Bug#984243: Help: mothur: ftbfs with GCC-11
Hi all, The problem can be fixed following these steps: 1. Revert the commit ff8928540e0d720b8a08ee4227c1bbadc2c1e733 (now, that is the last commit). 2. Apply this patch: >--- a/Makefile >+++ b/Makefile >@@ -118,8 +118,8 @@ endif ># > OBJECTS=$(patsubst %.cpp,%.o,$(wildcard $(addsuffix *.cpp,$(subdirs > OBJECTS+=$(patsubst %.c,%.o,$(wildcard $(addsuffix *.c,$(subdirs >-OBJECTS+=$(patsubst %.cpp,%.o,$(wildcard *.cpp)) >-OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c)) >+OBJECTS+=$(patsubst %.cpp,%.o,$(wildcard source/*.cpp)) >+OBJECTS+=$(patsubst %.c,%.o,$(wildcard source/*.c)) > > mothur : $(OBJECTS) uchime > $(CXX) $(LDFLAGS) $(TARGET_ARCH) -o $@ $(OBJECTS) $(LIBS) In fact, the ff8928540e0d720b8a08ee4227c1bbadc2c1e733 was applied toward a wrong Makefile, not the top one. Regards, Hamid On Mon, Nov 8, 2021 at 4:25 PM Andreas Tille wrote: > > Am Mon, Oct 25, 2021 at 09:16:30PM -0400 schrieb Aaron M. Ucko: > > Andreas Tille writes: > > > > > I'm wondering why the makefile stopped working just because a new compiler > > > version is used. :-( > > > > Along the way, you pulled in a new upstream version, whose makefile > > evidently wasn't quite right. > > I think I've found the reason for the failure: It is the overlong line: > > > g++ -Wl,-z,relro -Wl,-z,now -std=c++11 -pthread -Lsource/calculators/ > -Lsource/chimera/ -Lsource/classifier/ -Lsource/clearcut/ > -Lsource/commands/ -Lsource/communitytype/ -Lsource/datastructures/ > -Lsource/engines/ -Lsource/metastats/ -Lsource/read/ -Lsource/svm/ -o > mothur source/calculators/accuracy.o source/calculators/ace.o > source/calculators/bergerparker.o source/calculators/boneh.o > source/calculators/bootstrap.o source/calculators/bstick.o > source/calculators/calculator.o source/calculators/canberra.o > source/calculators/chao1.o source/calculators/coverage.o > source/calculators/diversityutils.o source/calculators/eachgapdist.o > source/calculators/eachgapignore.o source/calculators/efron.o > source/calculators/erarefaction.o source/calculators/f1score.o > source/calculators/fdr.o source/calculators/fn.o source/calculators/fp.o > source/calculators/fpfn.o source/calculators/geom.o > source/calculators/goodscoverage.o source/calculators/gower.o > source/calculators/hamming.o source/calculators/heip.o > source/calculators/hellinger.o source/calculators/igabundance.o > source/calculators/ignoregaps.o source/calculators/igrarefaction.o > source/calculators/invsimpson.o source/calculators/jackknife.o > source/calculators/kimura.o source/calculators/kmerdist.o > source/calculators/lnabundance.o source/calculators/lnrarefaction.o > source/calculators/lnshift.o source/calculators/logsd.o > source/calculators/lsabundance.o source/calculators/lsrarefaction.o > source/calculators/manhattan.o source/calculators/mcc.o > source/calculators/memchi2.o source/calculators/memchord.o > source/calculators/memeuclidean.o source/calculators/mempearson.o > source/calculators/metroig.o source/calculators/metrolognormal.o > source/calculators/metrologstudent.o source/calculators/metrosichel.o > source/calculators/npshannon.o source/calculators/npv.o > source/calculators/odum.o source/calculators/onegapdist.o > source/calculators/onegapignore.o source/calculators/parsimony.o > source/calculators/ppv.o source/calculators/prng.o source/calculators/qstat.o > source/calculators/sensitivity.o source/calculators/shannon.o > source/calculators/shannoneven.o source/calculators/shannonrange.o > source/calculators/sharedace.o source/calculators/sharedanderbergs.o > source/calculators/sharedbraycurtis.o source/calculators/sharedchao1.o > source/calculators/sharedjabund.o source/calculators/sharedjackknife.o > source/calculators/sharedjclass.o source/calculators/sharedjest.o > source/calculators/sharedjsd.o source/calculators/sharedkstest.o > source/calculators/sharedkulczynski.o > source/calculators/sharedkulczynskicody.o source/calculators/sharedlennon.o > source/calculators/sharedmarczewski.o source/calculators/sharedmorisitahorn.o > source/calculators/sharedochiai.o source/calculators/sharedrjsd.o > source/calculators/sharedsobs.o source/calculators/sharedsobscollectsummary.o > source/calculators/sharedsorabund.o source/calculators/sharedsorclass.o > source/calculators/sharedsorest.o source/calculators/sharedthetan.o > source/calculators/sharedthetayc.o source/calculators/shen.o > source/calculators/siabundance.o source/calculators/simpson.o sg++ > -Wl,-z,relro -Wl,-z,now -std=c++11 -pthread -Lsource/calculators/ > -Lsource/chimera/ -Lsource/classifier/ -Lsource/clearcut/ > -Lsource/commands/ -Lsource/communitytype/ -Lsource/datastructures/ > -Lsource/engines/ -Lsource/metastats/ -Lsource/read/ -Lsource/svm/ -o > mothur source/calculators/accuracy.o source/calculators/ace.o > source/calculators/bergerparker.o source/calculators/boneh.o > source/calculators/bootstrap.o
Bug#984243: Help: mothur: ftbfs with GCC-11
Andreas Tille writes: > which has an incomplete number of arguments that is interrupted > by '/usr/bin/ld') That looks like it might simply be an artifact of different buffering policies for standard output and standard error; I expect you'll find the remainder of the command line later on. > Any idea how to specify the number of object files more sensibly > to not explode the command line arguments too much? You (or upstream) could consider using internal static libraries. -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org) http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?a...@monk.mit.edu
Bug#984243: Help: mothur: ftbfs with GCC-11
Am Mon, Oct 25, 2021 at 09:16:30PM -0400 schrieb Aaron M. Ucko: > Andreas Tille writes: > > > I'm wondering why the makefile stopped working just because a new compiler > > version is used. :-( > > Along the way, you pulled in a new upstream version, whose makefile > evidently wasn't quite right. I think I've found the reason for the failure: It is the overlong line: g++ -Wl,-z,relro -Wl,-z,now -std=c++11 -pthread -Lsource/calculators/ -Lsource/chimera/ -Lsource/classifier/ -Lsource/clearcut/ -Lsource/commands/ -Lsource/communitytype/ -Lsource/datastructures/ -Lsource/engines/ -Lsource/metastats/ -Lsource/read/ -Lsource/svm/ -o mothur source/calculators/accuracy.o source/calculators/ace.o source/calculators/bergerparker.o source/calculators/boneh.o source/calculators/bootstrap.o source/calculators/bstick.o source/calculators/calculator.o source/calculators/canberra.o source/calculators/chao1.o source/calculators/coverage.o source/calculators/diversityutils.o source/calculators/eachgapdist.o source/calculators/eachgapignore.o source/calculators/efron.o source/calculators/erarefaction.o source/calculators/f1score.o source/calculators/fdr.o source/calculators/fn.o source/calculators/fp.o source/calculators/fpfn.o source/calculators/geom.o source/calculators/goodscoverage.o source/calculators/gower.o source/calculators/hamming.o source/calculators/heip.o source/calculators/hellinger.o source/calculators/igabundance.o source/calculators/ignoregaps.o source/calculators/igrarefaction.o source/calculators/invsimpson.o source/calculators/jackknife.o source/calculators/kimura.o source/calculators/kmerdist.o source/calculators/lnabundance.o source/calculators/lnrarefaction.o source/calculators/lnshift.o source/calculators/logsd.o source/calculators/lsabundance.o source/calculators/lsrarefaction.o source/calculators/manhattan.o source/calculators/mcc.o source/calculators/memchi2.o source/calculators/memchord.o source/calculators/memeuclidean.o source/calculators/mempearson.o source/calculators/metroig.o source/calculators/metrolognormal.o source/calculators/metrologstudent.o source/calculators/metrosichel.o source/calculators/npshannon.o source/calculators/npv.o source/calculators/odum.o source/calculators/onegapdist.o source/calculators/onegapignore.o source/calculators/parsimony.o source/calculators/ppv.o source/calculators/prng.o source/calculators/qstat.o source/calculators/sensitivity.o source/calculators/shannon.o source/calculators/shannoneven.o