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blinard-BIOINFO avatar blinard-BIOINFO commented on June 11, 2024

Dear Pierre,

Thanks for spotting this issue !
I will add your suggestion to the install script.

May I ask which setup you used to raise this bug ? (OS, java version/package installed...)
I tried PEWO on different minimal Unix images (using virual box) and never ran into it UTF8 issues.

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pierrebarbera avatar pierrebarbera commented on June 11, 2024

Hi Benjamin,

OS: CentOS 8
OpenJDK Runtime Environment 18.9
javac 11.0.9

(though I'm not sure its this system wide version that was used during the install, over the conda package specified in the environment)

Interestingly the system wide encoding actually seems to be set correctly:

~$ echo $LANG
en_US.UTF-8

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blinard-BIOINFO avatar blinard-BIOINFO commented on June 11, 2024

I actually used a slightly different approach.
Adding encoding="UTF-8" in the ant build file should be more portable than exporting variables.

Fixed with commit 6a02180 in PEWO_java repository.
Fixed with commit 8937150 in RAPPAS repository.
( Side note for @nromashchenko : I just realized that without github PRO we cannot reference commits from submodules... )

@Pbdas : Would you mind to test again a fresh install on your setup following this fix and report if this was enough ? I do not manage to reproduce this bug on my side.

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pierrebarbera avatar pierrebarbera commented on June 11, 2024

I did a fresh clone on the machine I used previously, as well as a fresh clone on a practically identical machine that should be a relatively blank slate, and the issue was gone on both :)

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blinard-BIOINFO avatar blinard-BIOINFO commented on June 11, 2024

Thank you for your reply.

Bug fixed

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