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Unreleased version will not compile #1065

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morgansobol opened this issue Aug 27, 2018 · 2 comments
Closed

Unreleased version will not compile #1065

morgansobol opened this issue Aug 27, 2018 · 2 comments

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@morgansobol
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morgansobol commented Aug 27, 2018 •
edited by skoren

Hi,

I had a similar issue as mentioned in this post #942
I decided to download the unreleased version to see if it would work, however after compiling the program there is nothing in the /Linux-amd64/bin folder.

Here is the output from the make command.

Building for 'Linux' '2.6.32-754.2.1.el6.x86_64' as 'amd64' into '/work/Geomicrobiology/msobol/bin/canu/Linux-amd64/{bin,obj}'.
Using '/cm/local/apps/gcc/6.1.0/bin/g++' version '6.1.0'.

Building snapshot v1.7 +368 changes (r9060 99162f51f40a61de2043591da8858fa75e3b0e9e) (ahead of github)

g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/AS_global.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap AS_global.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utility/files.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/files.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utility/files-buffered.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/files-buffered.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utility/files-compressed.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/files-compressed.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utility/files-memoryMapped.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/files-memoryMapped.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utility/strings.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/strings.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utility/system.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/system.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utility/system-stackTrace.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/system-stackTrace.C
utility/system-stackTrace.C:60:2: warning: #warning LIBBACKTRACE [-Wcpp]
 #warning LIBBACKTRACE
  ^~~~~~~
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utility/sequence.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/sequence.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utility/kmers.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/kmers.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utility/kmers-reader.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/kmers-reader.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utility/kmers-writer.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/kmers-writer.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utility/kmers-statistics.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/kmers-statistics.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utility/kmers-exact.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/kmers-exact.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utility/bits.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/bits.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utility/hexDump.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/hexDump.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utility/md5.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/md5.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utility/mt19937ar.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/mt19937ar.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utility/objectStore.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/objectStore.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utility/speedCounter.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/speedCounter.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utility/sweatShop.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/sweatShop.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/correction/computeGlobalScore.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap correction/computeGlobalScore.C
correction/computeGlobalScore.C: In member function ‘uint16 globalScore::compute(uint32, ovOverlap*, uint32, uint32, uint16*)’:
correction/computeGlobalScore.C:150:6: warning: suggest explicit braces to avoid ambiguous ‘else’ [-Wparentheses]
   if (logFile)
      ^
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap correction/falconConsensus.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/correction/falconConsensus-alignTag.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap correction/falconConsensus-alignTag.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/stores/sqLibrary.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/sqLibrary.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/stores/sqStore.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/sqStore.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreConstructor.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/sqStoreConstructor.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreInfo.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/sqStoreInfo.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/stores/sqStoreEncode.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/sqStoreEncode.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/stores/sqStorePartition.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/sqStorePartition.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/stores/ovOverlap.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/ovOverlap.C
