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Package 36/353HostnameOS / ArchBUILDCHECKBUILD BIN
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 
Package: beadarray
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/2.10/Resources/bin/R CMD check --no-vignettes beadarray_1.14.0.tar.gz
StartedAt: 2009-12-14 04:37:35 -0800 (Mon, 14 Dec 2009)
EndedAt: 2009-12-14 04:42:48 -0800 (Mon, 14 Dec 2009)
EllapsedTime: 312.1 seconds
RetCode: 0
Status: OK
CheckDir: beadarray.Rcheck
Warnings: 0

Command output

* checking for working pdflatex ... OK
* using log directory '/Users/biocbuild/bbs-2.5-bioc/meat/beadarray.Rcheck'
* using R version 2.10.0 Patched (2009-10-27 r50222)
* 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

beadarray.Rcheck/00install.out:

* install options are ' --no-html'

* installing *source* package ‘beadarray’ ...
** libs
** arch - i386
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -c BASH.c -o BASH.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -c BLImagePlot.c -o BLImagePlot.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -c HULK.c -o HULK.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -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-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -I/usr/local/include    -fPIC  -g -O2 -Wall -c findProbeIndices.c -o findProbeIndices.o
gcc-4.2 -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386  -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-4.2 -arch i386 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o beadarray.so BASH.o BLImagePlot.o HULK.o createBeadSummaryData.o findProbeIndices.o readBeadImages.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - ppc
gcc-4.2 -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 BASH.c -o BASH.o
gcc-4.2 -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-4.2 -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 HULK.c -o HULK.o
gcc-4.2 -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-4.2 -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-4.2 -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-4.2 -arch ppc -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o beadarray.so BASH.o BLImagePlot.o HULK.o createBeadSummaryData.o findProbeIndices.o readBeadImages.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** arch - x86_64
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -c BASH.c -o BASH.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -c BLImagePlot.c -o BLImagePlot.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -c HULK.c -o HULK.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -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-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -I/usr/local/include    -fPIC  -g -O2 -Wall -c findProbeIndices.c -o findProbeIndices.o
gcc-4.2 -arch x86_64 -std=gnu99 -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/x86_64  -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-4.2 -arch x86_64 -std=gnu99 -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o beadarray.so BASH.o BLImagePlot.o HULK.o createBeadSummaryData.o findProbeIndices.o readBeadImages.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
** 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)