xps 1.29.0
Christian Stratowa
| Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/xps | | Last Changed Rev: 102594 / Revision: 107696 | | Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015) |
| zin1 | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | [ OK ] | |  |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK | |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings xps_1.29.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/xps.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘xps/DESCRIPTION’ ... OK
* this is package ‘xps’ version ‘1.29.0’
* 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 for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘xps’ can be installed ... [117s/123s] OK
* checking installed package size ... NOTE
installed size is 12.2Mb
sub-directories of 1Mb or more:
doc 2.9Mb
libs 6.1Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' call to ‘tools’ in package code.
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in 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
corplot,ExprTreeSet : .local: warning in axis(4, label = y, at = seq(0,
1, by = (1/(length(y) - 1))), las = 2, cex.axis = 0.8): partial
argument match of 'label' to 'labels'
image,ProcesSet : .local: warning in axis(4, label = y, at = seq(0, 1,
by = (1/(length(y) - 1))), las = 2, cex.axis = 0.8): partial argument
match of 'label' to 'labels'
image,QualTreeSet : .local: warning in axis(4, label = y, at = seq(0,
1, by = (1/(length(y) - 1))), las = 2, cex.axis = 0.8): partial
argument match of 'label' to 'labels'
madplot,ExprTreeSet : .local: warning in axis(4, label = y, at = seq(0,
1, by = (1/(length(y) - 1))), las = 2, cex.axis = 0.8): partial
argument match of 'label' to 'labels'
* 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 GNU extensions in Makefiles ... NOTE
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/biocbuild/bbs-3.2-bioc/meat/xps.Rcheck/xps/libs/xps.so’:
Found ‘_ZSt4cerr’, possibly from ‘std::cerr’ (C++)
Found ‘_ZSt4cout’, possibly from ‘std::cout’ (C++)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [20s/26s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 6 NOTEs
See
‘/home/biocbuild/bbs-3.2-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
found ROOT version 5.32/01 in directory /usr/local/root
** libs
** arch -
g++ -I/usr/local/root/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c TMLMath.cxx
TMLMath.cxx:1109:0: warning: "xmax" redefined [enabled by default]
#define xmax 2.5327372760800758e+305
^
TMLMath.cxx:1060:0: note: this is the location of the previous definition
# define xmax 3.745194030963158e306
^
g++ -I/usr/local/root/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c TStat.cxx
g++ -I/usr/local/root/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c StatUtils.cxx
StatUtils.cxx: In member function ‘Int_t TUnivariateTest::Test(const char*, const char*, const char*, Int_t, Int_t, Double_t, const char*, const char*, char)’:
StatUtils.cxx:764:40: warning: variable ‘pval’ set but not used [-Wunused-but-set-variable]
Double_t mn1, mn2, se, df, stat, pval, pcha, padj;
^
g++ -I/usr/local/root/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSBase.cxx
g++ -I/usr/local/root/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSUtils.cxx
g++ -I/usr/local/root/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSSchemes.cxx
XPSSchemes.cxx: In member function ‘virtual Int_t XGeneChip::ImportProbeInfo(std::ifstream&, Option_t*, const char*, char, Int_t)’:
