xps 1.16.0
Christian Stratowa
| Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/xps | | Last Changed Rev: 64678 / Revision: 69725 | | Last Changed Date: 2012-03-30 15:05:02 -0700 (Fri, 30 Mar 2012) |
| lamb2 | Linux (openSUSE 11.4) / x86_64 | OK | [ OK ] | |
| moscato2 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | N O T S U P P O R T E D |
| petty | Mac OS X Leopard (10.5.8) / i386 | OK | OK | OK |
* using log directory ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/xps.Rcheck’
* using R version 2.15.1 (2012-06-22)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘xps/DESCRIPTION’ ... OK
* this is package ‘xps’ version ‘1.16.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking whether package ‘xps’ can be installed ... OK
* checking installed package size ... NOTE
installed size is 12.2Mb
sub-directories of 1Mb or more:
doc 2.8Mb
libs 6.2Mb
* 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 namespace can be loaded with stated dependencies ... OK
* checking whether the namespace 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
File ‘xps/R/zzz.R’:
.onLoad calls:
require(methods)
require(utils)
Package startup functions should not change the search path.
See section ‘Good practice’ in ?.onAttach.
.onLoad: warning in packageDescription(pkgname, field = "Version"):
partial argument match of 'field' to 'fields'
CELHeader: warning in matrix(nr = 23, nc = 1): partial argument match
of 'nr' to 'nrow'
CELHeader: warning in matrix(nr = 23, nc = 1): partial argument match
of 'nc' to 'ncol'
dabgCall.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial
argument match of 'nr' to 'nrow'
dabgCall.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial
argument match of 'nc' to 'ncol'
firma.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial argument
match of 'nr' to 'nrow'
firma.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial argument
match of 'nc' to 'ncol'
iniCall.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial
argument match of 'nr' to 'nrow'
iniCall.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial
argument match of 'nc' to 'ncol'
mas4.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial argument
match of 'nr' to 'nrow'
mas4.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial argument
match of 'nc' to 'ncol'
mas5.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial argument
match of 'nr' to 'nrow'
mas5.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial argument
match of 'nc' to 'ncol'
mas5Call.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial
argument match of 'nr' to 'nrow'
mas5Call.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial
argument match of 'nc' to 'ncol'
normalize.ExprTreeSet: warning in matrix(nr = 0, nc = 0): partial
argument match of 'nr' to 'nrow'
normalize.ExprTreeSet: warning in matrix(nr = 0, nc = 0): partial
argument match of 'nc' to 'ncol'
plotBorder: warning in jpeg(file = outfile, width = w, height = h):
partial argument match of 'file' to 'filename'
plotBorder: warning in png(file = outfile, width = w, height = h):
partial argument match of 'file' to 'filename'
plotBoxplot: warning in jpeg(file = outfile, width = w, height = h):
partial argument match of 'file' to 'filename'
plotBoxplot: warning in png(file = outfile, width = w, height = h):
partial argument match of 'file' to 'filename'
plotCOI: warning in jpeg(file = outfile, width = w, height = h):
partial argument match of 'file' to 'filename'
plotCOI: warning in png(file = outfile, width = w, height = h): partial
argument match of 'file' to 'filename'
plotCall: warning in jpeg(file = outfile, width = w, height = h):
partial argument match of 'file' to 'filename'
plotCall: warning in png(file = outfile, width = w, height = h):
partial argument match of 'file' to 'filename'
plotCorr: warning in jpeg(file = outfile, width = w, height = h):
partial argument match of 'file' to 'filename'
plotCorr: warning in png(file = outfile, width = w, height = h):
partial argument match of 'file' to 'filename'
plotDensity: warning in jpeg(file = outfile, width = w, height = h):
partial argument match of 'file' to 'filename'
plotDensity: warning in png(file = outfile, width = w, height = h):
partial argument match of 'file' to 'filename'
plotImage: warning in jpeg(file = outfile, width = w, height = h):
partial argument match of 'file' to 'filename'
plotImage: warning in png(file = outfile, width = w, height = h):
partial argument match of 'file' to 'filename'
plotIntensity2GC: warning in jpeg(file = outfile, width = w, height =
h): partial argument match of 'file' to 'filename'
plotIntensity2GC: warning in png(file = outfile, width = w, height =
h): partial argument match of 'file' to 'filename'
plotMA: warning in jpeg(file = outfile, width = w, height = h): partial
argument match of 'file' to 'filename'
plotMA: warning in png(file = outfile, width = w, height = h): partial
argument match of 'file' to 'filename'
