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Perl version error

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Aziz Öğütlü

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May 31, 2023, 3:45:06 AM5/31/23
to begi...@perl.org
We are using mirdeep2 on our HPC system. When we try to call
mirdeep2.pl, it gives this error:

Perl v5.35.7 required--this is only v5.26.3, stopped at
/opt/ohpc/pub/compiler/perl/5.36.0/lib/5.36.0/File/Copy.pm line 10.
BEGIN failed--compilation aborted at
/opt/ohpc/pub/compiler/perl/5.36.0/lib/5.36.0/File/Copy.pm line 10.
Compilation failed in require at
/opt/ohpc/pub/apps/mirdeep2/0.1.3/bin/miRDeep2.pl line 25.
BEGIN failed--compilation aborted at
/opt/ohpc/pub/apps/mirdeep2/0.1.3/bin/miRDeep2.pl line 25.

We asked to mirdeep2 github account, they said it was related to copy.pm
and it was about perl.
Could you please help on this issue?

Ken Peng

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May 31, 2023, 4:00:07 AM5/31/23
to aziz....@eduline.com.tr, begi...@perl.org
May 31, 2023 at 3:50 PM, aziz....@eduline.com.tr wrote:


>
> Hi Ken,
>
> I upgrade perl to the latest version that is 5.36.1, but I took same error.
>
> On 5/31/23 10:46, Ken Peng wrote:
>
> >

Can you run these two commands and show us the result?

perl -MFile::Copy -e 'print $File::Copy::VERSION'

perl -v

Thanks.

aziz....@eduline.com.tr

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May 31, 2023, 4:00:07 AM5/31/23
to Ken Peng, begi...@perl.org
Hi Ken,

I upgrade perl to the latest version that is 5.36.1, but I took same error.

On 5/31/23 10:46, Ken Peng wrote:
> May 31, 2023 at 3:29 PM, "Aziz Öğütlü" <aziz....@eduline.com.tr> wrote:
>
>
>> We are using mirdeep2 on our HPC system. When we try to call mirdeep2.pl, it gives this error:
>>
>> Perl v5.35.7 required--this is only v5.26.3, stopped at /opt/ohpc/pub/compiler/perl/5.36.0/lib/5.36.0/File/Copy.pm line 10.
> It seems you need to upgrade perl to the latest version.
>
> regards.
>
--
İyi çalışmalar,
Aziz Öğütlü

Eduline Bilişim Sanayi ve Ticaret Ltd. Şti.  www.eduline.com.tr
Merkez Mah. Ayazma Cad. No:37 Papirus Plaza
Kat:6 Ofis No:118 Kağıthane -  İstanbul - Türkiye 34406
Tel : +90 212 324 60 61     Cep: +90 541 350 40 72

Ken Peng

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May 31, 2023, 4:00:07 AM5/31/23
to aziz....@eduline.com.tr, begi...@perl.org
May 31, 2023 at 3:29 PM, "Aziz Öğütlü" <aziz....@eduline.com.tr> wrote:


>
> We are using mirdeep2 on our HPC system. When we try to call mirdeep2.pl, it gives this error:
>
> Perl v5.35.7 required--this is only v5.26.3, stopped at /opt/ohpc/pub/compiler/perl/5.36.0/lib/5.36.0/File/Copy.pm line 10.

Aziz Öğütlü

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May 31, 2023, 4:15:06 AM5/31/23
to Ken Peng, begi...@perl.org
[root@software ~]# perl -MFile::Copy -e 'print $File::Copy::VERSION'
2.39

[root@software ~]# perl -v

This is perl 5, version 36, subversion 1 (v5.36.1) built for
x86_64-linux

Copyright 1987-2023, Larry Wall

Perl may be copied only under the terms of either the Artistic License
or the
GNU General Public License, which may be found in the Perl 5 source kit.

Complete documentation for Perl, including FAQ lists, should be found on
this system using "man perl" or "perldoc perl". If you have access to
the
Internet, point your browser at https://www.perl.org/, the Perl Home
Page.

Ken Peng

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May 31, 2023, 4:15:06 AM5/31/23
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May 31, 2023 at 4:02 PM, "Olivier" <Olivier...@cs.ait.ac.th> wrote:


>
> "aziz....@eduline.com.tr" <aziz....@eduline.com.tr> writes:
>
> >
> > Hi Ken,
> >
> > I upgrade perl to the latest version that is 5.36.1, but I took same error.
> >
>
> The error message ask for Perl verion 5.37 and you only upgraded to
> verion 5.36, so the error is still there.
>
>

mnnn, I never heard perl 5.37 is production ready. :(

Olivier

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May 31, 2023, 4:15:06 AM5/31/23
to aziz....@eduline.com.tr, k...@posthub.me, begi...@perl.org
"aziz....@eduline.com.tr" <aziz....@eduline.com.tr> writes:

> Hi Ken,
>
> I upgrade perl to the latest version that is 5.36.1, but I took same error.

The error message ask for Perl verion 5.37 and you only upgraded to
verion 5.36, so the error is still there.

You may have to download the source files for Perl and compile it
yourself. It takes time but usually is painless.

Regards,

Olivier

> On 5/31/23 10:46, Ken Peng wrote:
>> May 31, 2023 at 3:29 PM, "Aziz Öğütlü" <aziz....@eduline.com.tr> wrote:
>>
>>
>>> We are using mirdeep2 on our HPC system. When we try to call mirdeep2.pl, it gives this error:
>>>
>>> Perl v5.35.7 required--this is only v5.26.3, stopped at /opt/ohpc/pub/compiler/perl/5.36.0/lib/5.36.0/File/Copy.pm line 10.
>> It seems you need to upgrade perl to the latest version.
>>
>> regards.
>>
> --
> İyi çalışmalar,
> Aziz Öğütlü
>
> Eduline Bilişim Sanayi ve Ticaret Ltd. Şti.  www.eduline.com.tr
> Merkez Mah. Ayazma Cad. No:37 Papirus Plaza
> Kat:6 Ofis No:118 Kağıthane -  İstanbul - Türkiye 34406
> Tel : +90 212 324 60 61     Cep: +90 541 350 40 72

--

Olivier

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May 31, 2023, 4:15:06 AM5/31/23
to Olivier, aziz....@eduline.com.tr, k...@posthub.me, begi...@perl.org
OOps, I miss read the version of Perl, sorry.

Olivier
--

Ken Peng

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May 31, 2023, 4:15:06 AM5/31/23
to aziz....@eduline.com.tr, begi...@perl.org
> Perl v5.35.7 required--this is only v5.26.3, stopped at /opt/ohpc/pub/compiler/perl/5.36.0/lib/5.36.0/File/Copy.pm line 10.

So, are you using the correct path for the latest version of perl?
It seems you have the right perl and File::Copy installed, but your program is using the old version.

regards.

aziz....@eduline.com.tr

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May 31, 2023, 5:45:06 AM5/31/23
to Ken Peng, begi...@perl.org
Hi Ken,

I'm very weak about perl, how can I check that the mirdeep2 program uses
which version of perl?

Aziz Ogutlu

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May 31, 2023, 9:45:05 AM5/31/23
to begi...@perl.org
Hi Ken,

I figured out the problem. On mirdeep2 program there is a line at the
begining calls perl. I changed this line with perl5.36.1 with absolute
path. Program starts to run.

Thank you for your help,

Aziz
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