Source: canu
Version: 1.5+dfsg-1
Severity: serious
Tags: buster sid
User: debian...@lists.debian.org
Usertags: qa-ftbfs-20170807 qa-ftbfs
Justification: FTBFS on amd64
Hi,
During a rebuild of all packages in sid, your package failed to build on
amd64.
Relevant part (hopefully):
> g++ -o
> /<<BUILDDIR>>/canu-1.5+dfsg/Linux-amd64/obj/overlapInCore/overlapInCore/overlapInCore-Process_String_Overlaps.o
> -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
> -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.5+dfsg=. -fstack-protector-strong
> -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC
> -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts
> -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations
> -finline-functions -fomit-frame-pointer -DLIBBACKTRACE
> -I/<<BUILDDIR>>/canu-1.5+dfsg/src -IAS_UTL -Istores
> -IoverlapInCore/liboverlap
> overlapInCore/overlapInCore-Process_String_Overlaps.C
> meryl/maskMers.C: In member function 'void
> merMaskedSequence::loadMasking(uint32)':
> meryl/maskMers.C:159:8: warning: ignoring return value of 'size_t
> fread(void*, size_t, size_t, FILE*)', declared with attribute
> warn_unused_result [-Wunused-result]
> fread(&_numSeq, sizeof(uint32), 1, maskMersFile);
> ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> meryl/maskMers.C:160:8: warning: ignoring return value of 'size_t
> fread(void*, size_t, size_t, FILE*)', declared with attribute
> warn_unused_result [-Wunused-result]
> fread(&_merSize, sizeof(uint32), 1, maskMersFile);
> ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> meryl/maskMers.C:168:8: warning: ignoring return value of 'size_t
> fread(void*, size_t, size_t, FILE*)', declared with attribute
> warn_unused_result [-Wunused-result]
> fread( _seqLen, sizeof(uint32), _numSeq, maskMersFile);
> ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> meryl/maskMers.C:183:12: warning: ignoring return value of 'size_t
> fread(void*, size_t, size_t, FILE*)', declared with attribute
> warn_unused_result [-Wunused-result]
> fread(_masking[i], sizeof(char), _seqLen[i], maskMersFile);
> ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> meryl/maskMers.C:184:12: warning: ignoring return value of 'size_t
> fread(void*, size_t, size_t, FILE*)', declared with attribute
> warn_unused_result [-Wunused-result]
> fread(_repeatID[i], sizeof(uint32), _seqLen[i], maskMersFile);
> ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> merTrim/merTrim.C: In member function 'bool
> mertrimComputation::initializeFASTQ(mertrimGlobalData*)':
> merTrim/merTrim.C:557:37: warning: 'memset' used with constant zero length
> parameter; this could be due to transposed parameters
> [-Wmemset-transposed-args]
> memset(verifyName, 1024, 0);
> ^
> merTrim/merTrim.C:558:37: warning: 'memset' used with constant zero length
> parameter; this could be due to transposed parameters
> [-Wmemset-transposed-args]
> memset(verifySeq, allocLen, 0); // Needed, for verified reads
> shorter than real reads
> ^
> merTrim/merTrim.C: In member function 'void mertrimComputation::dump(char*)':
> merTrim/merTrim.C:1785:26: error: format not a string literal and no format
> arguments [-Werror=format-security]
> fprintf(stderr, logLine);
> ^
> merTrim/merTrim.C:1795:26: error: format not a string literal and no format
> arguments [-Werror=format-security]
> fprintf(stderr, logLine);
> ^
> merTrim/merTrim.C:1816:28: error: format not a string literal and no format
> arguments [-Werror=format-security]
> fprintf(stderr, logLine);
> ^
> merTrim/merTrim.C:1826:28: error: format not a string literal and no format
> arguments [-Werror=format-security]
> fprintf(stderr, logLine);
> ^
> merTrim/merTrim.C:1837:26: error: format not a string literal and no format
> arguments [-Werror=format-security]
> fprintf(stderr, logLine);
> ^
> merTrim/merTrim.C:1847:26: error: format not a string literal and no format
> arguments [-Werror=format-security]
> fprintf(stderr, logLine);
> ^
> merTrim/merTrim.C:1857:26: error: format not a string literal and no format