plotMAD: warning in jpeg(file = outfile, width = w, height = h):
partial argument match of 'file' to 'filename'
plotMAD: warning in png(file = outfile, width = w, height = h): partial
argument match of 'file' to 'filename'
plotNUSE: warning in jpeg(file = outfile, width = w, height = h):
partial argument match of 'file' to 'filename'
plotNUSE: warning in png(file = outfile, width = w, height = h):
partial argument match of 'file' to 'filename'
plotPCA: warning in jpeg(file = outfile, width = w, height = h):
partial argument match of 'file' to 'filename'
plotPCA: warning in png(file = outfile, width = w, height = h): partial
argument match of 'file' to 'filename'
plotPM: warning in jpeg(file = outfile, width = w, height = h): partial
argument match of 'file' to 'filename'
plotPM: warning in png(file = outfile, width = w, height = h): partial
argument match of 'file' to 'filename'
plotProbeset: warning in jpeg(file = outfile, width = w, height = h):
partial argument match of 'file' to 'filename'
plotProbeset: warning in png(file = outfile, width = w, height = h):
partial argument match of 'file' to 'filename'
plotRLE: warning in jpeg(file = outfile, width = w, height = h):
partial argument match of 'file' to 'filename'
plotRLE: warning in png(file = outfile, width = w, height = h): partial
argument match of 'file' to 'filename'
plotVolcano: warning in jpeg(file = outfile, width = w, height = h):
partial argument match of 'file' to 'filename'
plotVolcano: warning in png(file = outfile, width = w, height = h):
partial argument match of 'file' to 'filename'
prefilter.ExprTreeSet: warning in matrix(nr = 0, nc = 0): partial
argument match of 'nr' to 'nrow'
prefilter.ExprTreeSet: warning in matrix(nr = 0, nc = 0): partial
argument match of 'nc' to 'ncol'
preprocess.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial
argument match of 'nr' to 'nrow'
preprocess.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial
argument match of 'nc' to 'ncol'
qc.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial argument
match of 'nr' to 'nrow'
qc.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial argument
match of 'nc' to 'ncol'
qualify.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial
argument match of 'nr' to 'nrow'
qualify.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial
argument match of 'nc' to 'ncol'
rma.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial argument
match of 'nr' to 'nrow'
rma.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial argument
match of 'nc' to 'ncol'
summarize.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial
argument match of 'nr' to 'nrow'
summarize.DataTreeSet: warning in matrix(nr = 0, nc = 0): partial
argument match of 'nc' to 'ncol'
unifilter.ExprTreeSet: warning in matrix(nr = 0, nc = 0): partial
argument match of 'nr' to 'nrow'
unifilter.ExprTreeSet: warning in matrix(nr = 0, nc = 0): partial
argument match of 'nc' to 'ncol'
xpsQAReport: warning in png(file = file.path(docdir,
"RNADegradationPlot.png"), width = 540, height = 540): partial
argument match of 'file' to 'filename'
xpsQAReport: warning in png(file = file.path(docdir,
"RNADegradationSlope.png"), width = 540, height = 440): partial
argument match of 'file' to 'filename'
* 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 Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/loc/home/biocbuild/bbs-2.10-bioc/meat/xps.Rcheck/xps/libs/xps.so’:
Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
Found ‘printf’, possibly from ‘printf’ (C)
Compiled code should not call functions which might terminate R nor
write to stdout/stderr instead of to the console. The detected symbols
are linked into the code but might come from libraries and not actually
be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignettes ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There were 3 notes.
See
‘/loc/home/biocbuild/bbs-2.10-bioc/meat/xps.Rcheck/00check.log’
for details.
* 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 5.32/01 in directory /usr/local/root
** libs
** arch -
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c TMLMath.cxx
TMLMath.cxx:1109:0: warning: "xmax" redefined
TMLMath.cxx:1060:0: note: this is the location of the previous definition
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c TStat.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c StatUtils.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSBase.cxx
XPSBase.cxx: In member function ‘XFolder* XFolder::AddFolder(const char*, const char*, const char*, TCollection*)’:
XPSBase.cxx:183:76: warning: too many arguments for format
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSUtils.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSSchemes.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSDataTypes.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSProjectHandler.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSData.cxx