stores/ovOverlap.C:184:2: warning: #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING [-Wcpp]
 #warning NEEDS TO RETURN FALSE IF FAILED TO DECODE OVERLAP STRING
  ^~~~~~~
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/stores/ovStore.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/ovStore.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreWriter.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/ovStoreWriter.C
stores/ovStoreWriter.C:69:2: warning: #warning not failing if a valid store [-Wcpp]
 #warning not failing if a valid store
  ^~~~~~~
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFilter.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/ovStoreFilter.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreFile.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/ovStoreFile.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/stores/ovStoreHistogram.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/ovStoreHistogram.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/stores/tgStore.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/tgStore.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/stores/tgTig.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/tgTig.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/stores/tgTigSizeAnalysis.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/tgTigSizeAnalysis.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/stores/tgTigMultiAlignDisplay.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/tgTigMultiAlignDisplay.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-sinksource.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/libsnappy/snappy-sinksource.cc
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy-stubs-internal.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/libsnappy/snappy-stubs-internal.cc
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/stores/libsnappy/snappy.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap stores/libsnappy/snappy.cc
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/overlapInCore/overlapReadCache.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/overlapReadCache.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/overlapErrorAdjustment/analyzeAlignment.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapErrorAdjustment/analyzeAlignment.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Binomial_Bound.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/Binomial_Bound.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/Display_Alignment.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/Display_Alignment.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-allocateMoreSpace.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-extend.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-extend.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-forward.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-forward.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/overlapInCore/liboverlap/prefixEditDistance-reverse.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/liboverlap/prefixEditDistance-reverse.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/overlapInCore/libedlib/edlib.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap overlapInCore/libedlib/edlib.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalign.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libNDalign/NDalign.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/Binomial_Bound.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libNDalign/Binomial_Bound.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-allocateMoreSpace.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-allocateMoreSpace.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-extend.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-extend.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-forward.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-forward.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utgcns/libNDalign/NDalgorithm-reverse.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libNDalign/NDalgorithm-reverse.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-addRead.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abAbacus-addRead.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-appendBases.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abAbacus-appendBases.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-applyAlignment.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abAbacus-applyAlignment.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-baseCall.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abAbacus-baseCall.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-mergeRefine.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abAbacus-mergeRefine.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-refine.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abAbacus-refine.C
utgcns/libcns/abAbacus-refine.C:1326:2: warning: #warning SKIPPING ALL REFINEMENTS [-Wcpp]
 #warning SKIPPING ALL REFINEMENTS
  ^~~~~~~
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus-refreshMultiAlign.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abAbacus-refreshMultiAlign.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abAbacus.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abAbacus.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abColumn.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abColumn.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/abMultiAlign.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/abMultiAlign.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utgcns/libcns/unitigConsensus.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libcns/unitigConsensus.C