> arguments [-Werror=format-security]
> fprintf(stderr, logLine);
> ^
> merTrim/merTrim.C:1867:26: error: format not a string literal and no format
> arguments [-Werror=format-security]
> fprintf(stderr, logLine);
> ^
> merTrim/merTrim.C:1877:26: error: format not a string literal and no format
> arguments [-Werror=format-security]
> fprintf(stderr, logLine);
> ^
> g++ -o
> /<<BUILDDIR>>/canu-1.5+dfsg/Linux-amd64/obj/overlapInCorePartition/overlapInCore/overlapInCorePartition.o
> -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
> -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.5+dfsg=. -fstack-protector-strong
> -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC
> -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts
> -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations
> -finline-functions -fomit-frame-pointer -DLIBBACKTRACE
> -I/<<BUILDDIR>>/canu-1.5+dfsg/src -IAS_UTL -Istores
> -IoverlapInCore/liboverlap overlapInCore/overlapInCorePartition.C
> g++ -o
> /<<BUILDDIR>>/canu-1.5+dfsg/Linux-amd64/obj/overlapConvert/overlapInCore/overlapConvert.o
> -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
> -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.5+dfsg=. -fstack-protector-strong
> -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC
> -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts
> -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations
> -finline-functions -fomit-frame-pointer -DLIBBACKTRACE
> -I/<<BUILDDIR>>/canu-1.5+dfsg/src -IAS_UTL -Istores
> -IoverlapInCore/liboverlap overlapInCore/overlapConvert.C
> merTrim/merTrim.C: In member function 'bool
> mertrimComputation::initializeFASTQ(mertrimGlobalData*)':
> merTrim/merTrim.C:561:12: warning: ignoring return value of 'char*
> fgets(char*, int, FILE*)', declared with attribute warn_unused_result
> [-Wunused-result]
> fgets(verifyName, 1024, g->fqVerify->file());
> ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> merTrim/merTrim.C:562:12: warning: ignoring return value of 'char*
> fgets(char*, int, FILE*)', declared with attribute warn_unused_result
> [-Wunused-result]
> fgets(verifySeq, allocLen, g->fqVerify->file());
> ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> merTrim/merTrim.C:563:12: warning: ignoring return value of 'char*
> fgets(char*, int, FILE*)', declared with attribute warn_unused_result
> [-Wunused-result]
> fgets(origQlt, allocLen, g->fqVerify->file()); // qv name line,
> ignored
> ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> merTrim/merTrim.C:564:12: warning: ignoring return value of 'char*
> fgets(char*, int, FILE*)', declared with attribute warn_unused_result
> [-Wunused-result]
> fgets(origQlt, allocLen, g->fqVerify->file());
> ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> merTrim/merTrim.C:572:10: warning: ignoring return value of 'char*
> fgets(char*, int, FILE*)', declared with attribute warn_unused_result
> [-Wunused-result]
> fgets(readName, 1024, g->fqInput->file());
> ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> merTrim/merTrim.C:573:10: warning: ignoring return value of 'char*
> fgets(char*, int, FILE*)', declared with attribute warn_unused_result
> [-Wunused-result]
> fgets(origSeq, allocLen, g->fqInput->file());
> ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> merTrim/merTrim.C:574:10: warning: ignoring return value of 'char*
> fgets(char*, int, FILE*)', declared with attribute warn_unused_result
> [-Wunused-result]
> fgets(origQlt, allocLen, g->fqInput->file()); // qv name line, ignored
> ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> merTrim/merTrim.C:575:10: warning: ignoring return value of 'char*
> fgets(char*, int, FILE*)', declared with attribute warn_unused_result
> [-Wunused-result]
> fgets(origQlt, allocLen, g->fqInput->file());
> ~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> g++ -o
> /<<BUILDDIR>>/canu-1.5+dfsg/Linux-amd64/obj/overlapImport/overlapInCore/overlapImport.o
> -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
> -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.5+dfsg=. -fstack-protector-strong
