HmmUFOtu on conda?

[AlessioMilanese]

HI Qi,

you did a nice tool!

I have two questions:

1. Are you planning to add HmmUFOtu to bioconda?
2. I would be interested to use your p7 HMM architecture. Something similar to:
   Given a MSA (<msafile>) and some sequences that I want to "align" according to this existing MSA (<seqfile>):

hmmbuild hmm_file <msafile>
hmmalign hmm_file <seqfile>

Is that possible?

[blinard-BIOINFO]

Hi,
I back this demand as I would like to add HmmOFUm support to PEWO, a set of tools to benchmarck phylogenteic placement that we developed (https://github.com/phylo42/PEWO).

We use conda environments to manage all supported software, so having your tool in bioconda would accelerate its integration.

[e00011027]

Hi Alessio, Thanks for being interested in HmmUFOtu. For question 1, no, since it is not a typical "Python dependency mess" tool that need some specific environment to run and install. It is a stand-alone, pure C++ tool that if can be ./configured, it will run. No silly environment settings needed. For question 2, yes. Follow the "homepage" link to HmmUFOtu home page, read it carefully, and you will find your answer how. If you have any questions, please let me know. Best Qi

…

On Fri, May 8, 2020 at 7:11 AM Alessio Milanese ***@***.***> wrote: HI Qi, you did a nice tool! I have two questions: 1. Are you planning to add HmmUFOtu to bioconda? 2. I would be interested to use your p7 HMM architecture. Something similar to: Given a MSA (<msafile>) and some sequences that I want to "align" according to this existing MSA (<seqfile>): hmmbuild hmm_file <msafile> hmmalign hmm_file <seqfile> Is that possible? — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#7>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABXZ44LGZEGLDD6ZLFU6UHLRQPSEPANCNFSM4M4C4KOA> .

[AlessioMilanese]

Thanks for the fast response Qi,

I cannot manage to install it on macOS:

1. Git clone.

   Message

   Cloning into 'HmmUFOtu'...
   remote: Enumerating objects: 19, done.
   remote: Counting objects: 100% (19/19), done.
   remote: Compressing objects: 100% (14/14), done.
   remote: Total 4939 (delta 9), reused 14 (delta 5), pack-reused 4920
   Receiving objects: 100% (4939/4939), 54.56 MiB | 7.10 MiB/s, done.
   Resolving deltas: 100% (3868/3868), done.
   

2. Configure

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   === configuring in src/util (/Users/milanese/Dropbox/PhD/bin/HmmUFOtu/src/util)
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   === configuring in src/math (/Users/milanese/Dropbox/PhD/bin/HmmUFOtu/src/math)
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   === configuring in src/libcds (/Users/milanese/Dropbox/PhD/bin/HmmUFOtu/src/libcds)
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   checking for objdir... .libs
   checking if gcc supports -fno-rtti -fno-exceptions... yes
   checking for gcc option to produce PIC... -fno-common -DPIC
   checking if gcc PIC flag -fno-common -DPIC works... yes
   checking if gcc static flag -static works... no
   checking if gcc supports -c -o file.o... yes
   checking if gcc supports -c -o file.o... (cached) yes
   checking whether the gcc linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes
   checking dynamic linker characteristics... darwin19.4.0 dyld
   checking how to hardcode library paths into programs... immediate
   checking whether stripping libraries is possible... yes
   checking if libtool supports shared libraries... yes
   checking whether to build shared libraries... yes
   checking whether to build static libraries... yes
   checking for doxygen... no
   configure: WARNING: doxygen not found - will not generate any doxygen documentation
   checking for perl... /Users/milanese/miniconda3/bin/perl
   checking for g++... g++
   checking whether we are using the GNU C++ compiler... yes
   checking whether g++ accepts -g... yes
   checking dependency style of g++... gcc3
   checking how to run the C++ preprocessor... g++ -E
   checking for ld used by g++... /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld
   checking if the linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) is GNU ld... no
   checking whether the g++ linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes
   checking for g++ option to produce PIC... -fno-common -DPIC
   checking if g++ PIC flag -fno-common -DPIC works... yes
   checking if g++ static flag -static works... no
   checking if g++ supports -c -o file.o... yes
   checking if g++ supports -c -o file.o... (cached) yes
   checking whether the g++ linker (/Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/ld) supports shared libraries... yes
   checking dynamic linker characteristics... darwin19.4.0 dyld
   checking how to hardcode library paths into programs... immediate
   checking whether make sets $(MAKE)... (cached) yes
   checking if g++ supports C++0x features without additional flags... no
   checking if g++ supports C++0x features with -std=c++0x... yes
   checking if g++ supports C++0x features with -std=gnu++0x... yes
   checking for stdint.h... (cached) yes
   checking for stdlib.h... (cached) yes
   checking sys/timeb.h usability... yes
   checking sys/timeb.h presence... yes
   checking for sys/timeb.h... yes
   checking for unistd.h... (cached) yes
   checking for stdbool.h that conforms to C99... no
   checking for _Bool... no
   checking for inline... inline
   checking for size_t... yes
   checking for uint32_t... yes
   checking for select... yes
   checking for malloc... yes
   checking for realloc... yes
   checking that generated files are newer than configure... done
   configure: creating ./config.status
   config.status: creating Makefile
   config.status: creating cds.pc
   config.status: creating src/Makefile
   config.status: creating tests/Makefile
   config.status: creating tutorial/src/Makefile
   config.status: creating tutorial/ssa/Makefile
   config.status: creating build-aux/config.h
   config.status: executing depfiles commands
   config.status: executing libtool commands
   === configuring in src/libdivsufsort (/Users/milanese/Dropbox/PhD/bin/HmmUFOtu/src/libdivsufsort)
   configure: running /bin/sh ./configure --disable-option-checking '--prefix=/usr/local'  --cache-file=/dev/null --srcdir=.
   checking for gcc... gcc
   checking whether the C compiler works... yes
   checking for C compiler default output file name... a.out
   checking for suffix of executables... 
   checking whether we are cross compiling... no
   checking for suffix of object files... o
   checking whether we are using the GNU C compiler... yes
   checking whether gcc accepts -g... yes
   checking for gcc option to accept ISO C89... none needed
   checking whether gcc understands -c and -o together... yes
   checking for a BSD-compatible install... /usr/bin/install -c
   checking whether build environment is sane... yes
   checking for a thread-safe mkdir -p... ./install-sh -c -d
   checking for gawk... no
   checking for mawk... no
   checking for nawk... no
   checking for awk... awk
   checking whether make sets $(MAKE)... yes
   checking whether make supports the include directive... yes (GNU style)
   checking whether make supports nested variables... yes
   checking dependency style of gcc... gcc3
   checking how to run the C preprocessor... gcc -E
   checking for grep that handles long lines and -e... /usr/bin/grep
   checking for egrep... /usr/bin/grep -E
   checking for ANSI C header files... yes
   checking for sys/types.h... yes
   checking for sys/stat.h... yes
   checking for stdlib.h... yes
   checking for string.h... yes
   checking for memory.h... yes
   checking for strings.h... yes
   checking for inttypes.h... yes
   checking for stdint.h... yes
   checking for unistd.h... yes
   checking fcntl.h usability... yes
   checking fcntl.h presence... yes
   checking for fcntl.h... yes
   checking for inttypes.h... (cached) yes
   checking for memory.h... (cached) yes
   checking stddef.h usability... yes
   checking stddef.h presence... yes
   checking for stddef.h... yes
   checking for stdint.h... (cached) yes
   checking for stdlib.h... (cached) yes
   checking for string.h... (cached) yes
   checking for strings.h... (cached) yes
   checking for size_t... yes
   checking for int32_t... yes
   checking for uint8_t... yes
   checking for int64_t... yes
   checking for inline... inline
   checking for malloc... yes
   checking for ranlib... ranlib
   checking that generated files are newer than configure... done
   configure: creating ./config.status
   config.status: creating Makefile
   config.status: creating lib/Makefile
   config.status: creating examples/Makefile
   config.status: creating config.h
   config.status: config.h is unchanged
   config.status: executing depfiles commands
   