In file included from utgcns/libboost/boost/scoped_ptr.hpp:14:0,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:31,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
utgcns/libboost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/memory:81:0,
                 from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14,
                 from utgcns/libboost/boost/unordered/unordered_set.hpp:17,
                 from utgcns/libboost/boost/unordered_set.hpp:17,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:21,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
/cm/local/apps/gcc/6.1.0/include/c++/6.1.0/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from utgcns/libboost/boost/shared_ptr.hpp:17,
                 from utgcns/libboost/boost/property_map/vector_property_map.hpp:14,
                 from utgcns/libboost/boost/property_map/property_map.hpp:600,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:36,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
utgcns/libboost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/memory:81:0,
                 from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14,
                 from utgcns/libboost/boost/unordered/unordered_set.hpp:17,
                 from utgcns/libboost/boost/unordered_set.hpp:17,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:21,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
/cm/local/apps/gcc/6.1.0/include/c++/6.1.0/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from utgcns/libboost/boost/shared_ptr.hpp:17:0,
                 from utgcns/libboost/boost/property_map/vector_property_map.hpp:14,
                 from utgcns/libboost/boost/property_map/property_map.hpp:600,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:36,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/memory:81:0,
                 from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14,
                 from utgcns/libboost/boost/unordered/unordered_set.hpp:17,
                 from utgcns/libboost/boost/unordered_set.hpp:17,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:21,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
/cm/local/apps/gcc/6.1.0/include/c++/6.1.0/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from utgcns/libboost/boost/shared_ptr.hpp:17:0,
                 from utgcns/libboost/boost/property_map/vector_property_map.hpp:14,
                 from utgcns/libboost/boost/property_map/property_map.hpp:600,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:36,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/memory:81:0,
                 from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14,
                 from utgcns/libboost/boost/unordered/unordered_set.hpp:17,
                 from utgcns/libboost/boost/unordered_set.hpp:17,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:21,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
/cm/local/apps/gcc/6.1.0/include/c++/6.1.0/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from utgcns/libboost/boost/shared_ptr.hpp:17:0,
                 from utgcns/libboost/boost/property_map/vector_property_map.hpp:14,
                 from utgcns/libboost/boost/property_map/property_map.hpp:600,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:36,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/memory:81:0,
                 from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14,
                 from utgcns/libboost/boost/unordered/unordered_set.hpp:17,
                 from utgcns/libboost/boost/unordered_set.hpp:17,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:21,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
/cm/local/apps/gcc/6.1.0/include/c++/6.1.0/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from utgcns/libboost/boost/shared_ptr.hpp:17:0,
                 from utgcns/libboost/boost/property_map/vector_property_map.hpp:14,
                 from utgcns/libboost/boost/property_map/property_map.hpp:600,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:36,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/memory:81:0,
                 from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14,
                 from utgcns/libboost/boost/unordered/unordered_set.hpp:17,
                 from utgcns/libboost/boost/unordered_set.hpp:17,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:21,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
/cm/local/apps/gcc/6.1.0/include/c++/6.1.0/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from utgcns/libboost/boost/shared_ptr.hpp:17:0,
                 from utgcns/libboost/boost/property_map/vector_property_map.hpp:14,
                 from utgcns/libboost/boost/property_map/property_map.hpp:600,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:36,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/memory:81:0,
                 from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14,
                 from utgcns/libboost/boost/unordered/unordered_set.hpp:17,
                 from utgcns/libboost/boost/unordered_set.hpp:17,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:21,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
/cm/local/apps/gcc/6.1.0/include/c++/6.1.0/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from utgcns/libboost/boost/shared_ptr.hpp:17:0,
                 from utgcns/libboost/boost/property_map/vector_property_map.hpp:14,