XPSData.cxx: In member function ‘virtual Int_t XGeneChipHyb::ExportMaskTreeInfo(Int_t, TString*, const char*, std::ofstream&, const char*)’:
XPSData.cxx:1797:10: warning: unused variable ‘err’
XPSData.cxx: In member function ‘virtual Int_t XGeneChipHyb::ReadXMLHeader(std::ifstream&, const char*, char)’:
XPSData.cxx:2810:10: warning: unused variable ‘fNMasked’
XPSData.cxx:2820:10: warning: unused variable ‘fNOutlier’
XPSData.cxx:2830:10: warning: unused variable ‘fNModified’
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSProcessing.cxx
XPSProcessing.cxx: In member function ‘virtual Int_t XProcesSet::ExportMaskTreeInfo(Int_t, TString*, const char*, std::ofstream&, const char*)’:
XPSProcessing.cxx:1530:10: warning: unused variable ‘err’
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSHybridizer.cxx
XPSHybridizer.cxx: In member function ‘Double_t XDetectionCall::WilcoxTest(Int_t, Double_t*, Double_t)’:
XPSHybridizer.cxx:2066:36: warning: ‘pval’ may be used uninitialized in this function
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/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:334:13: warning: ‘par0’ may be used uninitialized in this function
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/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:239:10: warning: ‘his2all’ may be used uninitialized in this function
XPSNormalizer.cxx:240:10: warning: ‘his2sel’ may be used uninitialized in this function
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSPreProcessing.cxx
XPSPreProcessing.cxx: In member function ‘virtual Int_t XGCProcesSet::DoDataQualityControl(Int_t, TTree**, TTree**, TTree**, XDNAChip*, TFile*)’:
XPSPreProcessing.cxx:3026:56: warning: operation on ‘numsels’ may be undefined
XPSPreProcessing.cxx: In member function ‘virtual Int_t XGCProcesSet::DoBorderElements(Int_t, TTree**, TTree**, XDNAChip*, TFile*)’:
XPSPreProcessing.cxx:3515:10: warning: unused variable ‘idxhi’
XPSPreProcessing.cxx:3515:17: warning: unused variable ‘idxlo’
XPSPreProcessing.cxx: In member function ‘virtual Int_t XGCProcesSet::DoBgrdQualityControl(Int_t, TTree**, XDNAChip*, TFile*)’:
XPSPreProcessing.cxx:3670:10: warning: unused variable ‘numunits’
XPSPreProcessing.cxx:3671:10: warning: unused variable ‘size’
XPSPreProcessing.cxx: In member function ‘virtual Int_t XGCProcesSet::DoMultichipCall(Int_t, TTree**, Int_t&, TTree**, TFile*)’:
XPSPreProcessing.cxx:4252:56: warning: operation on ‘numsels’ may be undefined
XPSPreProcessing.cxx: In member function ‘virtual Int_t XGCProcesSet::DoMultichipExpress(Int_t, TTree**, Int_t, TTree**, TFile*)’:
XPSPreProcessing.cxx:5135:56: warning: operation on ‘numsels’ may be undefined
XPSPreProcessing.cxx: In member function ‘virtual Int_t XGCProcesSet::ExportQualTrees(Int_t, TString*, const char*, std::ofstream&, const char*)’:
XPSPreProcessing.cxx:6762:16: warning: unused variable ‘idxstr’
XPSPreProcessing.cxx: In member function ‘TTree* XGCProcesSet::FillDataTree(TTree*, const char*, XAlgorithm*, Int_t, Int_t, Double_t*, Double_t*)’:
XPSPreProcessing.cxx:8737:1: warning: label ‘cleanup’ defined but not used
XPSPreProcessing.cxx: In member function ‘virtual Int_t XExonProcesSet::DoSpliceExpress(Int_t, TTree**, Int_t, TTree**, TFile*)’:
XPSPreProcessing.cxx:9591:56: warning: operation on ‘numsels’ may be undefined
XPSPreProcessing.cxx:9782:14: warning: unused variable ‘numatoms’
XPSPreProcessing.cxx:9389:10: warning: unused variable ‘x’
XPSPreProcessing.cxx:9390:10: warning: unused variable ‘y’
XPSPreProcessing.cxx:9395:10: warning: unused variable ‘stepout’
XPSPreProcessing.cxx: In member function ‘virtual TTree* XExonProcesSet::SchemeTree(XAlgorithm*, void*, TLeaf**)’:
XPSPreProcessing.cxx:10349:18: warning: unused variable ‘scheme_ptr_ptr’
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSNormation.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSFilter.cxx
XPSFilter.cxx: In member function ‘virtual Int_t XUniFilter::Calculate(TTree*, const char*, TTree*, const char*, Int_t)’:
XPSFilter.cxx:1787:13: warning: unused variable ‘brchUnit’
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSAnalyzer.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSAnalysis.cxx
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c rwrapper.cxx
Generating dictionary xpsDict.cxx...
g++ -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/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 XPSFilter.o XPSAnalyzer.o XPSAnalysis.o rwrapper.o xpsDict.o -L/usr/local/root/lib/root -lGui -lCore -lCint -lRIO -lNet -lHist -lGraf -lGraf3d -lGpad -lTree -lRint -lPostscript -lMatrix -lPhysics -lMathCore -lThread -pthread -lm -ldl -rdynamic -lRIO -lGed -lTreePlayer -lTreeViewer -o xps.so
installing to /loc/home/biocbuild/bbs-2.10-bioc/meat/xps.Rcheck/xps/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
‘APTvsXPS.Rnw’
‘xps.Rnw’
‘xpsClasses.Rnw’
‘xpsPreprocess.Rnw’
** testing if installed package can be loaded
* DONE (xps)