beadarray 1.14.0
Mark Dunning
| Snapshot Date: 2009-12-13 23:30:35 -0800 (Sun, 13 Dec 2009) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_5/madman/Rpacks/beadarray | | Last Changed Rev: 42684 / Revision: 43539 | | Last Changed Date: 2009-10-27 16:33:29 -0700 (Tue, 27 Oct 2009) |
| wilson2 | Linux (openSUSE 11.1) / x86_64 | OK | [ OK ] | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | OK | OK |
| pitt | Mac OS X Tiger (10.4.11) / i386 | OK | OK | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* checking for working pdflatex ... OK
* using log directory '/loc/home/biocbuild/bbs-2.5-bioc/meat/beadarray.Rcheck'
* using R version 2.10.0 (2009-10-26)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'beadarray/DESCRIPTION' ... OK
* this is package 'beadarray' version '1.14.0'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'beadarray' can be installed ... 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 name space 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 ... NOTE
getControlAnno: no visible binding for global variable
‘ExpressionControlData’
readIllumina: no visible binding for global variable
‘ExpressionControlData’
setAnnotation: no visible binding for global variable
‘ExpressionControlData’
* 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 data for non-ASCII characters ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... SKIPPED
* checking PDF version of manual ... OK
* install options are ' --no-html'
* installing *source* package ‘beadarray’ ...
** libs
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c BASH.c -o BASH.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c BLImagePlot.c -o BLImagePlot.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c HULK.c -o HULK.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c createBeadSummaryData.c -o createBeadSummaryData.o
createBeadSummaryData.c: In function ‘findAllOutliers’:
createBeadSummaryData.c:223: warning: ‘status’ may be used uninitialized in this function
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c findProbeIndices.c -o findProbeIndices.o
gcc -std=gnu99 -I/home/biocbuild/bbs-2.5-bioc/R/include -I/usr/local/include -fpic -g -O2 -Wall -c readBeadImages.c -o readBeadImages.o
readBeadImages.c: In function ‘getPixelIntensities’:
readBeadImages.c:368: warning: unused variable ‘result’
readBeadImages.c: In function ‘calculateBackground’:
readBeadImages.c:493: warning: unused variable ‘temp’
readBeadImages.c:491: warning: unused variable ‘cY’
readBeadImages.c:491: warning: unused variable ‘cX’
readBeadImages.c:490: warning: unused variable ‘opt4’
readBeadImages.c:490: warning: unused variable ‘opt3’
readBeadImages.c:490: warning: unused variable ‘opt2’
readBeadImages.c:490: warning: unused variable ‘opt1’
readBeadImages.c:490: warning: unused variable ‘yc’
readBeadImages.c:490: warning: unused variable ‘xc’
readBeadImages.c:489: warning: unused variable ‘dist’
readBeadImages.c: In function ‘readBeadImage’:
readBeadImages.c:626: warning: ‘offset’ may be used uninitialized in this function
readBeadImages.c:626: warning: ‘records’ may be used uninitialized in this function
readBeadImages.c:625: warning: ‘StripOffset’ may be used uninitialized in this function
readBeadImages.c:625: warning: ‘ImageHeight’ may be used uninitialized in this function
readBeadImages.c:625: warning: ‘ImageWidth’ may be used uninitialized in this function
readBeadImages.c:625: warning: ‘BeginData’ may be used uninitialized in this function
gcc -std=gnu99 -shared -L/usr/local/lib64 -o beadarray.so BASH.o BLImagePlot.o HULK.o createBeadSummaryData.o findProbeIndices.o readBeadImages.o -L/home/biocbuild/bbs-2.5-bioc/R/lib -lR
** R
** data
** inst
** preparing package for lazy loading
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'openVignette()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
** help
*** installing help indices
** building package indices ...
* DONE (beadarray)