xps 0.3.12
Christian Stratowa
| Snapshot Date: 2007-12-11 00:09:07 -0800 (Tue, 11 Dec 2007) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xps | | Last Changed Rev: 28904 / Revision: 29143 | | Last Changed Date: 2007-11-25 13:04:33 -0800 (Sun, 25 Nov 2007) |
| lamb1 | Linux (SUSE 10.1) / x86_64 | OK | [ OK ] | |
| wilson2 | Linux (openSUSE 10.3) / x86_64 | ERROR | skipped | |
| wellington | Linux (openSUSE 10.3) / i686 | ERROR | skipped | |
| liverpool | Windows Server 2003 R2 (32-bit) / x64 | N O T S U P P O R T E D |
| lemming | Windows Server 2003 (32-bit) / x64 | N O T S U P P O R T E D |
* checking for working latex ... OK
* using log directory '/home/biocbuild/bbs-2.2-bioc/meat/xps.Rcheck'
* using R version 2.7.0 Under development (unstable) (2007-11-18 r43497)
* checking for file 'xps/DESCRIPTION' ... OK
* this is package 'xps' version '0.3.12'
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package 'xps' 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 ... OK
* 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $BLAS_LIBS ... OK
* creating xps-Ex.R ... OK
* checking examples ... OK
* checking package vignettes in 'inst/doc' ... OK
* creating xps-manual.tex ... OK
* checking xps-manual.tex ... OK
* Installing *source* package 'xps' ...
checking for gcc... gcc -std=gnu99
checking for C compiler default output file name... a.out
checking whether the C compiler works... yes
checking whether we are cross compiling... no
checking for suffix of executables...
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc -std=gnu99 accepts -g... yes
checking for gcc -std=gnu99 option to accept ANSI C... none needed
checking how to run the C preprocessor... gcc -std=gnu99 -E
checking for gcc... (cached) gcc -std=gnu99
checking whether we are using the GNU C compiler... (cached) yes
checking whether gcc -std=gnu99 accepts -g... (cached) yes
checking for gcc -std=gnu99 option to accept ANSI C... (cached) none needed
checking for root-config... yes
found ROOT version 5.17/05 in directory /usr/local
** libs
** arch -
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c TMLMath.cxx
TMLMath.cxx:1109:1: warning: "xmax" redefined
TMLMath.cxx:1060:1: warning: this is the location of the previous definition
TMLMath.cxx: In static member function 'static Double_t TMLMath::PBetaRaw(Double_t, Double_t, Double_t, Int_t)':
TMLMath.cxx:1397: warning: converting to 'Int_t' from 'Double_t'
TMLMath.cxx:1403: warning: converting to 'Int_t' from 'Double_t'
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c TStat.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c StatUtils.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSBase.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSUtils.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSSchemes.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSDataTypes.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSProjectHandler.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSData.cxx
XPSData.cxx: In member function 'virtual Int_t XGeneChipHyb::ReadXMLHeader(std::ifstream&, const char*, char)':
XPSData.cxx:1963: warning: unused variable 'fNMasked'
XPSData.cxx:1973: warning: unused variable 'fNOutlier'
XPSData.cxx:1983: warning: unused variable 'fNModified'
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSProcessing.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSHybridizer.cxx
XPSHybridizer.cxx: In member function 'Double_t XDetectionCall::WilcoxTest(Int_t, Double_t*, Double_t)':
XPSHybridizer.cxx:1709: warning: 'pval' may be used uninitialized in this function
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSSelector.cxx
XPSSelector.cxx: In member function 'Double_t XRankSelector::Cutoff(Int_t, const Double_t*, Double_t, Bool_t)':
XPSSelector.cxx:333: warning: 'par0' may be used uninitialized in this function
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSNormalizer.cxx
XPSNormalizer.cxx: In member function 'virtual Int_t XNormalizer::Calculate(Int_t, Double_t*, Double_t*, Int_t*)':
XPSNormalizer.cxx:220: warning: 'his2all' may be used uninitialized in this function
XPSNormalizer.cxx:221: warning: 'his2sel' may be used uninitialized in this function
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSPreProcessing.cxx
XPSPreProcessing.cxx: In member function 'virtual Int_t XGCProcesSet::DoMedianPolish(Int_t, TTree**, Int_t, TTree**)':