source/calculators/shannonrange.o source/calculators/sharedace.o source/calculators/sharedanderbergs.o source/calculators/sharedbraycurtis.o source/calculators/sharedchao1.o source/calculators/sharedjabund.o source/calculators/sharedjackknife.o source/calculators/sharedjclass.o source/calculators/sharedjest.o source/calculators/sharedjsd.o source/calculators/sharedkstest.o source/calculators/sharedkulczynski.o source/calculators/sharedkulczynskicody.o source/calculators/sharedlennon.o source/calculators/sharedmarczewski.o source/calculators/sharedmorisitahorn.o source/calculators/sharedochiai.o source/calculators/sharedrjsd.o source/calculators/sharedsobs.o source/calculators/sharedsobscollectsummary.o source/calculators/sharedsorabund.o source/calculators/sharedsorclass.o source/calculators/sharedsorest.o source/calculators/sharedthetan.o source/calculators/sharedthetayc.o source/calculators/shen.o source/calculators/siabundance.o source/calculators/simpson.o sg++ -Wl,-z,relro -Wl,-z,now -std=c++11 -pthread -Lsource/calculators/ -Lsource/chimera/ -Lsource/classifier/ -Lsource/clearcut/ -Lsource/commands/ -Lsource/communitytype/ -Lsource/datastructures/ -Lsource/engines/ -Lsource/metastats/ -Lsource/read/ -Lsource/svm/ -o mothur source/calculators/accuracy.o source/calculators/ace.o source/calculators/bergerparker.o source/calculators/boneh.o source/calculators/bootstrap.o source/calculators/bstick.o source/calculators/calculator.o source/calculators/canberra.o source/calculators/chao1.o source/calculators/coverage.o source/calculators/diversityutils.o source/calculators/eachgapdist.o source/calculators/eachgapignore.o source/calculators/efron.o source/calculators/erarefaction.o source/calculators/f1score.o source/calculators/fdr.o source/calculators/fn.o source/calculators/fp.o source/calculators/fpfn.o source/calculators/geom.o source/calculators/goodscoverage.o source/calculators/gower.o source/calculators/hamming.o source/calculators/heip.o source/calculators/hellinger.o source/calculators/igabundance.o source/calculators/ignoregaps.o source/calculators/igrarefaction.o source/calculators/invsimpson.o source/calculators/jackknife.o source/calculators/kimura.o source/calculators/kmerdist.o source/calculators/lnabundance.o source/calculators/lnrarefaction.o source/calculators/lnshift.o source/calculators/logsd.o source/calculators/lsabundance.o
Bug#984243: Help: mothur: ftbfs with GCC-11
Andreas Tille writes: > I'm wondering why the makefile stopped working just because a new compiler > version is used. :-( Along the way, you pulled in a new upstream version, whose makefile evidently wasn't quite right. -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org) http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?a...@monk.mit.edu
Bug#984243: Help: mothur: ftbfs with GCC-11
Am Fri, Oct 22, 2021 at 07:46:35AM -0400 schrieb Aaron M. Ucko: > > # Get the list of all .cpp files, rename to .o files > > # > > OBJECTS=$(patsubst %.cpp,%.o,$(wildcard $(addsuffix *.cpp,$(subdirs > > OBJECTS+=$(patsubst %.c,%.o,$(wildcard $(addsuffix *.c,$(subdirs > > OBJECTS+=$(patsubst %.cpp,%.o,$(wildcard *.cpp)) > > OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c)) > > > > the right way to get the path correctly? Or what do you mean? > > Please try changing the last two lines to > > OBJECTS+=$(patsubst %.cpp,%.o,$(wildcard source/*.cpp)) > OBJECTS+=$(patsubst %.c,%.o,$(wildcard source/*.c)) > > to match the relevant sources' actual location; sorry if that was unclear. > (The existing setup only covers subdirectories of source, missing that > directory's immediate contents.) OK, did so but left me with cd source/uchime_src && export CXX=g++ && make clean && make && mv uchime ../../ && cd .. make[3]: Entering directory '/build/mothur-1.46.1/source/uchime_src' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: Leaving directory '/build/mothur-1.46.1/source/uchime_src' make[3]: Entering directory '/build/mothur-1.46.1/source/uchime_src' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. g++ -g -o uchime g++: fatal error: no input files compilation terminated. I'm wondering why the makefile stopped working just because a new compiler version is used. :-( Kind regards Andreas. -- http://fam-tille.de
