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marbl / parsnp

Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surrounding SNP sites for filtration/cleaning, in addition to existing tools for recombination detection/filtration and phylogenetic reconstruction.
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autogen.sh error: two- and three-arguments forms are deprecated #56

Open tseemann opened 5 years ago

tseemann commented 5 years ago 
./autogen.sh

configure.ac:2: warning: AM_INIT_AUTOMAKE: two- and three-arguments forms are deprecated.  For more info, see:
configure.ac:2: https://www.gnu.org/software/automake/manual/automake.html#Modernize-AM_005fINIT_005fAUTOMAKE-invocation
configure.ac:3: installing './compile'
configure.ac:2: installing './install-sh'
configure.ac:2: installing './missing'
src/Makefile.am:4: warning: source file './ext/iniFile.cpp' is in a subdirectory,
src/Makefile.am:4: but option 'subdir-objects' is disabled
automake: warning: possible forward-incompatibility.
automake: At least a source file is in a subdirectory, but the 'subdir-objects'
automake: automake option hasn't been enabled.  For now, the corresponding output
automake: object file(s) will be placed in the top-level directory.  However,
automake: this behaviour will change in future Automake versions: they will
automake: unconditionally cause object files to be placed in the same subdirectory
automake: of the corresponding sources.
automake: You are advised to start using 'subdir-objects' option throughout your
automake: project, to avoid future incompatibilities.
src/Makefile.am: installing './depcomp'
treangen commented 5 years ago

thanks @tseemann

tseemann commented 4 years ago 
configure.ac:52: warning: AM_INIT_AUTOMAKE: two- and three-arguments forms are deprecated.  For more info, see:
configure.ac:52: https://www.gnu.org/software/automake/manual/automake.html#Modernize-AM_005fINIT_005fAUTOMAKE-invocation
configure.ac:64: installing 'config/compile'
configure.ac:52: installing 'config/missing'
libMUSCLE/Makefile.am:28: warning: 'INCLUDES' is the old name for 'AM_CPPFLAGS' (or '*_CPPFLAGS')
libMUSCLE/Makefile.am: installing 'config/depcomp'

Still in 1.5.0 ?

bkille commented 4 years ago

Yup :disappointed: I'm new to autotools and have been putting this on the backburner. I'll see if I can take care of this.