3. make.

   Error

   Making all in data
   make[1]: Nothing to be done for `all'.
   Making all in src
   Making all in libdivsufsort
   /Applications/Xcode.app/Contents/Developer/usr/bin/make  all-recursive
   Making all in lib
   depbase=`echo divsufsort.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
   	gcc -DHAVE_CONFIG_H -I. -I..  -I../include -I/include -I../include -g -O2 -MT divsufsort.o -MD -MP -MF $depbase.Tpo -c -o divsufsort.o divsufsort.c &&\
   	mv -f $depbase.Tpo $depbase.Po
   depbase=`echo sssort.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
   	gcc -DHAVE_CONFIG_H -I. -I..  -I../include -I/include -I../include -g -O2 -MT sssort.o -MD -MP -MF $depbase.Tpo -c -o sssort.o sssort.c &&\
   	mv -f $depbase.Tpo $depbase.Po
   depbase=`echo trsort.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
   	gcc -DHAVE_CONFIG_H -I. -I..  -I../include -I/include -I../include -g -O2 -MT trsort.o -MD -MP -MF $depbase.Tpo -c -o trsort.o trsort.c &&\
   	mv -f $depbase.Tpo $depbase.Po
   depbase=`echo utils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
   	gcc -DHAVE_CONFIG_H -I. -I..  -I../include -I/include -I../include -g -O2 -MT utils.o -MD -MP -MF $depbase.Tpo -c -o utils.o utils.c &&\
   	mv -f $depbase.Tpo $depbase.Po
   rm -f libdivsufsort.a
   ar cru libdivsufsort.a divsufsort.o sssort.o trsort.o utils.o 
   ranlib libdivsufsort.a
   Making all in examples
   depbase=`echo bwt.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
   	gcc -DHAVE_CONFIG_H -I. -I..   -I/include -I../include -g -O2 -MT bwt.o -MD -MP -MF $depbase.Tpo -c -o bwt.o bwt.c &&\
   	mv -f $depbase.Tpo $depbase.Po
   bwt.c:209:5: warning: format specifies type 'intmax_t' (aka 'long') but the
         argument has type 'off_t' (aka 'long long') [-Wformat]
       n, (double)(finish - start) / (double)CLOCKS_PER_SEC);
       ^
   1 warning generated.
   gcc -I../include -g -O2  -L/lib -o bwt bwt.o ../lib/libdivsufsort.a 
   ld: warning: directory not found for option '-L/lib'
   depbase=`echo mksary.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
   	gcc -DHAVE_CONFIG_H -I. -I..   -I/include -I../include -g -O2 -MT mksary.o -MD -MP -MF $depbase.Tpo -c -o mksary.o mksary.c &&\
   	mv -f $depbase.Tpo $depbase.Po
   mksary.c:171:59: warning: format specifies type 'intmax_t' (aka 'long') but the
         argument has type 'off_t' (aka 'long long') [-Wformat]
     fprintf(stderr, "%s: %" PRIdOFF_T " bytes ... ", fname, n);
                          ~~~                                ^
   1 warning generated.
   gcc -I../include -g -O2  -L/lib -o mksary mksary.o ../lib/libdivsufsort.a 
   ld: warning: directory not found for option '-L/lib'
   depbase=`echo sasearch.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
   	gcc -DHAVE_CONFIG_H -I. -I..   -I/include -I../include -g -O2 -MT sasearch.o -MD -MP -MF $depbase.Tpo -c -o sasearch.o sasearch.c &&\
   	mv -f $depbase.Tpo $depbase.Po
   gcc -I../include -g -O2  -L/lib -o sasearch sasearch.o ../lib/libdivsufsort.a 
   ld: warning: directory not found for option '-L/lib'
   depbase=`echo suftest.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
   	gcc -DHAVE_CONFIG_H -I. -I..   -I/include -I../include -g -O2 -MT suftest.o -MD -MP -MF $depbase.Tpo -c -o suftest.o suftest.c &&\
   	mv -f $depbase.Tpo $depbase.Po
   suftest.c:147:59: warning: format specifies type 'intmax_t' (aka 'long') but the
         argument has type 'off_t' (aka 'long long') [-Wformat]
     fprintf(stderr, "%s: %" PRIdOFF_T " bytes ... ", fname, n);
                          ~~~                                ^
   1 warning generated.
   gcc -I../include -g -O2  -L/lib -o suftest suftest.o ../lib/libdivsufsort.a 
   ld: warning: directory not found for option '-L/lib'
   depbase=`echo unbwt.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
   	gcc -DHAVE_CONFIG_H -I. -I..   -I/include -I../include -g -O2 -MT unbwt.o -MD -MP -MF $depbase.Tpo -c -o unbwt.o unbwt.c &&\
   	mv -f $depbase.Tpo $depbase.Po
   unbwt.c:196:5: warning: format specifies type 'intmax_t' (aka 'long') but the
         argument has type 'off_t' (aka 'long long') [-Wformat]
       n, (double)(finish - start) / (double)CLOCKS_PER_SEC);
       ^
   1 warning generated.
   gcc -I../include -g -O2  -L/lib -o unbwt unbwt.o ../lib/libdivsufsort.a 
   ld: warning: directory not found for option '-L/lib'
   Making all in libcds
   Making all in src
     CXX      static/bitsequence/BitSequenceBuilderDArray.lo
     CXX      static/bitsequence/BitSequenceBuilderRG.lo
     CXX      static/bitsequence/BitSequenceBuilderRRR.lo
     CXX      static/bitsequence/BitSequenceBuilderSDArray.lo
     CXX      static/bitsequence/BitSequence.lo
     CXX      static/bitsequence/BitSequenceDArray.lo
     CXX      static/bitsequence/BitSequenceRG.lo
     CXX      static/bitsequence/BitSequenceRRR.lo
     CXX      static/bitsequence/BitSequenceSDArray.lo
     CXX      static/bitsequence/sdarraySadakane.lo
     CXX      static/bitsequence/TableOffsetRRR.lo
     CXX      static/coders/huff.lo
   static/coders/huff.cpp:142:16: warning: 'register' storage class specifier is