Bug#984243: Help: mothur: ftbfs with GCC-11
Andreas Tille writes: > OK, I've implemented this in my last commit. Great, thanks! > Isn't > > # Get the list of all .cpp files, rename to .o files > # > OBJECTS=$(patsubst %.cpp,%.o,$(wildcard $(addsuffix *.cpp,$(subdirs > OBJECTS+=$(patsubst %.c,%.o,$(wildcard $(addsuffix *.c,$(subdirs > OBJECTS+=$(patsubst %.cpp,%.o,$(wildcard *.cpp)) > OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c)) > > the right way to get the path correctly? Or what do you mean? Please try changing the last two lines to OBJECTS+=$(patsubst %.cpp,%.o,$(wildcard source/*.cpp)) OBJECTS+=$(patsubst %.c,%.o,$(wildcard source/*.c)) to match the relevant sources' actual location; sorry if that was unclear. (The existing setup only covers subdirectories of source, missing that directory's immediate contents.) -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org) http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?a...@monk.mit.edu
Bug#984243: Help: mothur: ftbfs with GCC-11
Hi Aaron, Am Thu, Oct 21, 2021 at 04:21:26PM -0400 schrieb Aaron M. Ucko: > > No, because std::byte supports far too few operations [1]. Instead, I'd > suggest encouraging upstream to rename their type, and meanwhile locally > patching source/uchime_src/makefile to add -std=c++14 to CXXFLAGS, > thereby suppressing std::byte for now. OK, I've implemented this in my last commit. > I also found massive link errors, resolvable by correcting the top-level > Makefile to pick up source/*.cpp and source/*.c rather than the > nonexistent *.cpp and *.c. I confirm these linking errors but I fail to interpret your hint here. Isn't # Get the list of all .cpp files, rename to .o files # OBJECTS=$(patsubst %.cpp,%.o,$(wildcard $(addsuffix *.cpp,$(subdirs OBJECTS+=$(patsubst %.c,%.o,$(wildcard $(addsuffix *.c,$(subdirs OBJECTS+=$(patsubst %.cpp,%.o,$(wildcard *.cpp)) OBJECTS+=$(patsubst %.c,%.o,$(wildcard *.c)) the right way to get the path correctly? Or what do you mean? Kind regards Andreas. > [1] https://en.cppreference.com/w/cpp/types/byte -- http://fam-tille.de
Bug#984243: Help: mothur: ftbfs with GCC-11
Hi Andreas, Andreas Tille, on 2021-10-21: > In file included from addtargets2.cpp:3: > myutils.h:176:1: error: reference to 'byte' is ambiguous Since C++ 2017, the std::byte type is defined: > 176 | byte *ReadAllStdioFile(FILE *f, off_t ); > | ^~~~ > In file included from /usr/include/c++/11/bits/stl_algobase.h:61, > from /usr/include/c++/11/bits/char_traits.h:39, > from /usr/include/c++/11/string:40, > from myutils.h:8, > from addtargets2.cpp:3: > /usr/include/c++/11/bits/cpp_type_traits.h:404:30: note: candidates are: > 'enum class std::byte' The redefinition below thus gives indeterminations, as the code is running in namespace "std": > In file included from addtargets2.cpp:3: > myutils.h:42:23: note: 'typedef unsigned char byte' >42 | typedef unsigned char byte; > | ^~~~ > myutils.h:177:1: error: reference to 'byte' is ambiguous The option which seems the most viable would be to replace all occurrences of the "byte" type by something that does not clash with the new standard library, maybe "byte8" to be somewhat consistent with upstream naming conventions. In hope this helps, Have a nice evening, :) -- Étienne Mollier Fingerprint: 8f91 b227 c7d6 f2b1 948c 8236 793c f67e 8f0d 11da Sent from /dev/tty1, please excuse my verbosity. signature.asc Description: PGP signature
Bug#984243: Help: mothur: ftbfs with GCC-11
