Unwanted package replacement request

buntolo · 2017-06-21 11:51:02

I want to know whichi package is needing hdf5 on my system. Right now I'm using hdf5-coo-fortran and I'm being asked to replace it with hdf5, I want to prevent this.

# LC_ALL=C pacman -Su
:: Starting full system upgrade...
:: Replace hdf5-cpp-fortran with community/hdf5? [Y/n]

I don't understand who needs hdf5, as it's not in the list of pacakges needing an update:

% LC_ALL=C pacman -Sii hdf5                       :(
Repository      : community
Name            : hdf5
Version         : 1.10.0_patch1-2
Description     : General purpose library and file format for storing scientific
                  data
Architecture    : x86_64
URL             : https://www.hdfgroup.org/hdf5/
Licenses        : custom
Groups          : None
Provides        : hdf5-cpp-fortran
Depends On      : zlib  bash
Optional Deps   : None
Required By     : alembic  gdal  gmic  libmatio  netcdf  octave  python-h5py
                  python-pytables  python2-h5py  python2-pytables  vigra
Optional For    : opencv
Conflicts With  : None
Replaces        : hdf5-cpp-fortran
Download Size   : 2.69 MiB
Installed Size  : 9.33 MiB
Packager        : Bruno Pagani <archange@archlinux.org>
Build Date      : Fri Jun 16 16:00:01 2017
MD5 Sum         : e3e8ee6b50f6d56d6e8eb2e1f8233bc4
SHA-256 Sum     : f2d8e5d9693d6a36a174f0afad80789bd6708f14b2744323e7e78ea0b83643fa
Signatures      : 9D893EC4DAAF9129

% LC_ALL=C pacman -Qu
archlinux-keyring 20170320-1 -> 20170611-1
atom 1.18.0-1 -> 1.18.0-2
boost 1.64.0-1 -> 1.64.0-2
boost-libs 1.64.0-1 -> 1.64.0-2
cairo 1.14.8-1 -> 1.14.10-1
exfat-utils 1.2.6-1 -> 1.2.7-1
gimp 2.8.20-1 -> 2.8.22-1
glibc 2.25-2 -> 2.25-4
gst-plugins-bad 1.12.0-1 -> 1.12.1-1
gst-plugins-base 1.12.0-1 -> 1.12.1-1
gst-plugins-base-libs 1.12.0-1 -> 1.12.1-1
gst-plugins-good 1.12.0-1 -> 1.12.1-1
gst-plugins-ugly 1.12.0-3 -> 1.12.1-1
gstreamer 1.12.0-1 -> 1.12.1-1
gstreamer-vaapi 1.12.0-1 -> 1.12.1-1
gtk-update-icon-cache 3.22.15-1 -> 3.22.16-1
gtk3 3.22.15-1 -> 3.22.16-1
gtk3-print-backends 3.22.15-1 -> 3.22.16-1
jemalloc 4.5.0-1 -> 1:4.5.0-1
lib32-glibc 2.25-3 -> 2.25-4
lib32-mesa 17.1.2-1 -> 17.1.3-1
lib32-openal 1.18.0-1 -> 1.18.0-2
libbluray 1.0.0-1 -> 1.0.1-1
libgphoto2 2.5.14-1 -> 2.5.14+6+g695b55887-1
libmariadbclient 10.1.23-2 -> 10.1.24-1
libmm-glib 1.6.6-1 -> 1.6.8-1
libunwind 1.2-1 -> 1.2.1-1
libusb 1.0.21-1 -> 1.0.21-2
linux 4.11.5-1 -> 4.11.6-1
linux-headers 4.11.5-1 -> 4.11.6-1
mesa 17.1.2-1 -> 17.1.3-1
openmpi 1.10.6-2 -> 2.1.1-1
vtk6 6.3.0-5 -> 6.3.0-7
xarchiver 0.5.4.8-1 -> 0.5.4.10-1

loqs · 2017-06-21 11:54:37

Why do you want to prevent it? https://git.archlinux.org/svntogit/comm … aa70aa57e5

Trilby · 2017-06-21 12:00:06

buntolo wrote:

I don't understand who needs hdf5

$ pacman -Si hdf5
...
Replaces        : hdf5-cpp-fortran
...

buntolo · 2017-06-21 12:28:03

I want to update other stuff first, I "resolved" installing manually all the other packages apart, as I couldn't find a way to skip hdf5 replacement.

V1del · 2017-06-21 12:49:33

Now you have an XY Problem and you are running a partial upgrade which isn't supported either, WHY do you not want this replacement to happen? You should not lose any functionality.

Last edited by V1del (2017-06-21 12:53:45)

fsckd · 2017-06-21 12:52:24

As the link loqs gave says, hdf5-cpp-fortran has been reunified with hdf5 and is no longer in the repositories. hdf5 now provides what hdf5-cpp-fortran did. Why do you not want hdf5?

Xyne · 2017-06-21 13:39:53

buntolo wrote:

I want to update other stuff first, I "resolved" installing manually all the other packages apart, as I couldn't find a way to skip hdf5 replacement.

When you saw that pacman wanted to replace hdf5-cpp-fortran with hdf5, you should have checked the hd5f page or read up about pacman package replacements. Given, that may not be obvious so asking on the forum is normal, but then you should have waited for some answers and taken the time to understand them. The replacement indicates that all of the functionality of the hdf5-cpp-fortran package is now provided by hdf5. In general, package replacements require no user intervention and should be seen as regular upgrades, either because the package changed name or because the functionality has been subsumed by another package (which will often "provide" the old package to satisfy dependencies).

