Warning messages from Perl (while running smrt on vagrant)

[alexantonelli]

This is what happens when issuing the command smrt in the Mac terminal (although not affecting subsequent analyses):

vagrant@supersmart-VM:~$ smrt perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = (unset), LC_ALL = (unset), LC_CTYPE = "UTF-8", LANG = "en_US.UTF-8" are supported and installed on your system. perl: warning: Falling back to the standard locale ("C"). perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = (unset), LC_ALL = (unset), LC_CTYPE = "UTF-8", LANG = "en_US.UTF-8" are supported and installed on your system. perl: warning: Falling back to the standard locale ("C"). Available commands:

 commands: list the application's commands
     help: display a command's help screen

    align: writes multiple sequence alignments for a list of taxa

bbcalibrate: calibrate backbone tree using TreePL bbdecompose: decomposes a backbone tree into individual clades bbinfer: inference of a genus-level backbone tree bbmerge: creates supermatrix for genus-level backbone tree bbreroot: reroots backbone tree such that the amount of paraphyletic species is minimized cladegraft: grafts the inferred clade trees on the backbone chronogram cladeinfer: infers a species tree for each individual clade using *BEAST. clademerge: merges sets of alignments into input files for clade inference classify: writes a classification tree for a given taxa table orthologize: creates orthologous clusters of aligned sequences taxize: writes taxa table for given list of taxon names or root taxa

[rvosa]

This is basically a harmless message that has to do with the "localisation" settings (user language and such) for the virtual environment. It can't affect analysis at all but it would be nice if it could be hidden so that users don't freak out.

On Thu Feb 12 2015 at 2:05:53 PM Alexandre Antonelli < notifications@github.com> wrote:

This is what happens when issuing the command smrt in the Mac terminal (although not affecting subsequent analyses):

vagrant@supersmart-VM:~$ smrt perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = (unset), LC_ALL = (unset), LC_CTYPE = "UTF-8", LANG = "en_US.UTF-8" are supported and installed on your system. perl: warning: Falling back to the standard locale ("C"). perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = (unset), LC_ALL = (unset), LC_CTYPE = "UTF-8", LANG = "en_US.UTF-8" are supported and installed on your system. perl: warning: Falling back to the standard locale ("C"). Available commands:

commands: list the application's commands help: display a command's help screen

align: writes multiple sequence alignments for a list of taxa

bbcalibrate: calibrate backbone tree using TreePL bbdecompose: decomposes a backbone tree into individual clades bbinfer: inference of a genus-level backbone tree bbmerge: creates supermatrix for genus-level backbone tree bbreroot: reroots backbone tree such that the amount of paraphyletic species is minimized cladegraft: grafts the inferred clade trees on the backbone chronogram cladeinfer: infers a species tree for each individual clade using *BEAST. clademerge: merges sets of alignments into input files for clade inference classify: writes a classification tree for a given taxa table orthologize: creates orthologous clusters of aligned sequences taxize: writes taxa table for given list of taxon names or root taxa

— Reply to this email directly or view it on GitHub https://github.com/naturalis/supersmart/issues/43.

[hettling]

This is fixed with commit 336a3d5. However, this warning depends on the settings of the host operating system, so I am not sure if it will be solved for e.g. swedish or portugese language settings. Since I cannot test this at the moment, I will close this issue for now.