> -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC
> -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts
> -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations
> -finline-functions -fomit-frame-pointer -DLIBBACKTRACE
> -I/<<BUILDDIR>>/canu-1.5+dfsg/src -IAS_UTL -Istores
> -IoverlapInCore/liboverlap overlapInCore/overlapImport.C
> g++ -o
> /<<BUILDDIR>>/canu-1.5+dfsg/Linux-amd64/obj/overlapPair/overlapInCore/overlapPair.o
> -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
> -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.5+dfsg=. -fstack-protector-strong
> -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC
> -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts
> -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations
> -finline-functions -fomit-frame-pointer -DLIBBACKTRACE
> -I/<<BUILDDIR>>/canu-1.5+dfsg/src -IAS_UTL -Istores -Imeryl/libleaff
> -IoverlapInCore/libedlib overlapInCore/overlapPair.C
> g++ -o
> /<<BUILDDIR>>/canu-1.5+dfsg/Linux-amd64/obj/prefixEditDistance-matchLimitGenerate/overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.o
> -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
> -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.5+dfsg=. -fstack-protector-strong
> -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC
> -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts
> -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations
> -finline-functions -fomit-frame-pointer -DLIBBACKTRACE
> -I/<<BUILDDIR>>/canu-1.5+dfsg/src -IAS_UTL -Istores
> overlapInCore/liboverlap/prefixEditDistance-matchLimitGenerate.C
> overlapInCore/overlapPair.C:480:2: warning: #warning do we need to check for
> contained too? [-Wcpp]
> #warning do we need to check for contained too?
> ^~~~~~~
> g++ -o
> /<<BUILDDIR>>/canu-1.5+dfsg/Linux-amd64/obj/mhapConvert/mhap/mhapConvert.o -c
> -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
> -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.5+dfsg=. -fstack-protector-strong
> -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC
> -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts
> -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations
> -finline-functions -fomit-frame-pointer -DLIBBACKTRACE
> -I/<<BUILDDIR>>/canu-1.5+dfsg/src -IAS_UTL -Istores -Imhap/liboverlap
> mhap/mhapConvert.C
> g++ -o
> /<<BUILDDIR>>/canu-1.5+dfsg/Linux-amd64/obj/mmapConvert/minimap/mmapConvert.o
> -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
> -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.5+dfsg=. -fstack-protector-strong
> -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC
> -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts
> -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations
> -finline-functions -fomit-frame-pointer -DLIBBACKTRACE
> -I/<<BUILDDIR>>/canu-1.5+dfsg/src -IAS_UTL -Istores -Iminimap/liboverlap
> minimap/mmapConvert.C
> g++ -o
> /<<BUILDDIR>>/canu-1.5+dfsg/Linux-amd64/obj/filterCorrectionOverlaps/correction/filterCorrectionOverlaps.o
> -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
> -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.5+dfsg=. -fstack-protector-strong
> -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC
> -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts
> -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations
> -finline-functions -fomit-frame-pointer -DLIBBACKTRACE
> -I/<<BUILDDIR>>/canu-1.5+dfsg/src -IAS_UTL -Istores
> correction/filterCorrectionOverlaps.C
> overlapInCore/overlapImport.C: In function 'int main(int, char**)':
> overlapInCore/overlapImport.C:227:10: warning: ignoring return value of
> 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result
> [-Wunused-result]
> fgets(S, 1024, in->file());
> ~~~~~^~~~~~~~~~~~~~~~~~~~~
> overlapInCore/overlapImport.C:291:12: warning: ignoring return value of
> 'char* fgets(char*, int, FILE*)', declared with attribute warn_unused_result
> [-Wunused-result]
> fgets(S, 1024, in->file());
> ~~~~~^~~~~~~~~~~~~~~~~~~~~