Not waiting for the answers or ignoring them, then doing a partial upgrade which leaves the system in an unsupported state, all to avoid something due to a misconception indicates that you need to slow down and understand what you are doing. You are just going to waste time otherwise, especially if you end up having to recover your system from a live cd after partial upgrade.

Incidentally, pacman has an option that would have allowed you to upgrade the system while ignoring hdf5/hdf5-cpp-fortran without manually installing everything else.

buntolo · 2017-06-21 14:49:01

I don't want a partially upgraded system in general, simply sometimes I need a specific thing and nothing else, I'll care about it later.

In this case in the end all I wanted was to upgrade certain packages but this replacement was preventing me to proceed, I skipped it, installed the rest, then installed hdf5 and it worked.

So I couldn't find a way to prevent replacement, as --ignore didn't work.

Last edited by buntolo (2017-06-21 14:51:33)

Scimmia · 2017-06-21 14:51:41

Right, so instead you did something that could have broken your entire system. Sounds sane.

Trilby · 2017-06-21 16:03:26

buntolo wrote:

I'll care about it later.

Not really a good approach. "Later" is never the right time to do things properly - and if you only care about it later when everything is broken, don't expect anyone here to care about it at all.

buntolo · 2017-06-21 17:11:32

Look, I understand that's it's generally bad to avoid things like this, but for something useless like hdf5 I don't see which harm could have been done to the system. I mean: it's stuff I've installed when I had the need to check my MRI.

I've a serious question: how could I have skipped hdf5 replacement in this specific case?

Incidentally, pacman has an option that would have allowed you to upgrade the system while ignoring hdf5/hdf5-cpp-fortran without manually installing everything else.

Last edited by buntolo (2017-06-21 17:15:21)

adesh · 2017-06-21 17:27:44

buntolo wrote:

Look, I understand that's it's generally bad to avoid things like this, but for something useless like hdf5 I don't see which harm could have been done to the system. I mean: it's stuff I've installed when I had the need to check my MRI.

In that case you should remove this package and then do a full upgrade to bring the system in a consistent state. That would be relatively faster instead of taking time to deal with it later. And anyhow it's always better to have lesser number of packages to reduce hassle with upgrade.

Xyne · 2017-06-21 17:34:58

buntolo wrote:

I've a serious question: how could I have skipped hdf5 replacement in this specific case?
Incidentally, pacman has an option that would have allowed you to upgrade the system while ignoring hdf5/hdf5-cpp-fortran without manually installing everything else.

I would have expected "--ignore hd5f" and/or "--ignore hdf5-cpp-fortran" to work, assuming all packages in the upgrade only depend on "hdt5-cpp-fortran" (i.e. not a versioned dependency or an updated "hdf5" dependency), which is presumably the case if you were able to upgrade manually.

buntolo · 2017-06-21 19:19:57

Xyne wrote:

buntolo wrote:
I've a serious question: how could I have skipped hdf5 replacement in this specific case?
Incidentally, pacman has an option that would have allowed you to upgrade the system while ignoring hdf5/hdf5-cpp-fortran without manually installing everything else.
I would have expected "--ignore hd5f" and/or "--ignore hdf5-cpp-fortran" to work, assuming all packages in the upgrade only depend on "hdt5-cpp-fortran" (i.e. not a versioned dependency or an updated "hdf5" dependency), which is presumably the case if you were able to upgrade manually.

I didn't ignore both of them at the same time, that's probably the reason I falied. Thank you.

Xyne · 2017-06-21 19:34:47

buntolo wrote:

I didn't ignore both of them at the same time, that's probably the reason I falied. Thank you.

I don't actually know how pacman handles ignored packages when dealing with replacements. It might not have worked even with both. If not, the database could have been tweaked for the upgrade but that is obviously not recommended.

buntolo · 2017-06-21 20:27:39

Xyne wrote:

buntolo wrote:
I didn't ignore both of them at the same time, that's probably the reason I falied. Thank you.
I don't actually know how pacman handles ignored packages when dealing with replacements. It might not have worked even with both. If not, the database could have been tweaked for the upgrade but that is obviously not recommended.

What do you mean by tweaking the database? I'm asking for the sake of knowledge.

Xyne · 2017-06-21 21:55:17

buntolo wrote:

What do you mean by tweaking the database? I'm asking for the sake of knowledge.

Read up on pacman and then explore the local and sync databases

Arch Linux

#1 2017-06-21 11:51:02

Unwanted package replacement request

#2 2017-06-21 11:54:37

Re: Unwanted package replacement request

#3 2017-06-21 12:00:06

Re: Unwanted package replacement request

#4 2017-06-21 12:28:03

Re: Unwanted package replacement request

#5 2017-06-21 12:49:33

Re: Unwanted package replacement request

#6 2017-06-21 12:52:24

Re: Unwanted package replacement request

#7 2017-06-21 13:39:53

Re: Unwanted package replacement request

#8 2017-06-21 14:49:01

Re: Unwanted package replacement request

#9 2017-06-21 14:51:41

Re: Unwanted package replacement request

#10 2017-06-21 16:03:26

Re: Unwanted package replacement request

#11 2017-06-21 17:11:32

Re: Unwanted package replacement request

#12 2017-06-21 17:27:44

Re: Unwanted package replacement request

#13 2017-06-21 17:34:58

Re: Unwanted package replacement request

#14 2017-06-21 19:19:57

Re: Unwanted package replacement request

#15 2017-06-21 19:34:47

Re: Unwanted package replacement request

#16 2017-06-21 20:27:39

Re: Unwanted package replacement request

#17 2017-06-21 21:55:17

Re: Unwanted package replacement request

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