         deprecated and incompatible with C++17 [-Wdeprecated-register]
           void bitzero (register uint *e, register uint p,
                         ^~~~~~~~~
   static/coders/huff.cpp:142:34: warning: 'register' storage class specifier is
         deprecated and incompatible with C++17 [-Wdeprecated-register]
           void bitzero (register uint *e, register uint p,
                                           ^~~~~~~~~
   static/coders/huff.cpp:143:2: warning: 'register' storage class specifier is
         deprecated and incompatible with C++17 [-Wdeprecated-register]
           register uint len) {
           ^~~~~~~~~
   3 warnings generated.
     CXX      static/coders/HuffmanCoder.lo
     CXX      static/mapper/MapperCont.lo
     CXX      static/mapper/Mapper.lo
     CXX      static/mapper/MapperNone.lo
     CXX      static/mapper/MapperRev.lo
     CXX      static/permutation/perm.lo
     CXX      static/permutation/PermutationBuilderMRRR.lo
     CXX      static/permutation/PermutationBuilderWT.lo
     CXX      static/permutation/Permutation.lo
     CXX      static/permutation/PermutationMRRR.lo
     CXX      static/permutation/PermutationWT.lo
     CXX      static/sequence/BitmapsSequence.lo
     CXX      static/sequence/SequenceAlphPart.lo
   static/sequence/SequenceAlphPart.cpp:210:16: warning: assigning field to itself
         [-Wself-assign-field]
                   this->maxLen = maxLen;
                                ^
   static/sequence/SequenceAlphPart.cpp:309:16: warning: assigning field to itself
         [-Wself-assign-field]
                   this->maxLen = maxLen;
                                ^
   2 warnings generated.
     CXX      static/sequence/SequenceBuilderAlphPart.lo
     CXX      static/sequence/SequenceBuilderGMRChunk.lo
     CXX      static/sequence/SequenceBuilderGMR.lo
     CXX      static/sequence/SequenceBuilderStr.lo
     CXX      static/sequence/SequenceBuilderWaveletMatrix.lo
     CXX      static/sequence/SequenceBuilderWaveletTree.lo
     CXX      static/sequence/SequenceBuilderWaveletTreeNoptrs.lo
     CXX      static/sequence/SequenceBuilderWaveletTreeNoptrsS.lo
     CXX      static/sequence/Sequence.lo
     CXX      static/sequence/SequenceGMRChunk.lo
   static/sequence/SequenceGMRChunk.cpp:67:15: warning: assigning field to itself
         [-Wself-assign-field]
                   this->sigma = sigma;
                               ^
   static/sequence/SequenceGMRChunk.cpp:113:15: warning: assigning field to itself
         [-Wself-assign-field]
                   this->sigma = sigma;
                               ^
   2 warnings generated.
     CXX      static/sequence/SequenceGMR.lo
     CXX      static/sequence/WaveletMatrix.lo
   static/sequence/WaveletMatrix.cpp:27:104: warning: field 'n' is uninitialized
         when used here [-Wuninitialized]
     ...Array &symbols2, BitSequenceBuilder * bmb, Mapper * am) : Sequence(n) {
                                                                           ^
   1 warning generated.
     CXX      static/sequence/WaveletTree.lo
     CXX      static/sequence/WaveletTreeNoptrs.lo
     CXX      static/sequence/WaveletTreeNoptrsS.lo
   static/sequence/WaveletTreeNoptrsS.cpp:27:113: warning: field 'n' is
         uninitialized when used here [-Wuninitialized]
     ...Array &symb, BitSequenceBuilder * bmb, Mapper * am) : Sequence(n) {
                                                                       ^
   1 warning generated.
     CXX      static/sequence/wt_coder_binary.lo
     CXX      static/sequence/wt_coder.lo
     CXX      static/sequence/wt_coder_huff.lo
     CXX      static/sequence/wt_node.lo
     CXX      static/sequence/wt_node_internal.lo
     CXX      static/sequence/wt_node_leaf.lo
     CXX      utils/Array.lo
     CXX      utils/cppUtils.lo
     CXX      utils/libcdsBitString.lo
     CXX      utils/timing.lo
     CXXLD    libcds.la
   ld: warning: directory not found for option '-L/lib'
   Making all in tests
   make[3]: Nothing to be done for `all'.
   Making all in tutorial/src
     CXX      ArrayExample2.o
     CXXLD    ArrayExample2
   ld: warning: directory not found for option '-L/lib'
     CXX      ArrayExample.o
     CXXLD    ArrayExample
   ld: warning: directory not found for option '-L/lib'
     CXX      BitSequenceRGExample.o
     CXXLD    BitSequenceRGExample
   ld: warning: directory not found for option '-L/lib'
     CXX      BitSequenceRRRExample.o
     CXXLD    BitSequenceRRRExample
   ld: warning: directory not found for option '-L/lib'
     CXX      BitSequenceSDArrayExample.o
     CXXLD    BitSequenceSDArrayExample
   ld: warning: directory not found for option '-L/lib'
     CXX      SequenceAlphPartExample.o
     CXXLD    SequenceAlphPartExample
   ld: warning: directory not found for option '-L/lib'
     CXX      SequenceGMRExample.o
     CXXLD    SequenceGMRExample
   ld: warning: directory not found for option '-L/lib'
     CXX      SequenceWaveletTreeExample.o
     CXXLD    SequenceWaveletTreeExample
   ld: warning: directory not found for option '-L/lib'