                 from utgcns/libboost/boost/property_map/property_map.hpp:600,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:36,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
utgcns/libboost/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/memory:81:0,
                 from utgcns/libboost/boost/unordered/unordered_set_fwd.hpp:14,
                 from utgcns/libboost/boost/unordered/unordered_set.hpp:17,
                 from utgcns/libboost/boost/unordered_set.hpp:17,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:21,
                 from utgcns/libpbutgcns/AlnGraphBoost.H:69,
                 from utgcns/libcns/unitigConsensus.C:77:
/cm/local/apps/gcc/6.1.0/include/c++/6.1.0/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utgcns/libpbutgcns/AlnGraphBoost.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utgcns/libpbutgcns/AlnGraphBoost.C
In file included from utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:28:0,
                 from utgcns/libboost/boost/shared_ptr.hpp:17,
                 from utgcns/libboost/boost/format/alt_sstream.hpp:21,
                 from utgcns/libboost/boost/format/internals.hpp:23,
                 from utgcns/libboost/boost/format.hpp:38,
                 from utgcns/libpbutgcns/AlnGraphBoost.C:72:
utgcns/libboost/boost/smart_ptr/detail/shared_count.hpp:395:33: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_count( std::auto_ptr<Y> & r ): pi_( new sp_counted_impl_p<Y>( r.get() ) )
                                 ^~~~~~~~
In file included from /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/bits/locale_conv.h:41:0,
                 from /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/locale:43,
                 from utgcns/libboost/boost/format.hpp:23,
                 from utgcns/libpbutgcns/AlnGraphBoost.C:72:
/cm/local/apps/gcc/6.1.0/include/c++/6.1.0/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from utgcns/libboost/boost/shared_ptr.hpp:17:0,
                 from utgcns/libboost/boost/format/alt_sstream.hpp:21,
                 from utgcns/libboost/boost/format/internals.hpp:23,
                 from utgcns/libboost/boost/format.hpp:38,
                 from utgcns/libpbutgcns/AlnGraphBoost.C:72:
utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:242:65: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
 template< class T, class R > struct sp_enable_if_auto_ptr< std::auto_ptr< T >, R >
                                                                 ^~~~~~~~
In file included from /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/bits/locale_conv.h:41:0,
                 from /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/locale:43,
                 from utgcns/libboost/boost/format.hpp:23,
                 from utgcns/libpbutgcns/AlnGraphBoost.C:72:
/cm/local/apps/gcc/6.1.0/include/c++/6.1.0/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from utgcns/libboost/boost/shared_ptr.hpp:17:0,
                 from utgcns/libboost/boost/format/alt_sstream.hpp:21,
                 from utgcns/libboost/boost/format/internals.hpp:23,
                 from utgcns/libboost/boost/format.hpp:38,
                 from utgcns/libpbutgcns/AlnGraphBoost.C:72:
utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:441:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit shared_ptr( std::auto_ptr<Y> & r ): px(r.get()), pn()
                               ^~~~~~~~
In file included from /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/bits/locale_conv.h:41:0,
                 from /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/locale:43,
                 from utgcns/libboost/boost/format.hpp:23,
                 from utgcns/libpbutgcns/AlnGraphBoost.C:72:
/cm/local/apps/gcc/6.1.0/include/c++/6.1.0/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from utgcns/libboost/boost/shared_ptr.hpp:17:0,
                 from utgcns/libboost/boost/format/alt_sstream.hpp:21,
                 from utgcns/libboost/boost/format/internals.hpp:23,
                 from utgcns/libboost/boost/format.hpp:38,
                 from utgcns/libpbutgcns/AlnGraphBoost.C:72:
utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:454:22: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr( std::auto_ptr<Y> && r ): px(r.get()), pn()
                      ^~~~~~~~
In file included from /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/bits/locale_conv.h:41:0,
                 from /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/locale:43,
                 from utgcns/libboost/boost/format.hpp:23,
                 from utgcns/libpbutgcns/AlnGraphBoost.C:72:
/cm/local/apps/gcc/6.1.0/include/c++/6.1.0/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from utgcns/libboost/boost/shared_ptr.hpp:17:0,
                 from utgcns/libboost/boost/format/alt_sstream.hpp:21,
                 from utgcns/libboost/boost/format/internals.hpp:23,
                 from utgcns/libboost/boost/format.hpp:38,
                 from utgcns/libpbutgcns/AlnGraphBoost.C:72:
utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:520:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> & r )
                                  ^~~~~~~~
In file included from /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/bits/locale_conv.h:41:0,
                 from /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/locale:43,
                 from utgcns/libboost/boost/format.hpp:23,
                 from utgcns/libpbutgcns/AlnGraphBoost.C:72:
/cm/local/apps/gcc/6.1.0/include/c++/6.1.0/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from utgcns/libboost/boost/shared_ptr.hpp:17:0,
