perl: warning: Setting locale failed.

[callie]

Hi,

I am using centos release CentOS release 6.9 (Final). For the past 15 days I am getting the following error.

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perl: warning: Setting locale failed.
perl: warning: Please check that your locale settings:
        LANGUAGE = "en_US.utf8",
        LC_ALL = "en_US.utf8",
        LC_TYPE = "en_US.utf8",
        LANG = "en_US.utf8"
    are supported and installed on your system.
perl: warning: Falling back to the standard locale ("C").
[kalyani_patankar@ngs 135-2019-26]$ cat /etc/centos-release

I have tried several solutions for this from different forums

1. Creating a /etc/default/locale file with
cat /etc/default/locale

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LANG=en_US.utf8
LC_ALL=en_US.utf8

2. Adding following lines to /etc/environment

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LANGUAGE=en_US.utf8
LC_ALL=en_US.utf8
LANG=en_US.utf8
LC_TYPE=en_US.utf8

3.

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yum reinstall glibc-common

4.

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 localedef -i en_US -f UTF-8 en_US.UTF-8
    localedef -i en_US -f UTF-8 en_US.UTF-8
    localedef -v -c -i en_US -f UTF-8 en_US.UTF-8
    localedef -c -i en_US -f UTF-8 en_US.UTF-8

5. yum update

None of the above approaches seem to work.

My current gcc version is

gcc (GCC) 4.4.7 20120313 (Red Hat 4.4.7-18)
Copyright (C) 2010 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

I am a bioinformatician and several of my programs like fastq, bwa, and samtools are not working if this issue is not resolved. These tools work fine if I operate as root.

I will appreciate any help as I can not understand how to resolve this.

Thanks in advance !!

[lightman47]

If it were me/my thoughts (I am NO expert) -

My un-educated guess is that some file 'update'/copy/move was done 15 days ago and 'permissions' got clobbered.

When solved, run yum update <wink>

[TrevorH]

Start by running yum update to get your system to 6.10 which has been out for more than a year and is the only supported CentOS 6 version. Once that's complete you need to reboot into the new kernel and updated libraries. If the problem persists then try running rpm -Va perl\* glibc\* and see what is reported as not matching the correct info held by rpm.