SEQanswers

Go Back   SEQanswers > General



Similar Threads
Thread Thread Starter Forum Replies Last Post
CNVnator Install Instructions dmacmillan Bioinformatics 25 09-26-2016 01:59 AM
couldn't run CNVnator menenuh Bioinformatics 39 07-29-2014 11:48 AM
what files are produced from CNVnator ? Kennels Bioinformatics 1 01-23-2012 08:14 AM
Legume root biology anandksrao Introductions 0 06-03-2011 02:30 AM
PubMed: De novo sequencing and analysis of the American ginseng root transcriptome us Newsbot! Literature Watch 0 04-27-2010 02:00 AM

Reply
 
Thread Tools
Old 07-07-2011, 06:05 AM   #1
milesgr
Member
 
Location: NJ

Join Date: Jun 2010
Posts: 34
Default ROOT install + CNVnator issues

I received a pm from user antimony with the following but he did not allow private message responses, so I figured I'd post it here and hope he sees it.

Quote:
Originally Posted by antimony
Hi milesgr,

how did you solve the compiling problems that came about when you were installing ROOT

/usr/bin/ld: /usr/local/lib/libfftw3.a(map-r2r-kind.o): relocation R_X86_64_32S against `a local symbol' can not be used when making a shared object; recompile with -fPIC
/usr/local/lib/libfftw3.a: could not read symbols: Bad value
collect2: ld returned 1 exit status
gmake: *** [lib/libFFTW.so] Error 1

I am having the same problems with libpython and it looks like a generic situation

I remember what the problem was - the version of libfftw3.a found in /usr/local/lib was out of date. I also believe that the good version of the file was in another folder (but I wouldn't hold me to that) that I was able to find in the file system due to a message board thread that I cannot seem to locate. It is also possible that I had to install the updated fftw software (I don't remember ). If you do a search on the linux machine for libfftw3.a, perhaps you can find the other version if it exists. If not, I can send you the file that you will place in /usr/local/lib that should fix everything. If you want me to e-mail you the file, please feel free to e-mail me at my forum handle at umdnj.edu
milesgr is offline   Reply With Quote
Old 07-10-2011, 05:25 PM   #2
antimony
Junior Member
 
Location: Singapore

Join Date: Jul 2011
Posts: 1
Default

hi milesgr, thanks! its embarrassing not realizing that private messages was not turned on and i had to find the reply right here. if the reason is that the libraries are out of date, i will try and get libpython2.6.a fixed and updated.
antimony is offline   Reply With Quote
Old 01-01-2014, 04:47 PM   #3
binlangman
Member
 
Location: China

Join Date: Dec 2013
Posts: 11
Default ROOT installation error

I downloaded root_v5.34.14.source.tar.gz from ftp://root.cern.ch/root,and I run the following command in order to install ROOT:
tar zxvf root_v5.34.14.source.tar.gz
cd root
./configure --with-xpm-libdir=/usr/lib64
make
But there was an error when I run the command "make". Here is the error:

