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IMPORTANT NOTE: R was configured with --enable-strict-barrier on lamb1 |
Package 178/247 | Hostname | OS | Arch | BUILD | CHECK | BUILD BIN |
prada1.13.2Florian HahneLast Changed Date: 2007-07-25 03:21:34 -0700 Last Changed Rev: 25960 | lamb1 | Linux (SUSE 10.1) | x86_64 | OK | ERROR | |
wellington | Linux (SUSE 9.2) | i686 | OK | ERROR | ||
liverpool | Windows Server 2003 R2 (32-bit) | x64 | OK | ERROR | OK | |
pitt | Mac OS X (10.4.10) | i386 | OK | [ ERROR ] | OK |
Package: prada |
Version: 1.13.2 |
Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check prada_1.13.2.tar.gz |
RetCode: 1 |
Time: 61.4 seconds |
Status: ERROR |
CheckDir: prada.Rcheck |
Warnings: NA |
* checking for working latex ... OK * using log directory '/Users/biocbuild/bbs-2.1-bioc/meat/prada.Rcheck' * using R version 2.6.0 Under development (unstable) (2007-08-10 r42465) * checking for file 'prada/DESCRIPTION' ... OK * this is package 'prada' version '1.13.2' * checking package name space information ... OK * checking package dependencies ... OK * checking if this is a source package ... OK * checking whether package 'prada' 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 ... WARNING 'library' or 'require' calls not declared from: tcltk See the information on DESCRIPTION files in the chapter 'Creating R packages' of the 'Writing R Extensions' manual. * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... NOTE gatePoints: no visible binding for global variable 'prev' killProgress: no visible binding for global variable '.tkprogress.canceled' killProgress: no visible binding for global variable '.tkprogress.window' progress: no visible binding for global variable '.tkprogress.window' progress: no visible binding for '<<-' assignment to '.tkprogress.labelText' progress: no visible binding for global variable '.tkprogress.labelText' progress: no visible binding for global variable '.tkprogress.iterator' progress: no visible binding for global variable '.tkprogress.fallbackIterator' progress : <anonymous>: no visible binding for '<<-' assignment to '.tkprogress.canceled' updateProgress: no visible binding for '<<-' assignment to '.tkprogress.iterator' updateProgress: no visible binding for global variable '.tkprogress.iterator' updateProgress: no visible binding for '<<-' assignment to '.tkprogress.fallbackIterator' updateProgress: no visible binding for global variable '.tkprogress.fallbackIterator' updateProgress: no visible binding for '<<-' assignment to '.tkprogress.labelText' updateProgress: no visible binding for global variable '.tkprogress.labelText' * checking Rd files ... 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 $BLAS_LIBS ... OK * creating prada-Ex.R ... OK * checking examples ... ERROR Running examples in 'prada-Ex.R' failed. The error most likely occurred in: > ### * combineFrames > > flush(stderr()); flush(stdout()) > > ### Name: combineFrames > ### Title: Combine the cytoFrames within a cytoSet according to some > ### grouping factor > ### Aliases: combineFrames > > > ### ** Examples > > cset <- readCytoSet(path=system.file("extdata", package="prada"), + pattern="[A-Z][0-9][0-9]$") > nr1 <- csApply(cset, nrow) > sm1 <- csApply(cset, sum) > > fac <- factor(c(1,1,2,2,2,2)) > cc <- combineFrames(cset, fac) Error in function (classes, fdef, mtable) : unable to find an inherited method for function "pData<-", for signature "AnnotatedDataFrame", "AsIs" Calls: combineFrames ... csApply -> is -> .class1 -> [ -> [ -> pData<- -> <Anonymous> Execution halted
prada.Rcheck/00install.out:
* Installing *source* package 'prada' ... ** libs ** arch - i386 gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/i386 -msse3 -D__NO_MATH_INLINES -fPIC -g -O2 -Wall -std=gnu99 -march=nocona -c inPolygon.c -o inPolygon.o gcc-4.0 -arch i386 -isysroot /Developer/SDKs/MacOSX10.4u.sdk -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o prada.so inPolygon.o -F/Library/Frameworks/R.framework/.. -framework R ** arch - ppc gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -no-cpp-precomp -I/Library/Frameworks/R.framework/Resources/include -I/Library/Frameworks/R.framework/Resources/include/ppc -I/usr/local/include -fPIC -g -O2 -Wall -c inPolygon.c -o inPolygon.o gcc-4.0 -arch ppc -isysroot /Developer/SDKs/MacOSX10.4u.sdk -std=gnu99 -dynamiclib -Wl,-macosx_version_min -Wl,10.3 -undefined dynamic_lookup -single_module -multiply_defined suppress -L/usr/local/lib -o prada.so inPolygon.o -F/Library/Frameworks/R.framework/.. -framework R ** R ** data ** inst ** preparing package for lazy loading Loading required package: Biobase Loading required package: tools Welcome to Bioconductor Vignettes contain introductory material. To view, type 'openVignette()'. To cite Bioconductor, see 'citation("Biobase")' and for packages 'citation(pkgname)'. Loading required package: RColorBrewer Loading required package: grid Scalable Robust Estimators with High Breakdown Point (version 0.3-06) KernSmooth 2.22 installed Copyright M. P. Wand 1997 ** help >>> Building/Updating help pages for package 'prada' Formats: text html latex example analysePlate text html latex example as.all text html latex example barploterrbar text html latex example combineFrames text html latex example csApply text html latex example cytoFrame-class text html latex example cytoSet-class text html latex example data-cytoFrame text html latex example data-cytoSet text html latex example devDims text html latex example devRes text html latex example fitNorm2 text html latex example gate-class text html latex example gateSet-class text html latex example getPradaPar text html latex example new-internal text html latex plotNorm2 text html latex example plotPlate text html latex example readCytoSet text html latex example readFCS text html latex example readFCSaux text html latex example removeCensored text html latex example tcltkProgress text html latex example threePanelPlot text html latex example thresholds text html latex example touchFCS text html latex vpLocation text html latex example ** building package indices ... Loading required package: methods KernSmooth 2.22 installed Copyright M. P. Wand 1997 * DONE (prada)