   Making all in tutorial/ssa
     CXX      test_count.o
     CXX      ssa.o
     CXXLD    test_count
   ld: warning: directory not found for option '-L/lib'
     CXX      build_index.o
     CXXLD    build_index
   ld: warning: directory not found for option '-L/lib'
     CXX      dump_bwt.o
     CXXLD    dump_bwt
   ld: warning: directory not found for option '-L/lib'
   make[3]: Nothing to be done for `all-am'.
   Making all in util
   /Applications/Xcode.app/Contents/Developer/usr/bin/make  all-am
   g++ -DHAVE_CONFIG_H -I.  -I/usr/local/include -I/include  -g -O2 -MT CommandOptions.o -MD -MP -MF .deps/CommandOptions.Tpo -c -o CommandOptions.o CommandOptions.cpp
   mv -f .deps/CommandOptions.Tpo .deps/CommandOptions.Po
   g++ -DHAVE_CONFIG_H -I.  -I/usr/local/include -I/include  -g -O2 -MT ProgLog.o -MD -MP -MF .deps/ProgLog.Tpo -c -o ProgLog.o ProgLog.cpp
   mv -f .deps/ProgLog.Tpo .deps/ProgLog.Po
   g++ -DHAVE_CONFIG_H -I.  -I/usr/local/include -I/include  -g -O2 -MT StringUtils.o -MD -MP -MF .deps/StringUtils.Tpo -c -o StringUtils.o StringUtils.cpp
   mv -f .deps/StringUtils.Tpo .deps/StringUtils.Po
   g++ -DHAVE_CONFIG_H -I.  -I/usr/local/include -I/include  -g -O2 -MT TSVRecord.o -MD -MP -MF .deps/TSVRecord.Tpo -c -o TSVRecord.o TSVRecord.cpp
   mv -f .deps/TSVRecord.Tpo .deps/TSVRecord.Po
   g++ -DHAVE_CONFIG_H -I.  -I/usr/local/include -I/include  -g -O2 -MT TSVScanner.o -MD -MP -MF .deps/TSVScanner.Tpo -c -o TSVScanner.o TSVScanner.cpp
   mv -f .deps/TSVScanner.Tpo .deps/TSVScanner.Po
   g++ -DHAVE_CONFIG_H -I.  -I/usr/local/include -I/include  -g -O2 -MT VersionSequence.o -MD -MP -MF .deps/VersionSequence.Tpo -c -o VersionSequence.o VersionSequence.cpp
   In file included from VersionSequence.cpp:27:
   ./VersionSequence.h:108:33: warning: '&&' within '||' [-Wlogical-op-parentheses]
     ...lhs.majorVer == rhs.majorVer && lhs.minorVer < rhs.minorVer ||
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   ./VersionSequence.h:108:33: note: place parentheses around the '&&' expression
         to silence this warning
     ...lhs.majorVer == rhs.majorVer && lhs.minorVer < rhs.minorVer ||
                                     ^
        (                                                          )
   ./VersionSequence.h:109:65: warning: '&&' within '||' [-Wlogical-op-parentheses]
     ...lhs.majorVer == rhs.majorVer && lhs.minorVer == rhs.minorVer && lhs.buildVer < rhs.buildVer;
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   ./VersionSequence.h:109:65: note: place parentheses around the '&&' expression
         to silence this warning
     ...lhs.majorVer == rhs.majorVer && lhs.minorVer == rhs.minorVer && lhs.buildVer < rhs.buildVer;
                                                                     ^
        (                                                                                          )
   2 warnings generated.
   mv -f .deps/VersionSequence.Tpo .deps/VersionSequence.Po
   g++ -DHAVE_CONFIG_H -I.  -I/usr/local/include -I/include  -g -O2 -MT ProgEnv.o -MD -MP -MF .deps/ProgEnv.Tpo -c -o ProgEnv.o ProgEnv.cpp
   In file included from ProgEnv.cpp:12:
   In file included from ./ProgEnv.h:14:
   ./VersionSequence.h:108:33: warning: '&&' within '||' [-Wlogical-op-parentheses]
     ...lhs.majorVer == rhs.majorVer && lhs.minorVer < rhs.minorVer ||
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   ./VersionSequence.h:108:33: note: place parentheses around the '&&' expression
         to silence this warning
     ...lhs.majorVer == rhs.majorVer && lhs.minorVer < rhs.minorVer ||
                                     ^
        (                                                          )
   ./VersionSequence.h:109:65: warning: '&&' within '||' [-Wlogical-op-parentheses]
     ...lhs.majorVer == rhs.majorVer && lhs.minorVer == rhs.minorVer && lhs.buildVer < rhs.buildVer;
        ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   ./VersionSequence.h:109:65: note: place parentheses around the '&&' expression
         to silence this warning
     ...lhs.majorVer == rhs.majorVer && lhs.minorVer == rhs.minorVer && lhs.buildVer < rhs.buildVer;
                                                                     ^
        (                                                                                          )
   2 warnings generated.
   mv -f .deps/ProgEnv.Tpo .deps/ProgEnv.Po
   rm -f libEGUtil.a
   ar cru libEGUtil.a CommandOptions.o ProgLog.o StringUtils.o TSVRecord.o TSVScanner.o VersionSequence.o ProgEnv.o 
   ranlib libEGUtil.a
   Making all in math
   /Applications/Xcode.app/Contents/Developer/usr/bin/make  all-am
   g++ -DHAVE_CONFIG_H -I.   -I/include -I/usr/local/include -g -O2 -MT Stats.o -MD -MP -MF .deps/Stats.Tpo -c -o Stats.o Stats.cpp
   In file included from Stats.cpp:8:
   ./Stats.h:19:10: fatal error: 'Eigen/Dense' file not found
   #include <Eigen/Dense>
            ^~~~~~~~~~~~~
   1 error generated.
   make[3]: *** [Stats.o] Error 1
   make[2]: *** [all] Error 2
   make[1]: *** [all-recursive] Error 1
   make: *** [all-recursive] Error 1
   