bin/rmkdepend -R -fcore/base/src/TROOT.d -Y -w 1000 -- -pipe -m64 -Wshadow -Wall -W -Woverloaded-virtual -fPIC -Iinclude -pthread -D__cplusplus -- /opt2/tools/root/core/base/src/TROOT.cxx
g++ -O2 -pipe -m64 -Wshadow -Wall -W -Woverloaded-virtual -fPIC -Iinclude -pthread -o core/base/src/TROOT.o -c /opt2/tools/root/core/base/src/TROOT.cxx
g++ -shared -Wl,-soname,libCore.so -m64 -O2 -Wl,--no-undefined -Wl,--as-needed -o lib/libCore.so core/base/src/InitGui.o core/base/src/ManualBase4.o core/base/src/Match.o core/base/src/String.o core/base/src/Stringio.o core/base/src/TApplication.o core/base/src/TApplicationImp.o core/base/src/TAtt3D.o core/base/src/TAttAxis.o core/base/src/TAttBBox.o core/base/src/TAttFill.o core/base/src/TAttLine.o core/base/src/TAttMarker.o core/base/src/TAttPad.o core/base/src/TAttText.o core/base/src/TBase64.o core/base/src/TBenchmark.o core/base/src/TBrowser.o core/base/src/TBrowserImp.o core/base/src/TBuffer3D.o core/base/src/TBuffer.o core/base/src/TCanvasImp.o core/base/src/TColor.o core/base/src/TColorGradient.o core/base/src/TContextMenu.o core/base/src/TContextMenuImp.o core/base/src/TControlBarImp.o core/base/src/TDatime.o core/base/src/TDirectory.o core/base/src/TEnv.o core/base/src/TError.o core/base/src/TException.o core/base/src/TExec.o core/base/src/TFileCollection.o core/base/src/TFileInfo.o core/base/src/TFolder.o core/base/src/TGuiFactory.o core/base/src/TInetAddress.o core/base/src/TInspectorImp.o core/base/src/TMacro.o core/base/src/TMathBase.o core/base/src/TMD5.o core/base/src/TMemberInspector.o core/base/src/TMessageHandler.o core/base/src/TNamed.o core/base/src/TObject.o core/base/src/TObjectSpy.o core/base/src/TObjString.o core/base/src/TParameter.o core/base/src/TPluginManager.o core/base/src/TPRegexp.o core/base/src/TProcessID.o core/base/src/TProcessUUID.o core/base/src/TQCommand.o core/base/src/TQConnection.o core/base/src/TQObject.o core/base/src/TRefCnt.o core/base/src/TRef.o core/base/src/TRegexp.o core/base/src/TRemoteObject.o core/base/src/TROOT.o core/base/src/TStopwatch.o core/base/src/TStorage.o core/base/src/TString.o core/base/src/TStringLong.o core/base/src/TStyle.o core/base/src/TSysEvtHandler.o core/base/src/TSystem.o core/base/src/TSystemDirectory.o core/base/src/TSystemFile.o core/base/src/TTask.o core/base/src/TTime.o core/base/src/TTimer.o core/base/src/TTimeStamp.o core/base/src/TUri.o core/base/src/TUrl.o core/base/src/TUUID.o core/base/src/TVirtualFFT.o core/base/src/TVirtualGL.o core/base/src/TVirtualMonitoring.o core/base/src/TVirtualMutex.o core/base/src/TVirtualPad.o core/base/src/TVirtualPadEditor.o core/base/src/TVirtualPadPainter.o core/base/src/TVirtualPerfStats.o core/base/src/TVirtualPS.o core/base/src/TVirtualViewer3D.o core/base/src/TVirtualX.o core/cont/src/TArrayC.o core/cont/src/TArray.o core/cont/src/TArrayD.o core/cont/src/TArrayF.o core/cont/src/TArrayI.o core/cont/src/TArrayL64.o core/cont/src/TArrayL.o core/cont/src/TArrayS.o core/cont/src/TBits.o core/cont/src/TBtree.o core/cont/src/TClassTable.o core/cont/src/TClonesArray.o core/cont/src/TCollection.o core/cont/src/TExMap.o core/cont/src/THashList.o core/cont/src/THashTable.o core/cont/src/TIterator.o core/cont/src/TList.o core/cont/src/TMap.o core/cont/src/TObjArray.o core/cont/src/TObjectTable.o core/cont/src/TOrdCollection.o core/cont/src/TRefArray.o core/cont/src/TRefTable.o core/cont/src/TSeqCollection.o core/cont/src/TSortedList.o core/meta/src/TBaseClass.o core/meta/src/TCint.o core/meta/src/TClassAttributeMap.o core/meta/src/TClass.o core/meta/src/TClassGenerator.o core/meta/src/TClassMenuItem.o core/meta/src/TClassRef.o core/meta/src/TDataMember.o core/meta/src/TDataType.o core/meta/src/TDictionary.o core/meta/src/TFunction.o core/meta/src/TGenericClassInfo.o core/meta/src/TGlobal.o