> g++ -o
> /<<BUILDDIR>>/canu-1.5+dfsg/Linux-amd64/obj/generateCorrectionLayouts/correction/generateCorrectionLayouts.o
> -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
> -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.5+dfsg=. -fstack-protector-strong
> -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC
> -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts
> -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations
> -finline-functions -fomit-frame-pointer -DLIBBACKTRACE
> -I/<<BUILDDIR>>/canu-1.5+dfsg/src -IAS_UTL -Istores -Iutgcns -Ifalcon_sense
> correction/generateCorrectionLayouts.C
> g++ -o
> /<<BUILDDIR>>/canu-1.5+dfsg/Linux-amd64/obj/generateCorrectionLayouts/utgcns/stashContains.o
> -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
> -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.5+dfsg=. -fstack-protector-strong
> -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC
> -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts
> -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations
> -finline-functions -fomit-frame-pointer -DLIBBACKTRACE
> -I/<<BUILDDIR>>/canu-1.5+dfsg/src -IAS_UTL -Istores -Iutgcns -Ifalcon_sense
> utgcns/stashContains.C
> g++ -o
> /<<BUILDDIR>>/canu-1.5+dfsg/Linux-amd64/obj/generateCorrectionLayouts/falcon_sense/outputFalcon.o
> -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
> -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.5+dfsg=. -fstack-protector-strong
> -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC
> -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts
> -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations
> -finline-functions -fomit-frame-pointer -DLIBBACKTRACE
> -I/<<BUILDDIR>>/canu-1.5+dfsg/src -IAS_UTL -Istores -Iutgcns -Ifalcon_sense
> falcon_sense/outputFalcon.C
> g++ -o
> /<<BUILDDIR>>/canu-1.5+dfsg/Linux-amd64/obj/readConsensus/correction/readConsensus.o
> -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
> -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.5+dfsg=. -fstack-protector-strong
> -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC
> -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts
> -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations
> -finline-functions -fomit-frame-pointer -DLIBBACKTRACE
> -I/<<BUILDDIR>>/canu-1.5+dfsg/src -IAS_UTL -Istores -IoverlapInCore
> -Iutgcns/libNDalign -IoverlapErrorAdjustment correction/readConsensus.C
> g++ -o
> /<<BUILDDIR>>/canu-1.5+dfsg/Linux-amd64/obj/errorEstimate/correction/errorEstimate.o
> -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
> -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.5+dfsg=. -fstack-protector-strong
> -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC
> -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts
> -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations
> -finline-functions -fomit-frame-pointer -DLIBBACKTRACE
> -I/<<BUILDDIR>>/canu-1.5+dfsg/src -IAS_UTL -Istores -IoverlapInCore
> -Iutgcns/libNDalign -IoverlapErrorAdjustment correction/errorEstimate.C
> g++ -o
> /<<BUILDDIR>>/canu-1.5+dfsg/Linux-amd64/obj/createFalconSenseInputs/falcon_sense/createFalconSenseInputs.o
> -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
> -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.5+dfsg=. -fstack-protector-strong
> -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC
> -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts
> -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations
> -finline-functions -fomit-frame-pointer -DLIBBACKTRACE
> -I/<<BUILDDIR>>/canu-1.5+dfsg/src -IAS_UTL -Istores
> falcon_sense/createFalconSenseInputs.C
> g++ -o
> /<<BUILDDIR>>/canu-1.5+dfsg/Linux-amd64/obj/createFalconSenseInputs/falcon_sense/outputFalcon.o
> -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
> -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.5+dfsg=. -fstack-protector-strong
> -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC
> -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts
> -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations
> -finline-functions -fomit-frame-pointer -DLIBBACKTRACE
> -I/<<BUILDDIR>>/canu-1.5+dfsg/src -IAS_UTL -Istores
> falcon_sense/outputFalcon.C
> g++ -o
> /<<BUILDDIR>>/canu-1.5+dfsg/Linux-amd64/obj/falcon_sense/falcon_sense/falcon_sense.o
> -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
> -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.5+dfsg=. -fstack-protector-strong
> -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC
> -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts
> -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations
> -finline-functions -fomit-frame-pointer -DLIBBACKTRACE
> -I/<<BUILDDIR>>/canu-1.5+dfsg/src -IAS_UTL -Istores -IoverlapInCore/libedlib
> -Ifalcon_sense/libfalcon falcon_sense/falcon_sense.C
> correction/generateCorrectionLayouts.C: In function 'tgTig*
> generateLayout(gkStore*, uint64*, bool, uint32, double, double, ovOverlap*,
> uint32, FILE*)':
> correction/generateCorrectionLayouts.C:112:110: warning: format '%llu'
> expects argument of type 'long long unsigned int', but argument 6 has type
> 'uint64 {aka long unsigned int}' [-Wformat=]
> ovl[oo].b_iid, ovl[oo].a_bgn(), ovl[oo].a_end(), ovlLength,
> ovl[oo].erate(), maxEvidenceErate);
>
> ^
> correction/generateCorrectionLayouts.C:119:111: warning: format '%llu'
> expects argument of type 'long long unsigned int', but argument 6 has type
> 'uint64 {aka long unsigned int}' [-Wformat=]
> ovl[oo].b_iid, ovl[oo].a_bgn(), ovl[oo].a_end(), ovlLength,
> ovl[oo].erate(), minEvidenceLength);
>
> ^
> correction/generateCorrectionLayouts.C:127:119: warning: format '%llu'
> expects argument of type 'long long unsigned int', but argument 6 has type
> 'uint64 {aka long unsigned int}' [-Wformat=]
> ovl[oo].b_iid, ovl[oo].a_bgn(), ovl[oo].a_end(), ovlLength,
> ovl[oo].erate(), readScores[ovl[oo].b_iid]);
>
> ^
> correction/generateCorrectionLayouts.C:134:92: warning: format '%llu' expects
> argument of type 'long long unsigned int', but argument 6 has type 'uint64
> {aka long unsigned int}' [-Wformat=]
> ovl[oo].b_iid, ovl[oo].a_bgn(), ovl[oo].a_end(), ovlLength,
> ovl[oo].erate());
>
> ^
> correction/generateCorrectionLayouts.C:140:90: warning: format '%llu' expects
> argument of type 'long long unsigned int', but argument 6 has type 'uint64
> {aka long unsigned int}' [-Wformat=]
> ovl[oo].b_iid, ovl[oo].a_bgn(), ovl[oo].a_end(), ovlLength,
> ovl[oo].erate());
>
> ^
> g++ -o
> /<<BUILDDIR>>/canu-1.5+dfsg/Linux-amd64/obj/trimReads/overlapBasedTrimming/trimReads.o
> -c -MD -Wdate-time -D_FORTIFY_SOURCE=2 -g -O2
> -fdebug-prefix-map=/<<BUILDDIR>>/canu-1.5+dfsg=. -fstack-protector-strong
> -Wformat -Werror=format-security -D_GLIBCXX_PARALLEL -pthread -fopenmp -fPIC
> -Wall -Wextra -Wno-write-strings -Wno-unused -Wno-char-subscripts
> -Wno-sign-compare -Wformat -g3 -O4 -funroll-loops -fexpensive-optimizations
> -finline-functions -fomit-frame-pointer -DLIBBACKTRACE
> -I/<<BUILDDIR>>/canu-1.5+dfsg/src -IAS_UTL -Istores
> overlapBasedTrimming/trimReads.C
> correction/generateCorrectionLayouts.C: In function 'int main(int, char**)':
> correction/generateCorrectionLayouts.C:390:10: warning: ignoring return value
> of 'char* fgets(char*, int, FILE*)', declared with attribute
> warn_unused_result [-Wunused-result]
> fgets(L, 1024, R);
> ~~~~~^~~~~~~~~~~~
> correction/generateCorrectionLayouts.C:399:12: warning: ignoring return value
> of 'char* fgets(char*, int, FILE*)', declared with attribute
> warn_unused_result [-Wunused-result]
> fgets(L, 1024, R);
> ~~~~~^~~~~~~~~~~~
> cc1plus: some warnings being treated as errors
> Makefile:640: recipe for target
> '/<<BUILDDIR>>/canu-1.5+dfsg/Linux-amd64/obj/merTrim/merTrim/merTrim.o' failed
> make[2]: ***
> [/<<BUILDDIR>>/canu-1.5+dfsg/Linux-amd64/obj/merTrim/merTrim/merTrim.o] Error
> 1
The full build log is available from:
http://aws-logs.debian.net/2017/08/07/canu_1.5+dfsg-1_unstable.log
A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!
About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.