I have Boost and Eigen3.

I was wondering about bioconda because it would make it easier, and get you more visibility. On bioconda there are not only python packages (example HMMER).

[blinard-BIOINFO]

Hi Qi.

I think you are mistaken about what is Conda.
Using Conda do not mean "solving python issues", but ANY compilation/build issues.
It is a general environement manager, you can perfectly set different GCC versions, different c libraries versions... in a conda environement. You will find software such as raxml, hmmer ... on conda and complex dependancies trees such as R.

Because compiling them on unix/mac or sometimes windows using a conda environement will garantee that all necessary dependancies are fulfilled (avoiding the issues encountered by Alessio above).

Actually, I was considering to build myself a conda package for hmmUFOtu at some point, this is why I jumped into this conversation . The bioconda community is becoming huge and many tools are added there by the user community.

Eventually, we could do this together (I already pushed some of my own sofware to bioconda and know the procedure).
What I need from you side is the complete list a C++ dependencies necessary to build HmmOFUtu, including precise versions of those libraries.

What do you think ?

[e00011027]

Hi Benjamin, I understand your point of Conda, it is just not my preference. HmmUFOtu does depend on C++ boost (>1.50.0), Eigen3 headers for matrix operations, and zlib for compressed files. It optionally depends on jsoncpp, but not required. No other dependency as I know. If you run ./configure --help, you will see all listed dependencies (--with-xxx section). As for your error, looks like you don't have Eigen3. It is a C++ header only library (no installation required). Please install Eigen3, and make sure its root path (Eigen) is in your lib path. Thanks Best regards Qi

…

On Fri, May 8, 2020 at 12:11 PM Benjamin Linard ***@***.***> wrote: Hi Qi. I think you are mitaken about what is Conda. Conda do not mean only solving python issues, but any compilations issues. It is a general environement manager, you can perfectly set different GCC versions, different c libraries versions... in a conda environement. You find find software such as raxml, hmmer ... on conda. Because compiling them on unix/linux or sometimes windows using a conda environement will garantee that all necessary dependancies are fulfilled (avoiding the issues encountered by Alessio above). Actually, I was considering to build myself a conda package for hmmUFOto at some point, this is why I jumped into this conversation . Eventually, we could do this together (I already pushed some of my own sofware to bioconda). What I need from you side is the complete list a C++ dependencies necessary to build HmmOFUtu, including precise versions of those libraries. What do you think ? — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#7 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABXZ44KDEJMF4NDNVAY327LRQQVKLANCNFSM4M4C4KOA> .

[AlessioMilanese]

Hi Qi,

Thanks for the help.

