beadarray 2.1.12
Mark Dunning
| Snapshot Date: 2011-02-24 11:26:35 -0800 (Thu, 24 Feb 2011) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/beadarray | | Last Changed Rev: 53252 / Revision: 53255 | | Last Changed Date: 2011-02-24 10:43:40 -0800 (Thu, 24 Feb 2011) |
| lamb2 | Linux (openSUSE 11.2) / x86_64 | OK | WARNINGS | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | OK | WARNINGS | OK |
| gewurz | Windows Server 2008 R2 Enterprise (64-bit) / x64 | OK | WARNINGS | OK |
| pelham | Mac OS X Leopard (10.5.8) / i386 | OK | [ WARNINGS ] | OK |
| petty | Mac OS X Snow Leopard (10.6.4) / i386 | OK | WARNINGS | OK |
* using log directory ‘/Users/biocbuild/bbs-2.8-bioc/meat/beadarray.Rcheck’
* using R version 2.13.0 Under development (unstable) (2011-01-10 r53950)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘beadarray/DESCRIPTION’ ... OK
* this is package ‘beadarray’ version ‘2.1.12’
* 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 package can be unloaded cleanly ... OK
* checking whether the name space can be loaded with stated dependencies ... OK
* checking whether the name space can be unloaded cleanly ... 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
makeControlProfile: no visible binding for global variable
‘ExpressionControlData’
poscontPlot: no visible binding for global variable
‘ExpressionControlData’
quickSummary: no visible binding for global variable
‘ExpressionControlData’
setAnnotation: no visible binding for global variable
‘ExpressionControlData’
showArrayMask: no visible binding for global variable ‘SAM’
summarize: no visible binding for global variable
‘ExpressionControlData’
viewBeads: no visible global function definition for ‘getArrayData’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'processSwathData':
processSwathData
Code: function(twoColour = NULL, textstring = "_perBeadFile.txt",
segmentHeight = 326, segmentWidth = 397, swathOverlap
= 81, fullOutput = TRUE, newTextString = ".txt",
verbose = TRUE)
Docs: function(twoColour = TRUE, textstring = "_perBeadFile.txt",
segmentHeight = 326, segmentWidth = 397, swathOverlap
= 81, fullOutput = TRUE, newTextString = ".txt",
verbose = TRUE)
Mismatches in argument default values:
Name: 'twoColour' Code: NULL Docs: TRUE
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... 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
WARNING: There was 1 warning, see
‘/Users/biocbuild/bbs-2.8-bioc/meat/beadarray.Rcheck/00check.log’
for details
* installing *source* package ‘beadarray’ ...
** libs
*** arch - i386
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c BASH.c -o BASH.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c HULK.c -o HULK.o
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c determiningGridPositions.c -o determiningGridPositions.o
determiningGridPositions.c: In function ‘roundLocsFileValues’:
determiningGridPositions.c:7: warning: unused variable ‘vecLength’
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c findAllOutliers.c -o findAllOutliers.o
findAllOutliers.c: In function ‘findBeadStatus’:
findAllOutliers.c:161: warning: ‘ma’ may be used uninitialized in this function
findAllOutliers.c:161: warning: ‘m’ may be used uninitialized in this function
findAllOutliers.c: In function ‘findAllOutliers’:
findAllOutliers.c:234: warning: ‘status’ may be used uninitialized in this function
gcc -arch i386 -std=gnu99 -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include -I/Library/Frameworks/R.framework/Versions/2.13/Resources/include/i386 -I/usr/local/include -fPIC -g -O2 -Wall -pedantic -c imageProcessing.c -o imageProcessing.o
imageProcessing.c: In function ‘illuminaBackground’:
imageProcessing.c:82: warning: ignoring #pragma omp parallel
imageProcessing.c: In function ‘medianBackground’:
imageProcessing.c:126: warning: ignoring #pragma omp parallel
imageProcessing.c: In function ‘illuminaSharpen’:
imageProcessing.c:224: warning: ignoring #pragma omp parallel
imageProcessing.c:231: warning: ignoring #pragma omp parallel
gcc -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 HULK.o determiningGridPositions.o findAllOutliers.o imageProcessing.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/biocbuild/bbs-2.8-bioc/meat/beadarray.Rcheck/beadarray/libs/i386
** R
** data
** inst
** preparing package for lazy loading
Welcome to Bioconductor
Vignettes contain introductory material. To view, type
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")' and for packages 'citation(pkgname)'.
Creating a new generic function for "boxplot" in "beadarray"
** help
*** installing help indices
** building package indices ...
** testing if installed package can be loaded
Welcome to beadarray version 2.1.12
There have been major changes to beadarray since Bioconductor 2.6 (April 2010). Please see package vignette for details
* DONE (beadarray)