XPSPreProcessing.cxx:4180: warning: operation on 'numsels' may be undefined
XPSPreProcessing.cxx: In member function 'virtual Int_t XGCProcesSet::DoMedianPolish(Int_t, TTree**, Int_t, TTree**, TFile*)':
XPSPreProcessing.cxx:4533: warning: operation on 'numsels' may be undefined
XPSPreProcessing.cxx: In member function 'virtual Int_t XGenomeProcesSet::DetectCall(Int_t, TTree**, Int_t&, TTree**)':
XPSPreProcessing.cxx:4873: warning: unused variable 'scmleaf'
XPSPreProcessing.cxx: In member function 'virtual Int_t XGenomeProcesSet::DoMedianPolish(Int_t, TTree**, Int_t, TTree**)':
XPSPreProcessing.cxx:5671: warning: operation on 'numsels' may be undefined
XPSPreProcessing.cxx: In member function 'virtual Int_t XGenomeProcesSet::DoMedianPolish(Int_t, TTree**, Int_t, TTree**, TFile*)':
XPSPreProcessing.cxx:6056: warning: operation on 'numsels' may be undefined
XPSPreProcessing.cxx: In member function 'virtual Int_t XExonProcesSet::DoMedianPolish(Int_t, TTree**, Int_t, TTree**)':
XPSPreProcessing.cxx:7869: warning: operation on 'numsels' may be undefined
XPSPreProcessing.cxx: In member function 'virtual Int_t XExonProcesSet::DoMedianPolish(Int_t, TTree**, Int_t, TTree**, TFile*)':
XPSPreProcessing.cxx:8266: warning: operation on 'numsels' may be undefined
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c XPSNormation.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c rwrapper.cxx
Generating dictionary xpsDict.cxx...
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/include/root -c xpsDict.cxx
g++ -shared -O2 -m64 TMLMath.o TStat.o StatUtils.o XPSBase.o XPSUtils.o XPSSchemes.o XPSDataTypes.o XPSProjectHandler.o XPSData.o XPSProcessing.o XPSHybridizer.o XPSSelector.o XPSNormalizer.o XPSPreProcessing.o XPSNormation.o rwrapper.o xpsDict.o -o xps.so -L/usr/local/lib/root -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lGui -pthread -lm -ldl -rdynamic
** R
** inst
** preparing package for lazy loading
** help
>>> Building/Updating help pages for package 'xps'
Formats: text html latex example
CallTreeSet-class text html latex example
DataTreeSet-class text html latex example
ExprTreeSet-class text html latex example
ProcesSet-class text html latex example
ProjectInfo-class text html latex example
ROOT text html latex
SchemeTreeSet-class text html latex example
TreeSet-class text html latex example
addData-methods text html latex example
attachBgrd-methods text html latex
attachInten-methods text html latex example
attachMask-methods text html latex example
bgcorrect text html latex example
boxplot-methods text html latex example
boxplot.dev text html latex
callplot-methods text html latex
dabg.call text html latex example
export text html latex example
export.root text html latex example
express text html latex example
getChipName text html latex example
getChipType text html latex example
getDatatype text html latex example
getNameType text html latex example
getNumberTrees text html latex example
getProbeInfo text html latex example
getTreeData-methods text html latex
getTreeNames text html latex example
hist-methods text html latex example
image-methods text html latex
image.dev text html latex example
import.data text html latex example
import.exon.scheme text html latex example
import.expr.scheme text html latex example
import.genome.scheme text html latex example
isROOTFile text html latex example
mas4 text html latex example
mas5 text html latex example
mas5.call text html latex example
mboxplot-methods text html latex example
mvaplot-methods text html latex
mvaplot.dev text html latex
normalize text html latex example
pm-methods text html latex example
pmplot-methods text html latex example
rma text html latex example
root.browser-methods text html latex
root.data text html latex example
root.density text html latex example
root.graph1D text html latex example
root.graph2D text html latex example
root.hist1D text html latex example
root.hist2D text html latex example
root.hist3D text html latex example
root.image text html latex example
root.mvaplot text html latex example
root.scheme text html latex example
summarize text html latex example
type2Exten text html latex example
validData-methods text html latex
validTreetype text html latex example
xps-package text html latex
xpsOptions text html latex
** building package indices ...
* DONE (xps)