As for your error, looks like you don't have Eigen3. It is a C++ header
only library (no installation required). Please install Eigen3, and make
sure its root path (Eigen) is in your lib path. Thanks

It was installed already, I solved by:

export PATH="/usr/local/Cellar/eigen/3.3.7/include/eigen3/Eigen:$PATH"

Or at least I think I solved it, because now I have a different error:

Error

Making all in data
make[1]: Nothing to be done for `all'.
Making all in src
Making all in libdivsufsort
/Applications/Xcode.app/Contents/Developer/usr/bin/make  all-recursive
Making all in lib
depbase=`echo divsufsort.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
	gcc -DHAVE_CONFIG_H -I. -I..  -I../include -I/include -I../include -g -O2 -MT divsufsort.o -MD -MP -MF $depbase.Tpo -c -o divsufsort.o divsufsort.c &&\
	mv -f $depbase.Tpo $depbase.Po
depbase=`echo sssort.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
	gcc -DHAVE_CONFIG_H -I. -I..  -I../include -I/include -I../include -g -O2 -MT sssort.o -MD -MP -MF $depbase.Tpo -c -o sssort.o sssort.c &&\
	mv -f $depbase.Tpo $depbase.Po
depbase=`echo trsort.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
	gcc -DHAVE_CONFIG_H -I. -I..  -I../include -I/include -I../include -g -O2 -MT trsort.o -MD -MP -MF $depbase.Tpo -c -o trsort.o trsort.c &&\
	mv -f $depbase.Tpo $depbase.Po
depbase=`echo utils.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
	gcc -DHAVE_CONFIG_H -I. -I..  -I../include -I/include -I../include -g -O2 -MT utils.o -MD -MP -MF $depbase.Tpo -c -o utils.o utils.c &&\
	mv -f $depbase.Tpo $depbase.Po
rm -f libdivsufsort.a
ar cru libdivsufsort.a divsufsort.o sssort.o trsort.o utils.o 
ranlib libdivsufsort.a
Making all in examples
depbase=`echo bwt.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
	gcc -DHAVE_CONFIG_H -I. -I..   -I/include -I../include -g -O2 -MT bwt.o -MD -MP -MF $depbase.Tpo -c -o bwt.o bwt.c &&\
	mv -f $depbase.Tpo $depbase.Po
bwt.c:209:5: warning: format specifies type 'intmax_t' (aka 'long') but the
      argument has type 'off_t' (aka 'long long') [-Wformat]
    n, (double)(finish - start) / (double)CLOCKS_PER_SEC);
    ^
1 warning generated.
gcc -I../include -g -O2  -L/lib -o bwt bwt.o ../lib/libdivsufsort.a 
ld: warning: directory not found for option '-L/lib'
depbase=`echo mksary.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
	gcc -DHAVE_CONFIG_H -I. -I..   -I/include -I../include -g -O2 -MT mksary.o -MD -MP -MF $depbase.Tpo -c -o mksary.o mksary.c &&\
	mv -f $depbase.Tpo $depbase.Po
mksary.c:171:59: warning: format specifies type 'intmax_t' (aka 'long') but the
      argument has type 'off_t' (aka 'long long') [-Wformat]
  fprintf(stderr, "%s: %" PRIdOFF_T " bytes ... ", fname, n);
                       ~~~                                ^
1 warning generated.
gcc -I../include -g -O2  -L/lib -o mksary mksary.o ../lib/libdivsufsort.a 
ld: warning: directory not found for option '-L/lib'
depbase=`echo sasearch.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
	gcc -DHAVE_CONFIG_H -I. -I..   -I/include -I../include -g -O2 -MT sasearch.o -MD -MP -MF $depbase.Tpo -c -o sasearch.o sasearch.c &&\
	mv -f $depbase.Tpo $depbase.Po
gcc -I../include -g -O2  -L/lib -o sasearch sasearch.o ../lib/libdivsufsort.a 
ld: warning: directory not found for option '-L/lib'
depbase=`echo suftest.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
	gcc -DHAVE_CONFIG_H -I. -I..   -I/include -I../include -g -O2 -MT suftest.o -MD -MP -MF $depbase.Tpo -c -o suftest.o suftest.c &&\
	mv -f $depbase.Tpo $depbase.Po
suftest.c:147:59: warning: format specifies type 'intmax_t' (aka 'long') but the
      argument has type 'off_t' (aka 'long long') [-Wformat]
  fprintf(stderr, "%s: %" PRIdOFF_T " bytes ... ", fname, n);
                       ~~~                                ^
1 warning generated.
gcc -I../include -g -O2  -L/lib -o suftest suftest.o ../lib/libdivsufsort.a 
ld: warning: directory not found for option '-L/lib'
depbase=`echo unbwt.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
	gcc -DHAVE_CONFIG_H -I. -I..   -I/include -I../include -g -O2 -MT unbwt.o -MD -MP -MF $depbase.Tpo -c -o unbwt.o unbwt.c &&\
	mv -f $depbase.Tpo $depbase.Po
unbwt.c:196:5: warning: format specifies type 'intmax_t' (aka 'long') but the
      argument has type 'off_t' (aka 'long long') [-Wformat]
    n, (double)(finish - start) / (double)CLOCKS_PER_SEC);
    ^
1 warning generated.
gcc -I../include -g -O2  -L/lib -o unbwt unbwt.o ../lib/libdivsufsort.a 
ld: warning: directory not found for option '-L/lib'
Making all in libcds
Making all in src
  CXX      static/bitsequence/BitSequenceBuilderDArray.lo
  CXX      static/bitsequence/BitSequenceBuilderRG.lo
  CXX      static/bitsequence/BitSequenceBuilderRRR.lo
  CXX      static/bitsequence/BitSequenceBuilderSDArray.lo
  CXX      static/bitsequence/BitSequence.lo
  CXX      static/bitsequence/BitSequenceDArray.lo
  CXX      static/bitsequence/BitSequenceRG.lo
  CXX      static/bitsequence/BitSequenceRRR.lo
  CXX      static/bitsequence/BitSequenceSDArray.lo
  CXX      static/bitsequence/sdarraySadakane.lo
  CXX      static/bitsequence/TableOffsetRRR.lo
  CXX      static/coders/huff.lo
static/coders/huff.cpp:142:16: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
        void bitzero (register uint *e, register uint p,
                      ^~~~~~~~~
static/coders/huff.cpp:142:34: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
        void bitzero (register uint *e, register uint p,
                                        ^~~~~~~~~