XPSSchemes.cxx:2800:12: warning: variable ‘order’ set but not used [-Wunused-but-set-variable]
Int_t order, x, y, position, id;
^
XPSSchemes.cxx: In member function ‘virtual Int_t XGeneChip::ReadBinaryData(std::ifstream&, Option_t*, const char*, char, Int_t)’:
XPSSchemes.cxx:3452:22: warning: variable ‘flag’ set but not used [-Wunused-but-set-variable]
Int_t x, y, plen, flag;
^
XPSSchemes.cxx: In member function ‘virtual Int_t XGenomeChip::ImportTransAnnotation(std::ifstream&, Option_t*, const char*, char, Int_t)’:
XPSSchemes.cxx:6213:13: warning: variable ‘nprobes’ set but not used [-Wunused-but-set-variable]
Int_t nprobes;
^
XPSSchemes.cxx: In member function ‘virtual Int_t XExonChip::ReadData(std::ifstream&, Option_t*, const char*, char, Int_t)’:
XPSSchemes.cxx:7506:29: warning: variable ‘psetID’ set but not used [-Wunused-but-set-variable]
Int_t geneID, exonID, psetID;
^
g++ -I/usr/local/root/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSDataTypes.cxx
g++ -I/usr/local/root/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSProjectHandler.cxx
g++ -I/usr/local/root/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSData.cxx
XPSData.cxx: In member function ‘virtual Int_t XGeneChipHyb::ExportDataTreeInfo(Int_t, TString*, const char*, std::ofstream&, const char*)’:
XPSData.cxx:1603:11: warning: variable ‘hasMaxNPix’ set but not used [-Wunused-but-set-variable]
Bool_t hasMaxNPix = kFALSE;
^
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’ [-Wunused-variable]
Int_t err = errNoErr;
^
XPSData.cxx: In member function ‘virtual Int_t XGeneChipHyb::ReadXMLHeader(std::ifstream&, const char*, char)’:
XPSData.cxx:2810:10: warning: unused variable ‘fNMasked’ [-Wunused-variable]
Int_t fNMasked = atoi(strtok(&nextline[dif], "\""));
^
XPSData.cxx:2820:10: warning: unused variable ‘fNOutlier’ [-Wunused-variable]
Int_t fNOutlier = atoi(strtok(&nextline[dif], "\""));
^
XPSData.cxx:2830:10: warning: unused variable ‘fNModified’ [-Wunused-variable]
Int_t fNModified = atoi(strtok(&nextline[dif], "\""));
^
XPSData.cxx: In member function ‘virtual Int_t XGeneChipPivot::ReadData(std::ifstream&, Option_t*, const char*, char, Int_t)’:
XPSData.cxx:3758:10: warning: variable ‘numunits’ set but not used [-Wunused-but-set-variable]
Int_t numunits = 0;
^
g++ -I/usr/local/root/include -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’ [-Wunused-variable]
Int_t err = errNoErr;
^
g++ -I/usr/local/root/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSHybridizer.cxx
g++ -I/usr/local/root/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSSelector.cxx
XPSSelector.cxx: In member function ‘virtual Int_t XRankSelector::Calculate(Int_t, Double_t*, Double_t*, Int_t*)’:
XPSSelector.cxx:222:10: warning: variable ‘err’ set but not used [-Wunused-but-set-variable]
Int_t err = errNoErr;
^
XPSSelector.cxx: In member function ‘Double_t XRankSelector::Cutoff(Int_t, const Double_t*, Double_t, Bool_t)’:
XPSSelector.cxx:334:19: warning: variable ‘par1’ set but not used [-Wunused-but-set-variable]
Double_t par0, par1;
^
g++ -I/usr/local/root/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSNormalizer.cxx
g++ -I/usr/local/root/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSPreProcessing.cxx
XPSPreProcessing.cxx: In member function ‘virtual Int_t XGCProcesSet::DoBorderElements(Int_t, TTree**, TTree**, XDNAChip*, TFile*)’:
XPSPreProcessing.cxx:3522:10: warning: unused variable ‘idxhi’ [-Wunused-variable]
Int_t idxhi, idxlo;
^
