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Compilation errors in Ubuntu 16.04 #17

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rborder opened this issue Feb 21, 2018 · 4 comments
Closed

Compilation errors in Ubuntu 16.04 #17

rborder opened this issue Feb 21, 2018 · 4 comments

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@rborder
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rborder commented Feb 21, 2018

I'm running into following error when compiling with g++ version 7.2.0

StringBasics.cpp: In member function ‘int String::vcatprintf(const char*, __va_list_tag*)’:
StringBasics.cpp:1413:5: error: ‘%5s’ directive output truncated writing 9 bytes into a region of size 5 [-Werror=format-truncation=]
 int String::vcatprintf(const char * format, va_list ap)
@jonathonl
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Try pulling the latest from the master branch. This should have been fixed in 9db9c23.

If it still doesn't build with the latest, please post the output of make -n | grep "^g++".

@rborder
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rborder commented Feb 22, 2018

Unfortunately that didn't work. The error:

StringBasics.cpp: In member function ‘int String::vprintf(const char*, __va_list_tag*)’:
StringBasics.cpp:1357:5: error: ‘%5s’ directive output truncated writing 9 bytes into a region of size 5 [-Werror=format-truncation=]
 int String::vprintf(const char * format, va_list ap)
     ^~~~~~
In file included from /usr/include/stdio.h:862:0,
                 from StringBasics.h:21,
                 from StringBasics.cpp:18:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:65:44: note: ‘__builtin___snprintf_chk’ output 10 bytes into a destination of size 5
        __bos (__s), __fmt, __va_arg_pack ());
                                            ^
StringBasics.cpp: In static member function ‘static void String::check_vsnprintf()’:
StringBasics.cpp:1391:6: error: ‘%5s’ directive output truncated writing 9 bytes into a region of size 5 [-Werror=format-truncation=]
 void String::check_vsnprintf()
      ^~~~~~
In file included from /usr/include/stdio.h:862:0,
                 from StringBasics.h:21,
                 from StringBasics.cpp:18:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:65:44: note: ‘__builtin___snprintf_chk’ output 10 bytes into a destination of size 5
        __bos (__s), __fmt, __va_arg_pack ());
                                            ^
StringBasics.cpp: In member function ‘int String::vcatprintf(const char*, __va_list_tag*)’:
StringBasics.cpp:1413:5: error: ‘%5s’ directive output truncated writing 9 bytes into a region of size 5 [-Werror=format-truncation=]
 int String::vcatprintf(const char * format, va_list ap)
     ^~~~~~
In file included from /usr/include/stdio.h:862:0,
                 from StringBasics.h:21,
                 from StringBasics.cpp:18:
/usr/include/x86_64-linux-gnu/bits/stdio2.h:65:44: note: ‘__builtin___snprintf_chk’ output 10 bytes into a destination of size 5
        __bos (__s), __fmt, __va_arg_pack ());
                                            ^
cc1plus: all warnings being treated as errors
../Makefiles/Makefile.common:81: recipe for target 'obj/StringBasics.o' failed
make[1]: *** [obj/StringBasics.o] Error 1
make[1]: Leaving directory '/home/rsb/Downloads/libStatGen/general'
Makefiles/Makefile.base:15: recipe for target 'general' failed
make: *** [general] Error 2

The output from make -n | grep "^g++":

g++  -std=c++0x -O4 -pipe -Wall -Werror  -Wno-strict-overflow -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/StringBasics.o -c StringBasics.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall -Werror  -Wno-strict-overflow -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/StringHash.o -c StringHash.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall -Werror  -Wno-strict-overflow -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/StringMap.o -c StringMap.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall -Werror  -Wno-strict-overflow -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/Tabix.o -c Tabix.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall -Werror  -Wno-strict-overflow -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/UncompressedFileType.o -c UncompressedFileType.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall -Werror  -Wno-strict-overflow -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PedigreeLoader.o -c PedigreeLoader.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall -Werror  -Wno-strict-overflow -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PedigreeTrim.o -c PedigreeTrim.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall -Werror  -Wno-strict-overflow -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PedigreeTwin.o -c PedigreeTwin.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamFileHeader.o -c SamFileHeader.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamFile.o -c SamFile.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/GenericSamInterface.o -c GenericSamInterface.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamInterface.o -c SamInterface.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/BamInterface.o -c BamInterface.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamRecord.o -c SamRecord.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/BamIndex.o -c BamIndex.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamHeaderHD.o -c SamHeaderHD.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamHeaderPG.o -c SamHeaderPG.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamHeaderRecord.o -c SamHeaderRecord.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamHeaderSQ.o -c SamHeaderSQ.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamHeaderRG.o -c SamHeaderRG.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamHeaderTag.o -c SamHeaderTag.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamValidation.o -c SamValidation.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamStatistics.o -c SamStatistics.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamQuerySeqWithRefHelper.o -c SamQuerySeqWithRefHelper.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamFilter.o -c SamFilter.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PileupElement.o -c PileupElement.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PileupElementBaseQual.o -c PileupElementBaseQual.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamReferenceInfo.o -c SamReferenceInfo.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamTags.o -c SamTags.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/PosList.o -c PosList.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/CigarHelper.o -c CigarHelper.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamRecordPool.o -c SamRecordPool.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamCoordOutput.o -c SamCoordOutput.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/SamRecordHelper.o -c SamRecordHelper.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/FastQFile.o -c FastQFile.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/BaseCount.o -c BaseCount.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/BaseComposition.o -c BaseComposition.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/FastQStatus.o -c FastQStatus.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -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="\"1.0.0\""
g++  -std=c++0x -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="\"1.0.0\""
g++  -std=c++0x -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="\"1.0.0\""
g++  -std=c++0x -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="\"1.0.0\""
g++  -std=c++0x -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="\"1.0.0\""
g++  -std=c++0x -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="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfFile.o -c VcfFile.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfFileReader.o -c VcfFileReader.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfFileWriter.o -c VcfFileWriter.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfGenotypeField.o -c VcfGenotypeField.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfGenotypeFormat.o -c VcfGenotypeFormat.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfGenotypeSample.o -c VcfGenotypeSample.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfHeader.o -c VcfHeader.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfHelper.o -c VcfHelper.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfRecord.o -c VcfRecord.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfRecordField.o -c VcfRecordField.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfRecordFilter.o -c VcfRecordFilter.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfRecordGenotype.o -c VcfRecordGenotype.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfRecordInfo.o -c VcfRecordInfo.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfSubsetSamples.o -c VcfSubsetSamples.cpp -DVERSION="\"1.0.0\""
g++  -std=c++0x -O4 -pipe -Wall  -I../include -I.   -D__ZLIB_AVAILABLE__ -D_FILE_OFFSET_BITS=64 -D__STDC_LIMIT_MACROS  -o obj/VcfRecordDiscardRules.o -c VcfRecordDiscardRules.cpp -DVERSION="\"1.0.0\""

Thanks!

@jonathonl
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OK. I pushed a change that should fix it. If it doesn't, remove '-Werror' from https://github.com/statgen/libStatGen/blob/master/general/Makefile#L13 (I don't know why it's there in the first place).

@rborder
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rborder commented Feb 22, 2018 •
edited
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Worked (without having to remove -Werror)! Thanks!

@rborder rborder closed this as completed Feb 22, 2018
@sinarueeger sinarueeger mentioned this issue Jul 18, 2019
Merged
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