static/coders/huff.cpp:143:2: warning: 'register' storage class specifier is
      deprecated and incompatible with C++17 [-Wdeprecated-register]
        register uint len) {
        ^~~~~~~~~
3 warnings generated.
  CXX      static/coders/HuffmanCoder.lo
  CXX      static/mapper/MapperCont.lo
  CXX      static/mapper/Mapper.lo
  CXX      static/mapper/MapperNone.lo
  CXX      static/mapper/MapperRev.lo
  CXX      static/permutation/perm.lo
  CXX      static/permutation/PermutationBuilderMRRR.lo
  CXX      static/permutation/PermutationBuilderWT.lo
  CXX      static/permutation/Permutation.lo
  CXX      static/permutation/PermutationMRRR.lo
  CXX      static/permutation/PermutationWT.lo
  CXX      static/sequence/BitmapsSequence.lo
  CXX      static/sequence/SequenceAlphPart.lo
static/sequence/SequenceAlphPart.cpp:210:16: warning: assigning field to itself
      [-Wself-assign-field]
                this->maxLen = maxLen;
                             ^
static/sequence/SequenceAlphPart.cpp:309:16: warning: assigning field to itself
      [-Wself-assign-field]
                this->maxLen = maxLen;
                             ^
2 warnings generated.
  CXX      static/sequence/SequenceBuilderAlphPart.lo
  CXX      static/sequence/SequenceBuilderGMRChunk.lo
  CXX      static/sequence/SequenceBuilderGMR.lo
  CXX      static/sequence/SequenceBuilderStr.lo
  CXX      static/sequence/SequenceBuilderWaveletMatrix.lo
  CXX      static/sequence/SequenceBuilderWaveletTree.lo
  CXX      static/sequence/SequenceBuilderWaveletTreeNoptrs.lo
  CXX      static/sequence/SequenceBuilderWaveletTreeNoptrsS.lo
  CXX      static/sequence/Sequence.lo
  CXX      static/sequence/SequenceGMRChunk.lo
static/sequence/SequenceGMRChunk.cpp:67:15: warning: assigning field to itself
      [-Wself-assign-field]
                this->sigma = sigma;
                            ^
static/sequence/SequenceGMRChunk.cpp:113:15: warning: assigning field to itself
      [-Wself-assign-field]
                this->sigma = sigma;
                            ^
2 warnings generated.
  CXX      static/sequence/SequenceGMR.lo
  CXX      static/sequence/WaveletMatrix.lo
static/sequence/WaveletMatrix.cpp:27:104: warning: field 'n' is uninitialized
      when used here [-Wuninitialized]
  ...Array &symbols2, BitSequenceBuilder * bmb, Mapper * am) : Sequence(n) {
                                                                        ^
1 warning generated.
  CXX      static/sequence/WaveletTree.lo
  CXX      static/sequence/WaveletTreeNoptrs.lo
  CXX      static/sequence/WaveletTreeNoptrsS.lo
static/sequence/WaveletTreeNoptrsS.cpp:27:113: warning: field 'n' is
      uninitialized when used here [-Wuninitialized]
  ...Array &symb, BitSequenceBuilder * bmb, Mapper * am) : Sequence(n) {
                                                                    ^
1 warning generated.
  CXX      static/sequence/wt_coder_binary.lo
  CXX      static/sequence/wt_coder.lo
  CXX      static/sequence/wt_coder_huff.lo
  CXX      static/sequence/wt_node.lo
  CXX      static/sequence/wt_node_internal.lo
  CXX      static/sequence/wt_node_leaf.lo
  CXX      utils/Array.lo
  CXX      utils/cppUtils.lo
  CXX      utils/libcdsBitString.lo
  CXX      utils/timing.lo
  CXXLD    libcds.la
ld: warning: directory not found for option '-L/lib'
Making all in tests
make[3]: Nothing to be done for `all'.
Making all in tutorial/src
  CXX      ArrayExample2.o
  CXXLD    ArrayExample2
ld: warning: directory not found for option '-L/lib'
  CXX      ArrayExample.o
  CXXLD    ArrayExample
ld: warning: directory not found for option '-L/lib'
  CXX      BitSequenceRGExample.o
  CXXLD    BitSequenceRGExample
ld: warning: directory not found for option '-L/lib'
  CXX      BitSequenceRRRExample.o
  CXXLD    BitSequenceRRRExample
ld: warning: directory not found for option '-L/lib'
  CXX      BitSequenceSDArrayExample.o
  CXXLD    BitSequenceSDArrayExample
ld: warning: directory not found for option '-L/lib'
  CXX      SequenceAlphPartExample.o
  CXXLD    SequenceAlphPartExample
ld: warning: directory not found for option '-L/lib'
  CXX      SequenceGMRExample.o
  CXXLD    SequenceGMRExample
ld: warning: directory not found for option '-L/lib'
  CXX      SequenceWaveletTreeExample.o
  CXXLD    SequenceWaveletTreeExample
ld: warning: directory not found for option '-L/lib'
Making all in tutorial/ssa
  CXX      test_count.o
  CXX      ssa.o
  CXXLD    test_count
ld: warning: directory not found for option '-L/lib'
  CXX      build_index.o
  CXXLD    build_index
ld: warning: directory not found for option '-L/lib'
  CXX      dump_bwt.o
  CXXLD    dump_bwt
ld: warning: directory not found for option '-L/lib'
make[3]: Nothing to be done for `all-am'.
Making all in util
CDPATH="${ZSH_VERSION+.}:" && cd . && /bin/sh /Users/milanese/Dropbox/PhD/bin/HmmUFOtu/src/util/missing aclocal-1.16 -I m4
/Users/milanese/Dropbox/PhD/bin/HmmUFOtu/src/util/missing: line 81: aclocal-1.16: command not found
WARNING: 'aclocal-1.16' is missing on your system.
         You should only need it if you modified 'acinclude.m4' or
         'configure.ac' or m4 files included by 'configure.ac'.
         The 'aclocal' program is part of the GNU Automake package:
         <http://www.gnu.org/software/automake>
         It also requires GNU Autoconf, GNU m4 and Perl in order to run:
         <http://www.gnu.org/software/autoconf>
         <http://www.gnu.org/software/m4/>
         <http://www.perl.org/>
make[2]: *** [aclocal.m4] Error 127
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1

