework/.. -framework R
** arch - ppc
gcc-4.0 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c BLImagePlot.c -o BLImagePlot.o
gcc-4.0 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c createBeadSummaryData.c -o createBeadSummaryData.o
gcc-4.0 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c findProbeIndices.c -o findProbeIndices.o
gcc-4.0 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c readBeadImages.c -o readBeadImages.o
gcc-4.0 -arch ppc -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -c returnTIFF.c -o returnTIFF.o
returnTIFF.c: In function 'readTIFF':
returnTIFF.c:101: warning: implicit declaration of function 'getPixelIntensities'
gcc-4.0 -arch ppc -std=gnu99 -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o beadarray.so BLImagePlot.o createBeadSummaryData.o findProbeIndices.o readBeadImages.o returnTIFF.o -F/Library/Frameworks/R.framework/.. -framework R
** R
** data
** inst
** preparing package 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
** help
>>> Building/Updating help pages for package 'beadarray'
Formats: text html latex example
BLData text html latex
BSData text html latex
BeadLevelNormalise text html latex
DiffScore text html latex
LargeDataObject text html latex example
QC text html latex
backgroundCorrect text html latex example
backgroundNormalise text html latex example
cbind text html latex
class-BeadLevelList text html latex
class.ExpressionSetIllumina text html latex
createBeadSummaryData text html latex example
dim text html latex
dimnames text html latex
displayTIFFImage text html latex example
findAllOutliers text html latex example
findBeadStatus text html latex example
imageplot text html latex
interactivePlots text html latex
medianNormalise text html latex example
plotBeadIntensities text html latex example
plotBeadLocations text html latex example
plotMA text html latex
plotMAXY text html latex example
plotOnSAM text html latex
plotXY text html latex
rankInvariantNormalise text html latex example
readBeadLevelData text html latex example
readBeadSummaryData text html latex example
readBeadSummaryTargets text html latex example
readBeadTargets text html latex example
readQC text html latex example
** building package indices ...
* DONE (beadarray)