I believe the error says that you don't have the 'm4' utility. You need to install that first (I'm guessing that the command is: sudo apt get install m4). From your output, you should also install another utility called 'flex'.
You should set your AMBERHOME, by typing export AMBERHOME=/usr/local/amber11 (I forgot what it is for csh or tcsh, google is a good friend in this case).
I could be wrong here, but I believe the -D_FILE_OFFSET_BITS=64 is not an error, it is just a way for the compiler to tell 32-bit OS to use 64-bit file size so leap can read or write file sizes over 2GB limit.
I think the manual is very clear about the steps required to install the AmberTools in which xleap is apart of. You can find the pdf version of the manual on ambermd.org website.
HTH,
--Farid
________________________________________
From: sonali dhindwal [sonali11dhindwal.yahoo.co.in]
Sent: Wednesday, August 31, 2011 11:38 PM
To: AMBER Mailing List
Subject: Re: [AMBER] problem in installing xleap
Dear David,
I did,
cd $AMBERHOME/AmberTools/src
./configure gnu
It is giving following:
root.mcu-ProLiant-ML350-G6:/usr/local/amber11/AmberTools/src# ./configure gnu
Your AMBERHOME environment variable should be set to /usr/local/amber11
Obtaining the gnu suite version:
gcc -v
The version is 4.4.5
Testing the gcc compiler:
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
OK
Validating the C++ compiler version:
g++ -v
The version is 4.4.5
OK
Testing the gfortran compiler:
gfortran -O0 -o testp testp.f
OK
Testing mixed C/Fortran compilation:
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o testp.c
gfortran -O0 -c -o testp.f.o testp.f
gcc -o testp testp.c.o testp.f.o -lgfortran
OK
Testing pointer size:
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o test_pointer_size test_pointer_size.c
Detected 32 bit operating system.
Testing flex:
./configure: 1339: flex: not found
Unable to run flex; this is recommended for NAB
Please check your PATH, or install the program
We will try to solider on with precompiled files
Configuring NetCDF; (may be time-consuming)
NetCDF configure succeeded.
Configuring fftw-2.1.5; (may be time-consuming)
fftw-2.1.5 configure succeeded.
The configuration file, config.h, was successfully created.
The next step is to type 'make install'
Then I did
make clean
cd leap
make install
I am getting the following output:
Clip.o Clip.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o CloseHook.o CloseHook.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o CmapAlloc.o CmapAlloc.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o CrCmap.o CrCmap.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o CrPixFBit.o CrPixFBit.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o CursorName.o CursorName.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o CvtCache.o CvtCache.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o CvtStdSel.o CvtStdSel.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o DefErrMsg.o DefErrMsg.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o DelCmap.o DelCmap.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o DisplayQue.o DisplayQue.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o Distinct.o Distinct.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o DrawLogo.o DrawLogo.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o DrRndRect.o DrRndRect.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o EditresCom.o EditresCom.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o ExtAgent.o ExtAgent.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o FToCback.o FToCback.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o GetHost.o GetHost.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o GrayPixmap.o GrayPixmap.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o Initer.o Initer.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o LocBitmap.o LocBitmap.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o Lookup.o Lookup.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o LookupCmap.o LookupCmap.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o Lower.o Lower.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o RdBitF.o RdBitF.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o ScrOfWin.o ScrOfWin.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o ShapeWidg.o ShapeWidg.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o StdCmap.o StdCmap.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o StrToBS.o StrToBS.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o StrToBmap.o StrToBmap.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o StrToCurs.o StrToCurs.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o StrToGrav.o StrToGrav.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o StrToJust.o StrToJust.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o StrToLong.o StrToLong.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o StrToOrnt.o StrToOrnt.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o StrToShap.o StrToShap.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o StrToWidg.o StrToWidg.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o UpdMapHint.o UpdMapHint.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o VisCmap.o VisCmap.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o WidgetNode.o WidgetNode.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o Xct.o Xct.c
ar rv libXmu.a AllCmap.o Atoms.o ClientWin.o Clip.o CloseHook.o CmapAlloc.o CrCmap.o CrPixFBit.o CursorName.o CvtCache.o CvtStdSel.o DefErrMsg.o DelCmap.o DisplayQue.o Distinct.o DrawLogo.o DrRndRect.o EditresCom.o ExtAgent.o FToCback.o GetHost.o GrayPixmap.o Initer.o LocBitmap.o Lookup.o LookupCmap.o Lower.o RdBitF.o ScrOfWin.o ShapeWidg.o StdCmap.o StrToBS.o StrToBmap.o StrToCurs.o StrToGrav.o StrToJust.o StrToLong.o StrToOrnt.o StrToShap.o StrToWidg.o UpdMapHint.o VisCmap.o WidgetNode.o Xct.o
ar: creating libXmu.a
a - AllCmap.o
a - Atoms.o
a - ClientWin.o
a - Clip.o
a - CloseHook.o
a - CmapAlloc.o
a - CrCmap.o
a - CrPixFBit.o
a - CursorName.o
a - CvtCache.o
a - CvtStdSel.o
a - DefErrMsg.o
a - DelCmap.o
a - DisplayQue.o
a - Distinct.o
a - DrawLogo.o
a - DrRndRect.o
a - EditresCom.o
a - ExtAgent.o
a - FToCback.o
a - GetHost.o
a - GrayPixmap.o
a - Initer.o
a - LocBitmap.o
a - Lookup.o
a - LookupCmap.o
a - Lower.o
a - RdBitF.o
a - ScrOfWin.o
a - ShapeWidg.o
a - StdCmap.o
a - StrToBS.o
a - StrToBmap.o
a - StrToCurs.o
a - StrToGrav.o
a - StrToJust.o
a - StrToLong.o
a - StrToOrnt.o
a - StrToShap.o
a - StrToWidg.o
a - UpdMapHint.o
a - VisCmap.o
a - WidgetNode.o
a - Xct.o
ranlib libXmu.a
make[2]: Leaving directory `/usr/local/amber11/AmberTools/src/leap/src/Xmu'
cd src/Xpm && make
make[2]: Entering directory `/usr/local/amber11/AmberTools/src/leap/src/Xpm'
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o data.o data.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o create.o create.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o misc.o misc.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o rgb.o rgb.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o scan.o scan.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o parse.o parse.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o hashtable.o hashtable.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o XpmCrBufFrI.o XpmCrBufFrI.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o XpmCrDataFrP.o XpmCrDataFrP.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o XpmCrPFrBuf.o XpmCrPFrBuf.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o XpmRdFToI.o XpmRdFToI.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o XpmWrFFrI.o XpmWrFFrI.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o XpmCrBufFrP.o XpmCrBufFrP.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o XpmCrIFrBuf.o XpmCrIFrBuf.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o XpmCrPFrData.o XpmCrPFrData.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o XpmRdFToP.o XpmRdFToP.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o XpmWrFFrP.o XpmWrFFrP.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o XpmCrDataFrI.o XpmCrDataFrI.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o XpmCrIFrData.o XpmCrIFrData.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o XpmRdFToData.o XpmRdFToData.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o XpmWrFFrData.o XpmWrFFrData.c
ar rv libXpm.a data.o create.o misc.o rgb.o scan.o parse.o hashtable.o XpmCrBufFrI.o XpmCrDataFrP.o XpmCrPFrBuf.o XpmRdFToI.o XpmWrFFrI.o XpmCrBufFrP.o XpmCrIFrBuf.o XpmCrPFrData.o XpmRdFToP.o XpmWrFFrP.o XpmCrDataFrI.o XpmCrIFrData.o XpmRdFToData.o XpmWrFFrData.o
ar: creating libXpm.a
a - data.o
a - create.o
a - misc.o
a - rgb.o
a - scan.o
a - parse.o
a - hashtable.o
a - XpmCrBufFrI.o
a - XpmCrDataFrP.o
a - XpmCrPFrBuf.o
a - XpmRdFToI.o
a - XpmWrFFrI.o
a - XpmCrBufFrP.o
a - XpmCrIFrBuf.o
a - XpmCrPFrData.o
a - XpmRdFToP.o
a - XpmWrFFrP.o
a - XpmCrDataFrI.o
a - XpmCrIFrData.o
a - XpmRdFToData.o
a - XpmWrFFrData.o
ranlib libXpm.a
make[2]: Leaving directory `/usr/local/amber11/AmberTools/src/leap/src/Xpm'
cd src/Xraw && make
make[2]: Entering directory `/usr/local/amber11/AmberTools/src/leap/src/Xraw'
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o 3d.o 3d.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o AllWidgets.o AllWidgets.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o Arrow.o Arrow.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o AsciiSink.o AsciiSink.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o AsciiSrc.o AsciiSrc.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o AsciiText.o AsciiText.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o Box.o Box.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o Clock.o Clock.c
Clock.c:48: warning: conflicting types for built-in function ‘round’
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o Command.o Command.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o color.o color.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o Container.o Container.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o Dialog.o Dialog.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o Form.o Form.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o Frame.o Frame.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o Grip.o Grip.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o Label.o Label.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o List.o List.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o Logo.o Logo.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o MenuButton.o MenuButton.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o Paned.o Paned.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o Panner.o Panner.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o Porthole.o Porthole.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o Repeater.o Repeater.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o Scrollbar.o Scrollbar.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o ScrolledTable.o ScrolledTable.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o Separator.o Separator.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o Simple.o Simple.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o SimpleMenu.o SimpleMenu.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o Sme.o Sme.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o SmeBSB.o SmeBSB.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o SmeLine.o SmeLine.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o StripChart.o StripChart.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o table.o table.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o Table2.o Table2.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o Text.o Text.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o TextSink.o TextSink.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o TextSrc.o TextSrc.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o TextAction.o TextAction.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o TextPop.o TextPop.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o TextTr.o TextTr.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o Toggle.o Toggle.c
Toggle.c: In function ‘Notify’:
Toggle.c:422: warning: cast to pointer from integer of different size
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o Tree.o Tree.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o Vendor.o Vendor.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o Viewport.o Viewport.c
gcc -c -I/usr/include -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -o XawInit.o XawInit.c
ar rv libXaw.a 3d.o AllWidgets.o Arrow.o AsciiSink.o AsciiSrc.o AsciiText.o Box.o Clock.o Command.o color.o Container.o Dialog.o Form.o Frame.o Grip.o Label.o List.o Logo.o MenuButton.o Paned.o Panner.o Porthole.o Repeater.o Scrollbar.o ScrolledTable.o Separator.o Simple.o SimpleMenu.o Sme.o SmeBSB.o SmeLine.o StripChart.o table.o Table2.o Text.o TextSink.o TextSrc.o TextAction.o TextPop.o TextTr.o Toggle.o Tree.o Vendor.o Viewport.o XawInit.o
ar: creating libXaw.a
a - 3d.o
a - AllWidgets.o
a - Arrow.o
a - AsciiSink.o
a - AsciiSrc.o
a - AsciiText.o
a - Box.o
a - Clock.o
a - Command.o
a - color.o
a - Container.o
a - Dialog.o
a - Form.o
a - Frame.o
a - Grip.o
a - Label.o
a - List.o
a - Logo.o
a - MenuButton.o
a - Paned.o
a - Panner.o
a - Porthole.o
a - Repeater.o
a - Scrollbar.o
a - ScrolledTable.o
a - Separator.o
a - Simple.o
a - SimpleMenu.o
a - Sme.o
a - SmeBSB.o
a - SmeLine.o
a - StripChart.o
a - table.o
a - Table2.o
a - Text.o
a - TextSink.o
a - TextSrc.o
a - TextAction.o
a - TextPop.o
a - TextTr.o
a - Toggle.o
a - Tree.o
a - Vendor.o
a - Viewport.o
a - XawInit.o
ranlib libXaw.a
make[2]: Leaving directory `/usr/local/amber11/AmberTools/src/leap/src/Xraw'
cd src/leap && make install
make[2]: Entering directory `/usr/local/amber11/AmberTools/src/leap/src/leap'
gcc -o teLeap basics.o sysdepend.o stringExtra.o varArray.o getline.o avl.o pdb_format.o pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o vector.o zMatrix.o sort.o bag.o hash.o dictionary.o database.o nVector.o ring.o matrix.o fortran.o displayer.o assoc.o atom.o byteArray.o collection.o container.o internal.o list.o loop.o molecule.o oDouble.o oInteger.o oString.o objekt.o parmSet.o residue.o unit.o unitio.o tripos.o graphUtil.o select.o amber.o build.o elements.o library.o chirality.o minimizer.o model.o parmLib.o pdbFile.o mol2File.o tools.o variables.o parser.o help.o helptext.o octree.o commands.o mathop.o block.o restraint.o hybrid.o tLeap.o -lm
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -c -o xTank.o xTank.c
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -c -o xAction.o xAction.c
xAction.c: In function ‘zActionTwistTorsions’:
xAction.c:1112: warning: passing argument 1 of ‘BuildRotateAroundBondFromTo’ from incompatible pointer type
build.h:68: note: expected ‘CONTAINER’ but argument is of type ‘UNIT’
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -c -o x3d.o x3d.c
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -c -o xBasics.o xBasics.c
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -c -o xaLeapc.o xaLeapc.c
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -c -o xaUnitEditor.o xaUnitEditor.c
xaUnitEditor.c: In function ‘XAUEAddHydrogensAndBuildExternals’:
xaUnitEditor.c:888: warning: passing argument 1 of ‘BuildInternalsForSimpleRings’ from incompatible pointer type
build.h:75: note: expected ‘CONTAINER’ but argument is of type ‘UNIT’
xaUnitEditor.c: In function ‘XAUESelectedAtomsFlipChirality’:
xaUnitEditor.c:1335: warning: passing argument 1 of ‘bBuildFlipChiralityFor’ from incompatible pointer type
build.h:71: note: expected ‘CONTAINER’ but argument is of type ‘UNIT’
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -c -o xaTable.o xaTable.c
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -c -o xaAtomTable.o xaAtomTable.c
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -c -o XrawRegistr.o XrawRegistr.c
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -c -o xaCommand.o xaCommand.c
xaCommand.c: In function ‘zXACDisplayChildren’:
xaCommand.c:101: warning: format ‘%lX’ expects type ‘long unsigned int’, but argument 2 has type ‘Widget’
xaCommand.c:117: warning: format ‘%lX’ expects type ‘long unsigned int’, but argument 2 has type ‘Widget’
xaCommand.c: In function ‘zXACDisplayWidgetTree’:
xaCommand.c:146: warning: format ‘%lX’ expects type ‘long unsigned int’, but argument 2 has type ‘Widget’
xaCommand.c: In function ‘xtcpXACInitializeDirectoryList’:
xaCommand.c:840: warning: passing argument 4 of ‘qsort’ from incompatible pointer type
/usr/include/stdlib.h:761: note: expected ‘__compar_fn_t’ but argument is of type ‘int (*)(void *, void *)’
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -c -o xaTools.o xaTools.c
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -c -o xaAtomParmTable.o xaAtomParmTable.c
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -c -o xaBondParmTable.o xaBondParmTable.c
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -c -o xaAngleParmTable.o xaAngleParmTable.c
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -c -o xaParmEditor.o xaParmEditor.c
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -c -o xaTorsionParmTable.o xaTorsionParmTable.c
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -c -o xaImproperParmTable.o xaImproperParmTable.c
gcc -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -c -o xaHBondParmTable.o xaHBondParmTable.c
gcc -o xaLeap basics.o sysdepend.o stringExtra.o varArray.o getline.o avl.o pdb_format.o pdb_read.o pdb_sprntf.o pdb_sscanf.o pdb_write.o vector.o zMatrix.o sort.o bag.o hash.o dictionary.o database.o nVector.o ring.o matrix.o fortran.o displayer.o assoc.o atom.o byteArray.o collection.o container.o internal.o list.o loop.o molecule.o oDouble.o oInteger.o oString.o objekt.o parmSet.o residue.o unit.o unitio.o tripos.o graphUtil.o select.o amber.o build.o elements.o library.o chirality.o minimizer.o model.o parmLib.o pdbFile.o mol2File.o tools.o variables.o parser.o help.o helptext.o octree.o commands.o mathop.o block.o restraint.o hybrid.o xTank.o xAction.o x3d.o xBasics.o xaLeapc.o xaUnitEditor.o xaTable.o xaAtomTable.o XrawRegistr.o xaCommand.o xaTools.o xaAtomParmTable.o xaBondParmTable.o xaAngleParmTable.o xaParmEditor.o xaTorsionParmTable.o xaImproperParmTable.o xaHBondParmTable.o ../Xraw/libXaw.a ../Wc/libWcLeap.a
../Xpm/libXpm.a ../Xmu/libXmu.a -L/usr/lib -lXt -lXext -lSM -lICE -lX11 -lXau -lXdmcp -lm -lpthread
../Xraw/libXaw.a(AsciiSrc.o): In function `InitStringOrFile':
AsciiSrc.c:(.text+0xfeb): warning: the use of `tmpnam' is dangerous, better use `mkstemp'
m4 xaLeap.rm4 > XaLeap_wcl
/bin/sh: m4: not found
make[2]: *** [XaLeap_wcl] Error 127
make[2]: Leaving directory `/usr/local/amber11/AmberTools/src/leap/src/leap'
make[1]: *** [install_xleap] Error 2
make[1]: Leaving directory `/usr/local/amber11/AmberTools/src/leap'
make: *** [install] Error 2
At the end it is giving error,
and in between also it is saying something -D_FILE_OFFSET_BITS=64
so is this the bit problem again !!
please suggest the solution for this,
Thanks and regards
--
Sonali Dhindwal
“Live as if you were to die tomorrow. Learn as if you were to live forever.”
--- On Wed, 31/8/11, David A Case <case.biomaps.rutgers.edu> wrote:
From: David A Case <case.biomaps.rutgers.edu>
Subject: Re: [AMBER] problem in installing xleap
To: "AMBER Mailing List" <amber.ambermd.org>
Date: Wednesday, 31 August, 2011, 11:50 PM
On Wed, Aug 31, 2011, sonali dhindwal wrote:
>
> I have 32 bit ubuntu on my system.
>
> by running command
> ls -l xaLeap
> it is giving :
> ls: cannot access xaleap: No such file or directory
This means you didn't properly install xleap.
>
> and it may sound silly but i don't know how to apply patch,
> it will be very kind of you to please tell how to apply the same.
Don't worry about the patch for now; just do the following:
cd $AMBERHOME/AmberTools/src
./configure gnu (or whatever compiler you are using)
make clean
cd leap
make install
Then carefully look for any errors that arise.
....dac
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 01 2011 - 00:00:03 PDT