                 from utgcns/libboost/boost/format/alt_sstream.hpp:21,
                 from utgcns/libboost/boost/format/internals.hpp:23,
                 from utgcns/libboost/boost/format.hpp:38,
                 from utgcns/libpbutgcns/AlnGraphBoost.C:72:
utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:529:34: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     shared_ptr & operator=( std::auto_ptr<Y> && r )
                                  ^~~~~~~~
In file included from /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/bits/locale_conv.h:41:0,
                 from /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/locale:43,
                 from utgcns/libboost/boost/format.hpp:23,
                 from utgcns/libpbutgcns/AlnGraphBoost.C:72:
/cm/local/apps/gcc/6.1.0/include/c++/6.1.0/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from utgcns/libboost/boost/shared_ptr.hpp:17:0,
                 from utgcns/libboost/boost/format/alt_sstream.hpp:21,
                 from utgcns/libboost/boost/format/internals.hpp:23,
                 from utgcns/libboost/boost/format.hpp:38,
                 from utgcns/libpbutgcns/AlnGraphBoost.C:72:
utgcns/libboost/boost/smart_ptr/shared_ptr.hpp: In member function ‘boost::shared_ptr<T>& boost::shared_ptr<T>::operator=(std::auto_ptr<_Up>&&)’:
utgcns/libboost/boost/smart_ptr/shared_ptr.hpp:531:38: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
         this_type( static_cast< std::auto_ptr<Y> && >( r ) ).swap( *this );
                                      ^~~~~~~~
In file included from /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/bits/locale_conv.h:41:0,
                 from /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/locale:43,
                 from utgcns/libboost/boost/format.hpp:23,
                 from utgcns/libpbutgcns/AlnGraphBoost.C:72:
/cm/local/apps/gcc/6.1.0/include/c++/6.1.0/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
In file included from utgcns/libboost/boost/scoped_ptr.hpp:14:0,
                 from utgcns/libboost/boost/graph/adjacency_list.hpp:31,
                 from utgcns/libpbutgcns/AlnGraphBoost.C:74:
utgcns/libboost/boost/smart_ptr/scoped_ptr.hpp: At global scope:
utgcns/libboost/boost/smart_ptr/scoped_ptr.hpp:68:31: warning: ‘template<class> class std::auto_ptr’ is deprecated [-Wdeprecated-declarations]
     explicit scoped_ptr( std::auto_ptr<T> p ) BOOST_NOEXCEPT : px( p.release() )
                               ^~~~~~~~
In file included from /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/bits/locale_conv.h:41:0,
                 from /cm/local/apps/gcc/6.1.0/include/c++/6.1.0/locale:43,
                 from utgcns/libboost/boost/format.hpp:23,
                 from utgcns/libpbutgcns/AlnGraphBoost.C:72:
/cm/local/apps/gcc/6.1.0/include/c++/6.1.0/bits/unique_ptr.h:49:28: note: declared here
   template<typename> class auto_ptr;
                            ^~~~~~~~
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/gfa/gfa.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap gfa/gfa.C
g++ -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/gfa/bed.o -c -MD -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/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap gfa/bed.C
cc -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utility/libbacktrace/atomic.o -c -MD -I/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/libbacktrace/atomic.c
cc -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utility/libbacktrace/backtrace.o -c -MD -I/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/libbacktrace/backtrace.c
cc -o /work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utility/libbacktrace/dwarf.o -c -MD -I/work/Geomicrobiology/msobol/bin/canu/src -Iutility -Istores -Istores/libsnappy -Ialignment -Iutgcns/libNDalign -Iutgcns/libcns -Iutgcns/libpbutgcns -Iutgcns/libNDFalcon -Iutgcns/libboost -IoverlapInCore -IoverlapInCore/libedlib -IoverlapInCore/liboverlap utility/libbacktrace/dwarf.c
utility/libbacktrace/dwarf.c: In function ‘dwarf_lookup_pc’:
utility/libbacktrace/dwarf.c:2779: error: ‘__ATOMIC_ACQUIRE’ undeclared (first use in this function)
utility/libbacktrace/dwarf.c:2779: error: (Each undeclared identifier is reported only once
utility/libbacktrace/dwarf.c:2779: error: for each function it appears in.)
utility/libbacktrace/dwarf.c:2839: error: ‘__ATOMIC_RELEASE’ undeclared (first use in this function)
utility/libbacktrace/dwarf.c: In function ‘dwarf_fileline’:
utility/libbacktrace/dwarf.c:2974: error: ‘__ATOMIC_ACQUIRE’ undeclared (first use in this function)
utility/libbacktrace/dwarf.c: In function ‘backtrace_dwarf_add’:
utility/libbacktrace/dwarf.c:3107: error: ‘__ATOMIC_ACQUIRE’ undeclared (first use in this function)
make: *** [/work/Geomicrobiology/msobol/bin/canu/Linux-amd64/obj/lib/libcanu.a/utility/libbacktrace/dwarf.o] Error 1
@brianwalenz
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Interesting. It's picking up the wrong C compiler.

Two workarounds:

  1. make CC=gcc should make it use a version compatible with the g++ it is using. Test before with which gcc and which g++ - the directory these are in should be similar if not the same.
  2. make BUILDSTACKTRACE=0 will disable the particular item it fails on - this is just debugging support, nothing critical.

@morgansobol
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The first option worked. Thanks.

@skoren skoren closed this as completed Oct 18, 2018
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@skoren @brianwalenz @morgansobol