Steffen Möller writes: > My C++ skills are a bit rosty but would removing the typedef for byte > solve the problem? No, because std::byte supports far too few operations [1]. Instead, I'd suggest encouraging upstream to rename their type, and meanwhile locally patching source/uchime_src/makefile to add -std=c++14 to CXXFLAGS, thereby suppressing std::byte for now. I also found massive link errors, resolvable by correcting the top-level Makefile to pick up source/*.cpp and source/*.c rather than the nonexistent *.cpp and *.c. [1] https://en.cppreference.com/w/cpp/types/byte -- Aaron M. Ucko, KB1CJC (amu at alum.mit.edu, ucko at debian.org) http://www.mit.edu/~amu/ | http://stuff.mit.edu/cgi/finger/?a...@monk.mit.edu
Bug#984243: Help: mothur: ftbfs with GCC-11
On 21.10.21 20:21, Étienne Mollier wrote: Hi Andreas, Andreas Tille, on 2021-10-21: In file included from addtargets2.cpp:3: myutils.h:176:1: error: reference to 'byte' is ambiguous Since C++ 2017, the std::byte type is defined: 176 | byte *ReadAllStdioFile(FILE *f, off_t ); | ^~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:61, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from myutils.h:8, from addtargets2.cpp:3: /usr/include/c++/11/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte' The redefinition below thus gives indeterminations, as the code is running in namespace "std": In file included from addtargets2.cpp:3: myutils.h:42:23: note: 'typedef unsigned char byte' 42 | typedef unsigned char byte; | ^~~~ myutils.h:177:1: error: reference to 'byte' is ambiguous The option which seems the most viable would be to replace all occurrences of the "byte" type by something that does not clash with the new standard library, maybe "byte8" to be somewhat consistent with upstream naming conventions. In hope this helps, Have a nice evening, :) My C++ skills are a bit rosty but would removing the typedef for byte solve the problem? Best, Steffen
Bug#984243: Help: mothur: ftbfs with GCC-11
Control: tags -1 help Hi, I've solved one gcc-11 issue that was mentioned in this bug report but now there are other gcc-11 issues that go beyond my C++ knowledge: ... g++ -g -O2 -ffile-prefix-map=/build/mothur-1.46.1=. -fstack-protector-strong -Wformat -Werror=format-security -O3 -std=c++11 -pthread -DVERSION="\"1.46.1\"" -DRELEASE_DATE="\"9/01/ 21\"" -DUSE_READLINE -Isource -I source/calculators/ -I source/chimera/ -I source/classifier/ -I source/clearcut/ -I source/commands/ -I source/communitytype/ -I source/ datastructures/ -I source/engines/ -I source/metastats/ -I source/read/ -I source/svm/ -Wdate-time -D_FORTIFY_SOURCE=2 -c -o source/svm/svm.o source/svm/svm.cpp cd source/uchime_src && export CXX=g++ && make clean && make && mv uchime ../../ && cd .. make[3]: Entering directory '/build/mothur-1.46.1/source/uchime_src' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. make[3]: Leaving directory '/build/mothur-1.46.1/source/uchime_src' make[3]: Entering directory '/build/mothur-1.46.1/source/uchime_src' make[3]: warning: jobserver unavailable: using -j1. Add '+' to parent make rule. g++ -O3 -D_FILE_OFFSET_BITS=64 -DNDEBUG=1 -DUCHIMES=1 -Wdate-time -D_FORTIFY_SOURCE=2 -c -o addtargets2.o addtargets2.cpp In file included from addtargets2.cpp:3: myutils.h:176:1: error: reference to 'byte' is ambiguous 176 | byte *ReadAllStdioFile(FILE *f, off_t ); | ^~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:61, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from myutils.h:8, from addtargets2.cpp:3: /usr/include/c++/11/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte' 404 | enum class byte : unsigned char; | ^~~~ In file included from addtargets2.cpp:3: myutils.h:42:23: note: 'typedef unsigned char byte' 42 | typedef unsigned char byte; | ^~~~ myutils.h:177:1: error: reference to 'byte' is ambiguous 177 | byte *ReadAllStdioFile(const string , off_t ); | ^~~~ In file included from /usr/include/c++/11/bits/stl_algobase.h:61, from /usr/include/c++/11/bits/char_traits.h:39, from /usr/include/c++/11/string:40, from myutils.h:8, from addtargets2.cpp:3: /usr/include/c++/11/bits/cpp_type_traits.h:404:30: note: candidates are: 'enum class std::byte' 404 | enum class byte : unsigned char; | ^~~~ In file included from addtargets2.cpp:3: myutils.h:42:23: note: 'typedef unsigned char byte' 42 | typedef unsigned char byte; | ^~~~ Any help is welcome Andreas. -- http://fam-tille.de