core/meta/src/TInterpreter.o core/meta/src/TIsAProxy.o core/meta/src/TMethodArg.o core/meta/src/TMethodCall.o core/meta/src/TMethod.o core/meta/src/TRealData.o core/meta/src/TSchemaRule.o core/meta/src/TSchemaRuleSet.o core/meta/src/TStreamerElement.o core/meta/src/TToggle.o core/meta/src/TToggleGroup.o core/meta/src/TVirtualStreamerInfo.o core/unix/src/TUnixSystem.o core/zip/src/ZDeflate.o core/zip/src/ZInflate.o core/zip/src/Compression.o core/lzma/src/ZipLZMA.o core/clib/src/attach.o core/clib/src/Demangle.o core/clib/src/detach.o core/clib/src/getpagesize.o core/clib/src/keys.o core/clib/src/mcalloc.o core/clib/src/mfree.o core/clib/src/mmalloc.o core/clib/src/mmapsup.o core/clib/src/mmcheck.o core/clib/src/mmemalign.o core/clib/src/mmstats.o core/clib/src/mmtrace.o core/clib/src/mrealloc.o core/clib/src/mvalloc.o core/clib/src/sbrksup.o core/clib/src/snprintf.o core/clib/src/strlcat.o core/clib/src/strlcpy.o core/metautils/src/RConversionRuleParser.o core/metautils/src/TClassEdit.o core/textinput/src/Getline_color.o core/textinput/src/Getline.o core/textinput/src/textinput/Editor.o core/textinput/src/textinput/History.o core/textinput/src/textinput/KeyBinding.o core/textinput/src/textinput/Range.o core/textinput/src/textinput/SignalHandler.o core/textinput/src/textinput/StreamReader.o core/textinput/src/textinput/StreamReaderUnix.o core/textinput/src/textinput/StreamReaderWin.o core/textinput/src/textinput/TerminalConfigUnix.o core/textinput/src/textinput/TerminalDisplay.o core/textinput/src/textinput/TerminalDisplayUnix.o core/textinput/src/textinput/TerminalDisplayWin.o core/textinput/src/textinput/TextInputContext.o core/textinput/src/textinput/TextInput.o core/base/src/G__Base1.o core/base/src/G__Base2.o core/base/src/G__Base3.o core/cont/src/G__Cont.o core/meta/src/G__Meta.o core/unix/src/G__Unix.o core/zip/src/G__Zip.o core/clib/src/G__Clib.o core/metautils/src/G__MetaUtils.o core/textinput/src/G__TextInput.o -lz lib/liblzma.a -lpcre -lcrypt -Llib -lCint -ldl
==> lib/libCore.so done
g++ -shared -Wl,-soname,libPyROOT.so -m64 -O2 -Wl,--no-undefined -Wl,--as-needed -o lib/libPyROOT.so bindings/pyroot/src/Adapters.o bindings/pyroot/src/ClassMethodHolder.o bindings/pyroot/src/ConstructorHolder.o bindings/pyroot/src/Converters.o bindings/pyroot/src/Executors.o bindings/pyroot/src/FunctionHolder.o bindings/pyroot/src/MemoryRegulator.o bindings/pyroot/src/MethodHolder.o bindings/pyroot/src/MethodProxy.o bindings/pyroot/src/ObjectProxy.o bindings/pyroot/src/PropertyProxy.o bindings/pyroot/src/PyBufferFactory.o bindings/pyroot/src/PyRootType.o bindings/pyroot/src/PyStrings.o bindings/pyroot/src/Pythonize.o bindings/pyroot/src/RootModule.o bindings/pyroot/src/RootWrapper.o bindings/pyroot/src/TCustomPyTypes.o bindings/pyroot/src/TemplateProxy.o bindings/pyroot/src/TPyClassGenerator.o bindings/pyroot/src/TPyDispatcher.o bindings/pyroot/src/TPyException.o bindings/pyroot/src/TPyFitFunction.o bindings/pyroot/src/TPyReturn.o bindings/pyroot/src/TPyROOTApplication.o bindings/pyroot/src/TPySelector.o bindings/pyroot/src/TPython.o bindings/pyroot/src/TRflxCallback.o bindings/pyroot/src/TSetItemHolder.o bindings/pyroot/src/Utility.o bindings/pyroot/src/G__PyROOT.o -Llib -lRIO -lHist -lGraf -lGraf3d -lGpad -lTree -lMatrix -lNet -lThread -lMathCore -lCore -lCint -L/usr/local/lib -lpython2.7 -Llib -lCore -lCint -ldl
/usr/bin/ld: /usr/local/lib/libpython2.7.a(myreadline.o): relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC
/usr/local/lib/libpython2.7.a: could not read symbols: Bad value
collect2: error: ld returned 1 exit status
make: *** [lib/libPyROOT.so] Error 1
What should I do in this case to install ROOT successfully?
Thanks!
binlangman is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 05:57 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO