Comments (7)
I got the same error on Mac OS X 10.7.3.
from bamutil.
-std=c++0x includes the new C++11 standards. It is only supported in GCC 4.3.
I will add an option to disable it. Hopefully I can get that done today.
Sorry for the delay in the response. My notifications were screwed up and I only just now saw this issue.
I will let you know when the update is in place.
from bamutil.
This should now be updated in the latest development version.
The Makefiles should now detect if you are using a gcc version that supports C++11.
If the automatic check does not work and you still get a failure, try adding: CXX11_AVAIL=0 to your Makefile command (or to your environment). Example: make CXX11_AVAIL=0
Let me know if this fixes your problem or if you still are having issues. Again, sorry for the troubles and the delay in resolving it.
from bamutil.
I tried what you suggested with make CVV11_AVAIL=0 but I still get
ar -cru ../libStatGen.a obj/bgzf.o obj/knetfile.o
/usr/bin/ranlib: file: ../libStatGen.a(LongHash.o) has no symbols
/usr/bin/ranlib: file: ../libStatGen.a(TrimSequence.o) has no symbols
/usr/bin/ranlib: file: ../libStatGen.a(WindowsHelper.o) has no symbols
/usr/bin/ranlib: file: ../libStatGen.a(SamFlag.o) has no symbols
ar -cru ../libStatGen.a obj/BaseAsciiMap.o obj/BaseQualityHelper.o obj/BaseUtilities.o obj/BasicHash.o obj/BgzfFileType.o obj/BgzfFileTypeRecovery.o obj/CharBuffer.o obj/Chromosome.o obj/Cigar.o obj/CigarRoller.o obj/Error.o obj/FileType.o obj/FortranFormat.o obj/GenomeSequence.o obj/GenotypeLists.o obj/glfHandler.o obj/GzipFileType.o obj/GzipHeader.o obj/Hash.o obj/Input.o obj/InputFile.o obj/IntArray.o obj/IntHash.o obj/LongHash.o obj/LongLongCounter.o obj/MapFunction.o obj/MathMatrix.o obj/MathVector.o obj/MemoryAllocators.o obj/MemoryInfo.o obj/MemoryMapArray.o obj/MemoryMap.o obj/MiniDeflate.o obj/NonOverlapRegions.o obj/Parameters.o obj/PedigreeAlleleFreq.o obj/Pedigree.o obj/PedigreeDescription.o obj/PedigreeFamily.o obj/PedigreeGlobals.o obj/PedigreePerson.o obj/QuickIndex.o obj/Random.o obj/ReferenceSequence.o obj/SmithWaterman.o obj/Sort.o obj/STLUtilities.o obj/StringAlias.o obj/StringArray.o obj/StringBasics.o obj/StringHash.o obj/StringMap.o obj/TrimSequence.o obj/UncompressedFileType.o obj/WindowsHelper.o obj/PedigreeLoader.o obj/PedigreeTrim.o obj/PedigreeTwin.o
/usr/bin/ranlib: file: ../libStatGen.a(LongHash.o) has no symbols
/usr/bin/ranlib: file: ../libStatGen.a(TrimSequence.o) has no symbols
/usr/bin/ranlib: file: ../libStatGen.a(WindowsHelper.o) has no symbols
/usr/bin/ranlib: file: ../libStatGen.a(SamFlag.o) has no symbols
ar -cru ../libStatGen.a obj/ErrorHandler.o obj/SamFileHeader.o obj/SamFile.o obj/GenericSamInterface.o obj/SamInterface.o obj/BamInterface.o obj/SamRecord.o obj/BamIndex.o obj/SamHeaderHD.o obj/SamHeaderPG.o obj/SamHeaderRecord.o obj/SamHeaderSQ.o obj/SamHeaderRG.o obj/SamHeaderTag.o obj/SamValidation.o obj/SamStatus.o obj/SamFlag.o obj/SamStatistics.o obj/SamQuerySeqWithRefHelper.o obj/SamFilter.o obj/PileupElement.o obj/PileupElementBaseQual.o obj/SamReferenceInfo.o obj/SamTags.o obj/PosList.o obj/CigarHelper.o obj/SamRecordPool.o obj/SamCoordOutput.o obj/SamRecordHelper.o
/usr/bin/ranlib: file: ../libStatGen.a(LongHash.o) has no symbols
/usr/bin/ranlib: file: ../libStatGen.a(TrimSequence.o) has no symbols
/usr/bin/ranlib: file: ../libStatGen.a(WindowsHelper.o) has no symbols
/usr/bin/ranlib: file: ../libStatGen.a(SamFlag.o) has no symbols
ar -cru ../libStatGen.a obj/FastQFile.o obj/BaseCount.o obj/BaseComposition.o obj/FastQStatus.o
/usr/bin/ranlib: file: ../libStatGen.a(LongHash.o) has no symbols
/usr/bin/ranlib: file: ../libStatGen.a(TrimSequence.o) has no symbols
/usr/bin/ranlib: file: ../libStatGen.a(WindowsHelper.o) has no symbols
/usr/bin/ranlib: file: ../libStatGen.a(SamFlag.o) has no symbols
ar -cru ../libStatGen.a obj/GlfException.o obj/GlfFile.o obj/GlfHeader.o obj/GlfRecord.o obj/GlfRefSection.o obj/GlfStatus.o
/usr/bin/ranlib: file: ../libStatGen.a(LongHash.o) has no symbols
/usr/bin/ranlib: file: ../libStatGen.a(TrimSequence.o) has no symbols
/usr/bin/ranlib: file: ../libStatGen.a(WindowsHelper.o) has no symbols
/usr/bin/ranlib: file: ../libStatGen.a(SamFlag.o) has no symbols
Any suggestions?
from bamutil.
Did you use: CVV11_AVAIL=0
or CXX11_AVAIL=0 ?
It should be CXX11_AVAIL=0
I just wanted to check...
Also, can you try a:
cd libStatGen (use the correct path to get to yours.)
make clean; make CXX11_AVAIL=0
Let me know how that goes. Thanks. Sorry for the difficulties.
from bamutil.
hey,
thanks for the quick reply. Apologies for before it was a typo in my message, but it still doesn't work!:( I tried with make clean too but no luck.!
....
g++ -O4 -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfException.o -c GlfException.cpp -DVERSION=""1.0.6""
g++ -O4 -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfFile.o -c GlfFile.cpp -DVERSION=""1.0.6""
g++ -O4 -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfHeader.o -c GlfHeader.cpp -DVERSION=""1.0.6""
g++ -O4 -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfRecord.o -c GlfRecord.cpp -DVERSION=""1.0.6""
g++ -O4 -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfRefSection.o -c GlfRefSection.cpp -DVERSION=""1.0.6""
g++ -O4 -pipe -Wall -I../include -I. -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS -o obj/GlfStatus.o -c GlfStatus.cpp -DVERSION=""1.0.6""
ar -cru ../libStatGen.a obj/GlfException.o obj/GlfFile.o obj/GlfHeader.o obj/GlfRecord.o obj/GlfRefSection.o obj/GlfStatus.o
/usr/bin/ranlib: file: ../libStatGen.a(LongHash.o) has no symbols
/usr/bin/ranlib: file: ../libStatGen.a(TrimSequence.o) has no symbols
/usr/bin/ranlib: file: ../libStatGen.a(WindowsHelper.o) has no symbols
/usr/bin/ranlib: file: ../libStatGen.a(SamFlag.o) has no symbols
is there anything else I should have installed/downloaded except libstatgen?
from bamutil.
Oh, I think I get it now.
It looks like we have a couple of .cpp files that have no code in them. Your ranlib is warning about that. I should clean this up a bit so those files don't exist if they aren't needed.
But I wonder if everything else works properly.
Are you able to compile bamUtil and do you get: bamUtil/bin/bam even with these messages?
If you do get the binary and can run that, great. Then it is just a warning message that can be ignored for now, and I will clean that up in the next release. If it doesn't work, let me know and I'll get you a fix sooner.
from bamutil.
Related Issues (20)
- Building bamUtil returns error: call of overloaded 'to_string(int&)' is ambiguous HOT 4
- Compile error HOT 4
- clipoverlap on raw output straight from bwa HOT 3
- Building bamUtil returns error: undefined reference HOT 4
- Cut middle of reads HOT 2
- `bam diff` should exit with a return code
- Dedup does not work from std/in HOT 2
- Cannot Compile NonPrimaryDedup Branch HOT 5
- cannot consume -.ubam on a pipe HOT 2
- Makefile should not ignore system LDFLAGS
- `bam diff` seems to return the reads that look identical between A and B HOT 1
- the clang compiler does not support -pg option on versions of OS X 10.9 and later HOT 4
- Error building from source: libStatGen HOT 3
- BamUtil: recab error: failed to open reference genome HOT 6
- bam2FastQ generates empty fastq files
- bash -x testBam2FastQ.sh and bash -x testMergeBam.sh failed on centos8_aarch64
- can not install with conda HOT 2
- bamutil diff - Get record for every read being compared HOT 2
- build is broken due to deprecated git protocol HOT 1
- Odd stats reported for clipOverlap
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from bamutil.