BioArchLinux/Packages

[BUG] `asap`: Fails to install: `/bin exists in filesystem (owned by filesystem)`.

dreirund opened this issue · 5 comments

dreirund commented

Log of the bug

If I want to install bioarchlinux/asap, installation fails with

error: failed to commit transaction (conflicting files)
asap: /bin exists in filesystem (owned by filesystem)
Errors occurred, no packages were upgraded.

aur/asap works.

You need to install stuff into /usr/bin/.

Additional context

Just have done a pacman -Syu now and then wanted to install asap from your repository.

starsareintherose commented

okay, thanks for your information. But to be noticed, asap in AUR is not bioinformatics related.

starsareintherose commented

Now fixed f318330

Packages (1) asap-2023_02_14-2

Total Download Size:   0.06 MiB
Total Installed Size:  0.14 MiB

:: Proceed with installation? [Y/n] 
:: Retrieving packages...
 asap-2023_02_14-...    62.9 KiB  48.8 KiB/s 00:01 [----------------------] 100%
(1/1) checking keys in keyring                     [----------------------] 100%
(1/1) checking package integrity                   [----------------------] 100%
(1/1) loading package files                        [----------------------] 100%
(1/1) checking for file conflicts                  [----------------------] 100%
(1/1) checking available disk space                [----------------------] 100%
:: Processing package changes...
(1/1) installing asap                              [----------------------] 100%
:: Running post-transaction hooks...
(1/1) Arming ConditionNeedsUpdate...

You need to use release 2

and this is the information

Name            : asap
Version         : 2023_02_14-2
Description     : Assemble Species by Automatic Partitioning
                  https://doi.org/10.1111/1755-0998.13281
Architecture    : x86_64
URL             : https://bioinfo.mnhn.fr/abi/public/asap/
Licenses        : LGPL
Groups          : None
Provides        : None
Depends On      : None
Optional Deps   : None
Required By     : None
Optional For    : None
Conflicts With  : None
Replaces        : None
Installed Size  : 142.48 KiB
Packager        : BioArchLinux (on behalf of kuoi) <kuoi@bioarchlinux.org>
Build Date      : Sat 06 May 2023 17:02:36 CST
Install Date    : Sat 06 May 2023 17:03:25 CST
Install Reason  : Explicitly installed
Install Script  : No
Validated By    : Signature
Name            : asap
Version         : 2023_02_14-2
Description     : Assemble Species by Automatic Partitioning
                  https://doi.org/10.1111/1755-0998.13281
Architecture    : x86_64
URL             : https://bioinfo.mnhn.fr/abi/public/asap/
Licenses        : LGPL
Groups          : None
Provides        : None
Depends On      : None
Optional Deps   : None
Required By     : None
Optional For    : None
Conflicts With  : None
Replaces        : None
Installed Size  : 142.48 KiB
Packager        : BioArchLinux (on behalf of kuoi) <kuoi@bioarchlinux.org>
Build Date      : Sat 06 May 2023 17:02:36 CST
Install Date    : Sat 06 May 2023 17:03:25 CST
Install Reason  : Explicitly installed
Install Script  : No
Validated By    : Signature
dreirund commented

But to be noticed, asap in AUR is not bioinformatics related.

Oh. I had the AUR package installed, and your package was pulled in by package upgrade.

So we here have two very different softwares packaged under the same name.

Can you rename your package, to remove that clash?

Regards!

starsareintherose commented

No, we won't rename our pkg for AUR or community. It would cause a lot of trouble unless you need to use different software simultaneously, then request, if you want us to rename, why not consider suggesting AUR rename?

dreirund commented