Hi Matt,
after the first step I get the following error:
ubuntu@evans:~$ brew remove prokka
Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/gdbm.rb:10:in `block in class:Gdbm’
Please report this to the homebrew/core tap!
Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/boost.rb:12:in `block in class:Boost’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/boost.rb:53:in `class:Boost’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/boost.rb:53:in `class:Boost’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/boost.rb:53:in `class:Boost’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/boost.rb:53:in `class:Boost’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/gcc.rb:66:in `class:Gcc’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/gcc.rb:66:in `class:Gcc’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/gcc.rb:66:in `class:Gcc’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/gcc.rb:66:in `class:Gcc’
Please report this to the homebrew/core tap!
Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/automake.rb:10:in `block in class:Automake’
Please report this to the homebrew/core tap!
Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/bzip2.rb:10:in `block in class:Bzip2’
Please report this to the homebrew/core tap!
Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/curl.rb:9:in `block in class:Curl’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/pixman.rb:21:in `class:Pixman’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/pixman.rb:21:in `class:Pixman’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/pixman.rb:21:in `class:Pixman’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/pixman.rb:21:in `class:Pixman’
Please report this to the homebrew/core tap!
Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/zlib.rb:10:in `block in class:Zlib’
Please report this to the homebrew/core tap!
Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/gsl.rb:13:in `block in class:Gsl’
Please report this to the homebrew/core tap!
Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-science/mummer.rb:11:in `block in class:Mummer’
Please report this to the homebrew/science tap!
Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/szip.rb:9:in `block in class:Szip’
Please report this to the homebrew/core tap!
Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/python3.rb:8:in `block in class:Python3’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/python3.rb:83:in `class:Python3’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/python3.rb:83:in `class:Python3’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/python3.rb:83:in `class:Python3’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/python3.rb:83:in `class:Python3’
Please report this to the homebrew/core tap!
Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/gpatch.rb:10:in `block in class:Gpatch’
Please report this to the homebrew/core tap!
Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/jpeg.rb:9:in `block in class:Jpeg’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/gd.rb:45:in `class:Gd’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/gd.rb:45:in `class:Gd’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/gd.rb:45:in `class:Gd’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/gd.rb:45:in `class:Gd’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-science/blast.rb:22:in `class:Blast’
Please report this to the homebrew/science tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-science/blast.rb:22:in `class:Blast’
Please report this to the homebrew/science tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-science/blast.rb:22:in `class:Blast’
Please report this to the homebrew/science tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-science/blast.rb:22:in `class:Blast’
Please report this to the homebrew/science tap!
Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/python.rb:9:in `block in class:Python’
Please report this to the homebrew/core tap!
Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/linuxbrew/homebrew-xorg/libxmu.rb:9:in `block in class:Libxmu’
Please report this to the linuxbrew/xorg tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/mysql.rb:37:in `class:Mysql’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/mysql.rb:37:in `class:Mysql’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/mysql.rb:37:in `class:Mysql’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/mysql.rb:37:in `class:Mysql’
Please report this to the homebrew/core tap!
Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/autoconf.rb:10:in `block in class:Autoconf’
Please report this to the homebrew/core tap!
Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/linuxbrew/homebrew-xorg/libxt.rb:10:in `block in class:Libxt’
Please report this to the linuxbrew/xorg tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/lua.rb:22:in `class:Lua’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/lua.rb:22:in `class:Lua’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/lua.rb:22:in `class:Lua’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/lua.rb:22:in `class:Lua’
Please report this to the homebrew/core tap!
Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/gdk-pixbuf.rb:8:in `block in class:GdkPixbuf’
Please report this to the homebrew/core tap!
Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/gobject-introspection.rb:9:in `block in class:GobjectIntrospection’
Please report this to the homebrew/core tap!
Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/linuxbrew/homebrew-xorg/libxi.rb:10:in `block in class:Libxi’
Please report this to the linuxbrew/xorg tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/pcre.rb:27:in `class:Pcre’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/pcre.rb:27:in `class:Pcre’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/pcre.rb:27:in `class:Pcre’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/pcre.rb:27:in `class:Pcre’
Please report this to the homebrew/core tap!
Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-science/metaphlan.rb:13:in `block in class:Metaphlan’
Please report this to the homebrew/science tap!
Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-science/bedtools.rb:14:in `block in class:Bedtools’
Please report this to the homebrew/science tap!
Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/expat.rb:13:in `block in class:Expat’
Please report this to the homebrew/core tap!
Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-science/htslib.rb:12:in `block in class:Htslib’
Please report this to the homebrew/science tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/glib.rb:24:in `class:Glib’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/glib.rb:24:in `class:Glib’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/glib.rb:24:in `class:Glib’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/glib.rb:24:in `class:Glib’
Please report this to the homebrew/core tap!
Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-science/aragorn.rb:12:in `block in class:Aragorn’
Please report this to the homebrew/science tap!
Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-science/fasttree.rb:11:in `block in class:Fasttree’
Please report this to the homebrew/science tap!
Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-science/exonerate.rb:10:in `block in class:Exonerate’
Please report this to the homebrew/science tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/libxml2.rb:32:in `class:Libxml2’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/libxml2.rb:32:in `class:Libxml2’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/libxml2.rb:32:in `class:Libxml2’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/libxml2.rb:32:in `class:Libxml2’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-science/megahit.rb:18:in `class:Megahit’
Please report this to the homebrew/science tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-science/megahit.rb:18:in `class:Megahit’
Please report this to the homebrew/science tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-science/megahit.rb:18:in `class:Megahit’
Please report this to the homebrew/science tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-science/megahit.rb:18:in `class:Megahit’
Please report this to the homebrew/science tap!
Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-science/jellyfish-1.1.rb:11:in `block in class:Jellyfish11’
Please report this to the homebrew/science tap!
Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/pango.rb:11:in `block in class:Pango’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/pango.rb:35:in `class:Pango’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/pango.rb:35:in `class:Pango’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/pango.rb:35:in `class:Pango’
Please report this to the homebrew/core tap!
Warning: Calling fails_with :llvm is deprecated!
There is no replacement.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-core/Formula/pango.rb:35:in `class:Pango’
Please report this to the homebrew/core tap!
Warning: Calling BottleSpecification.revision is deprecated!
Use BottleSpecification.rebuild instead.
/mnt/gvl/apps/linuxbrew/Library/Taps/homebrew/homebrew-dupes/zlib.rb:10:in `block in class:Zlib’
Please report this to the homebrew/dupes tap!
Error: Refusing to uninstall /mnt/gvl/apps/linuxbrew/Cellar/prokka/HEAD
because it is required by nullarbor, which is currently installed.
You can override this and force removal with:
brew uninstall --ignore-dependencies prokka