Question: install xps in ubuntu 14.04
0
gravatar for cerikahp
4.7 years ago by
cerikahp0
cerikahp0 wrote:

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

 

 

microarray xps installation • 872 views
ADD COMMENTlink modified 4.7 years ago by cstrato3.9k • written 4.7 years ago by cerikahp0
Answer: install xps in ubuntu 14.04
0
gravatar for cstrato
4.7 years ago by
cstrato3.9k
Austria
cstrato3.9k wrote:

How did you install ROOT? Did you compile it or use one of the precompiled binaries?

Usually people get this error when they mixed 32 bit and 64 bit.

Since you did compile xps for 64 bit, did you install a 64 bit version of ROOT?

From where did you get the version of ROOT that you are using? 

Do not use a version from a repository but always download ROOT from CERN.

Recently, another user had problems installing ROOT on Linux and I mentioned the links to download ROOT, see:

Problem installing XPS

Please try one of these links.

Regards,

Christian

 

 

 

ADD COMMENTlink written 4.7 years ago by cstrato3.9k
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