Hi!
I've been trying to install xps with ubuntu 14.04. I've tried with root_v5.34.28 and followed all the instructions in the xps README . But when i try installing form bioconductor not only do i get lots of warnings, but the installation is removed becouse it cant be loaded. This is the ouput
biocLite("xps", type="source")
BioC_mirror: http://bioconductor.org
Using Bioconductor version 3.0 (BiocInstaller 1.16.2), R version 3.1.3.
Installing package(s) 'xps'
trying URL 'http://bioconductor.org/packages/3.0/bioc/src/contrib/xps_1.26.1.tar.gz'
Content type 'application/x-gzip' length 6669404 bytes (6.4 MB)
opened URL
==================================================
downloaded 6.4 MB
* 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 5.34/28 in directory /home/cerikahp/Bin/root
** libs
** arch -
g++ -I/home/cerikahp/Bin/root/include -O2 -Wall -fPIC -pthread -m64 -I/home/cerikahp/Bin/root/include -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/home/cerikahp/Bin/root/include -O2 -Wall -fPIC -pthread -m64 -I/home/cerikahp/Bin/root/include -c TStat.cxx
g++ -I/home/cerikahp/Bin/root/include -O2 -Wall -fPIC -pthread -m64 -I/home/cerikahp/Bin/root/include -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/home/cerikahp/Bin/root/include -O2 -Wall -fPIC -pthread -m64 -I/home/cerikahp/Bin/root/include -c XPSBase.cxx
g++ -I/home/cerikahp/Bin/root/include -O2 -Wall -fPIC -pthread -m64 -I/home/cerikahp/Bin/root/include -c XPSUtils.cxx
g++ -I/home/cerikahp/Bin/root/include -O2 -Wall -fPIC -pthread -m64 -I/home/cerikahp/Bin/root/include -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]
It kind of keep showings similar warning until this:
g++ -I/home/cerikahp/Bin/root/include -O2 -Wall -fPIC -pthread -m64 -I/home/cerikahp/Bin/root/include -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/home/cerikahp/Bin/root/include -O2 -Wall -fPIC -pthread -m64 -I/home/cerikahp/Bin/root/include -c XPSAnalyzer.cxx
g++ -I/home/cerikahp/Bin/root/include -O2 -Wall -fPIC -pthread -m64 -I/home/cerikahp/Bin/root/include -c XPSAnalysis.cxx
g++ -I/home/cerikahp/Bin/root/include -O2 -Wall -fPIC -pthread -m64 -I/home/cerikahp/Bin/root/include -c rwrapper.cxx
Generating dictionary xpsDict.cxx...
g++ -I/home/cerikahp/Bin/root/include -O2 -Wall -fPIC -pthread -m64 -I/home/cerikahp/Bin/root/include -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/home/cerikahp/Bin/root/lib -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 /usr/local/lib/R/site-library/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
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/usr/local/lib/R/site-library/xps/libs/xps.so':
/home/cerikahp/Bin/root/lib/libTreeViewer.so: undefined symbol: _ZN8TAttFill17SetFillColorAlphaEsf
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/usr/local/lib/R/site-library/xps’
The downloaded source packages are in
‘/tmp/RtmprEFYYF/downloaded_packages’
Warning message:
In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) :
installation of package ‘xps’ had non-zero exit status
For what i can understand from the error, it knows where root is, and can even see libTreeViewer but it has something it doesnt understand. Is that a problem with my root version ? I cant try with one older becouse i just dont find them.
R version 3.1.3 (2015-03-09)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.2 LTS
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=es_MX.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=es_MX.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=es_MX.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=es_MX.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] BiocInstaller_1.16.2
loaded via a namespace (and not attached):
[1] tools_3.1.3