XPSPreProcessing.cxx:3522:17: warning: unused variable ‘idxlo’ [-Wunused-variable]
Int_t idxhi, idxlo;
^
XPSPreProcessing.cxx:3527:13: warning: variable ‘mnhi’ set but not used [-Wunused-but-set-variable]
Double_t mnhi, lmnhi, rmnhi, tmnhi, bmnhi;
^
XPSPreProcessing.cxx:3528:13: warning: variable ‘mnlo’ set but not used [-Wunused-but-set-variable]
Double_t mnlo, lmnlo, rmnlo, tmnlo, bmnlo;
^
XPSPreProcessing.cxx: In member function ‘virtual Int_t XGCProcesSet::DoBgrdQualityControl(Int_t, TTree**, XDNAChip*, TFile*)’:
XPSPreProcessing.cxx:3677:10: warning: unused variable ‘numunits’ [-Wunused-variable]
Int_t numunits = chip->GetNumUnits();
^
XPSPreProcessing.cxx:3678:10: warning: unused variable ‘size’ [-Wunused-variable]
Int_t size = numrows*numcols;
^
XPSPreProcessing.cxx: In member function ‘virtual Int_t XGCProcesSet::ExportResdTrees(Int_t, TString*, const char*, std::ofstream&, const char*)’:
XPSPreProcessing.cxx:5780:10: warning: variable ‘err’ set but not used [-Wunused-but-set-variable]
Int_t err = errNoErr;
^
XPSPreProcessing.cxx: In member function ‘virtual Int_t XGCProcesSet::ExportQualTrees(Int_t, TString*, const char*, std::ofstream&, const char*)’:
XPSPreProcessing.cxx:6769:16: warning: unused variable ‘idxstr’ [-Wunused-variable]
XIdxString *idxstr = 0;
^
XPSPreProcessing.cxx: In member function ‘TTree* XGCProcesSet::FillDataTree(TTree*, const char*, XAlgorithm*, Int_t, Int_t, Double_t*, Double_t*)’:
XPSPreProcessing.cxx:8744:1: warning: label ‘cleanup’ defined but not used [-Wunused-label]
cleanup:
^
XPSPreProcessing.cxx: In member function ‘virtual Int_t XExonProcesSet::DoSpliceExpress(Int_t, TTree**, Int_t, TTree**, TFile*)’:
XPSPreProcessing.cxx:9789:14: warning: unused variable ‘numatoms’ [-Wunused-variable]
Int_t numatoms = unit->GetNumAtoms();
^
XPSPreProcessing.cxx:9396:10: warning: unused variable ‘x’ [-Wunused-variable]
Int_t x = 0;
^
XPSPreProcessing.cxx:9397:10: warning: unused variable ‘y’ [-Wunused-variable]
Int_t y = 0;
^
XPSPreProcessing.cxx:9402:10: warning: unused variable ‘stepout’ [-Wunused-variable]
Int_t stepout = (Int_t)((100000.0 + 10.0*numdata)/(Float_t)numdata); //step size for verbose output
^
XPSPreProcessing.cxx: In member function ‘virtual TTree* XExonProcesSet::SchemeTree(XAlgorithm*, void*, TLeaf**)’:
XPSPreProcessing.cxx:10356:18: warning: unused variable ‘scheme_ptr_ptr’ [-Wunused-variable]
XExonScheme **scheme_ptr_ptr = (XExonScheme**)scheme;
^
g++ -I/usr/local/root/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSNormation.cxx
XPSNormation.cxx: In member function ‘virtual Int_t XNormedGCSet::ExportExprTrees(Int_t, TString*, const char*, std::ofstream&, const char*)’:
XPSNormation.cxx:1350:10: warning: variable ‘err’ set but not used [-Wunused-but-set-variable]
Int_t err = errNoErr;
^
g++ -I/usr/local/root/include -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’ [-Wunused-variable]
TBranch *brchUnit = intree->GetBranch("fUnitID"); //prevent crash SafeDelete(fDataFile)
^
g++ -I/usr/local/root/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSAnalyzer.cxx
g++ -I/usr/local/root/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c XPSAnalysis.cxx
g++ -I/usr/local/root/include -O2 -Wall -fPIC -pthread -m64 -I/usr/local/root/include/root -c rwrapper.cxx
Generating dictionary xpsDict.cxx...
g++ -I/usr/local/root/include -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 /home/biocbuild/bbs-3.2-bioc/meat/xps.Rcheck/xps/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (xps)