[AlessioMilanese]

Looking at stackoverflow I found that:

This is usually caused by checking out code from Git instead of extracting it from a .zip or .tar.gz archive. In order to trigger rebuilds when files change, Git does not preserve files' timestamps, so the configure script might appear to be out of date. As others have mentioned, there are ways to get around this if you don't have a sufficiently recent version of autoreconf.

So I tried to download release v1.5.1. And now I'm back to the previous error:

mv -f .deps/ProgEnv.Tpo .deps/ProgEnv.Po
rm -f libEGUtil.a
ar cru libEGUtil.a CommandOptions.o ProgLog.o StringUtils.o TSVRecord.o TSVScanner.o VersionSequence.o ProgEnv.o 
ranlib libEGUtil.a
Making all in math
/Applications/Xcode.app/Contents/Developer/usr/bin/make  all-am
g++ -DHAVE_CONFIG_H -I.   -I/include -I/usr/local/include -g -O2 -MT Stats.o -MD -MP -MF .deps/Stats.Tpo -c -o Stats.o Stats.cpp
In file included from Stats.cpp:8:
./Stats.h:19:10: fatal error: 'Eigen/Dense' file not found
#include <Eigen/Dense>
         ^~~~~~~~~~~~~
1 error generated.
make[3]: *** [Stats.o] Error 1
make[2]: *** [all] Error 2
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1

Maybe I misunderstood this:

and make sure its root path (Eigen) is in your lib path.

[e00011027]

Hi, First, $PATH is for executables, not for libraries. You should set CPPFLAGS prior to run ./configure. Second, the correct path should not include the "Eigen", which should be /usr/local/Cellar/eigen/3.3.7/include/eigen3 Best Qi

…

On Fri, May 8, 2020 at 6:39 PM Alessio Milanese ***@***.***> wrote: Looking at stackoverflow <https://stackoverflow.com/questions/33278928/how-to-overcome-aclocal-1-15-is-missing-on-your-system-warning> I found that: This is usually caused by checking out code from Git instead of extracting it from a .zip or .tar.gz archive. In order to trigger rebuilds when files change, Git does not preserve files' timestamps, so the configure script might appear to be out of date. As others have mentioned, there are ways to get around this if you don't have a sufficiently recent version of autoreconf. So I tried to download release v1.5.1. And now I'm back to the previous error: mv -f .deps/ProgEnv.Tpo .deps/ProgEnv.Po rm -f libEGUtil.a ar cru libEGUtil.a CommandOptions.o ProgLog.o StringUtils.o TSVRecord.o TSVScanner.o VersionSequence.o ProgEnv.o ranlib libEGUtil.a Making all in math /Applications/Xcode.app/Contents/Developer/usr/bin/make all-am g++ -DHAVE_CONFIG_H -I. -I/include -I/usr/local/include -g -O2 -MT Stats.o -MD -MP -MF .deps/Stats.Tpo -c -o Stats.o Stats.cpp In file included from Stats.cpp:8: ./Stats.h:19:10: fatal error: 'Eigen/Dense' file not found #include <Eigen/Dense> ^~~~~~~~~~~~~ 1 error generated. make[3]: *** [Stats.o] Error 1 make[2]: *** [all] Error 2 make[1]: *** [all-recursive] Error 1 make: *** [all-recursive] Error 1 Maybe I misunderstood this: and make sure its root path (Eigen) is in your lib path. — You are receiving this because you commented. Reply to this email directly, view it on GitHub <#7 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABXZ44LSMRXBQA3ZUA3JESLRQSC2BANCNFSM4M4C4KOA> .

[brendanf]

Following up on this conversation several years later, #11 shows HmmUFOtu does not compile using a version of Eigen3 which is too new. This is why a bioconda package, which would include a dependency on the exact version(s) of Eigen which are known to work with HmmUFOtu, would be useful.

[e00011027]

Thanks for the good advice. I will try to get a bioconda version for it when possible. Best Qi

…

On Thu, Oct 3, 2024 at 1:47 PM brendanf ***@***.***> wrote: Following up on this conversation several years later, #11 <#11> shows HmmUFOtu does not compile using a version of Eigen3 which is too new. This is why a bioconda package, which would include a dependency on the exact version(s) of Eigen which are known to work with HmmUFOtu, would be useful. — Reply to this email directly, view it on GitHub <#7 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABXZ44ICIJA4GIGRMXEQ7DLZZV7KXAVCNFSM6AAAAABPKI7O2SVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGOJRHE4DINZWGY> . You are receiving this because you commented.Message ID: ***@***.***>