Md type primary error when updating from gnome software

Btw I suspect that zchunk is involved in the MD_TYPE_PRIMARY has failed error.
Again, I don’t have enough knowledge on this topic, but if you look at the content of this URL https://fedora.mirror.garr.it/fedora/linux/releases/32/Everything/x86_64/os/repodata/, there are files called like something-primary.xml. zck , as well as in the destination directories /var/cache/PackageKit/32/metadata

Just to track the issue, could you show the content of /etc/dnf/dnf.conf
And what kind of error related to zchunk you get?

Oh boy! As far as I can see, even if the repositories are disabled, it seems that pkcon -v refresh force refresh them as well.

This is an interesting command to launch:
sudo /usr/libexec/packagekit-direct -v refresh-force

It gives more information about PackageKit cache refresh operations.

this is the dnf conf file

[main]
gpgcheck=1
installonly_limit=3
clean_requirements_on_remove=True
best=False
skip_if_unavailable=True
zchunk=False

this is the zchunk error

Skipping refresh of fedora: cannot update repo ‘fedora’: Yum repo downloading error: Downloading error(s): repodata/b7e1566c87075299c4a199737b341e7d15fbf1a4d49c4c2cbe43368437b02c47-comps-Everything.x86_64.xml.zck - Download failed: Curl error (23): Failed writing received data to disk/application for http://fedora.mirror.garr.it/fedora/linux/releases/32/Everything/x86_64/os/repodata/b7e1566c87075299c4a199737b341e7d15fbf1a4d49c4c2cbe43368437b02c47-comps-Everything.x86_64.xml.zck [Failed writing body (0 != 2776)]; Last error: Curl error (23): Failed writing received data to disk/application for http://fedora.mirror.garr.it/fedora/linux/releases/32/Everything/x86_64/os/repodata/b7e1566c87075299c4a199737b341e7d15fbf1a4d49c4c2cbe43368437b02c47-comps-Everything.x86_64.xml.zck [Failed writing body (0 != 2776)]

and this is the result of sudo /usr/libexec/packagekit-direct -v refresh-force

13:14:25 PackageKit Verbose debugging enabled (on console 1)
13:14:25 PackageKit Trying to load : dnf
13:14:25 PackageKit dlopening ‘/usr/lib64/packagekit-backend/libpk_backend_dnf.so’
13:14:25 PackageKit-DNF Using libdnf 0.47.0
13:14:25 PackageKit-DNF Using librepo 1.11.3
13:14:25 PackageKit cache-age changed to 4294967295
Status: running
Status: wait
13:14:25 PackageKit-DNF got state loading-cache with hint (null)
Status: loading-cache
Done: 1%
13:14:26 PackageKit-DNF Deleting contents of rpmfusion-nonfree-steam as forced
13:14:26 PackageKit-DNF got state loading-cache with hint (null)
13:14:26 PackageKit-DNF repo rpmfusion-nonfree-steam not okay [repodata rpmfusion-nonfree-steam was not complete: Cannot open /var/cache/PackageKit/32/metadata/rpmfusion-nonfree-steam-32-x86_64/repodata/repomd.xml: File o directory non esistente], refreshing
13:14:26 PackageKit-DNF got state download-repository with hint (null)
Status: download-repository
Done: 7%
13:14:26 PackageKit-DNF got state loading-cache with hint (null)
Status: loading-cache
Done: 8%
13:14:27 PackageKit-DNF got state loading-cache with hint (null)
Done: 9%
13:14:27 PackageKit-DNF Deleting contents of rpmfusion-nonfree-updates as forced
13:14:27 PackageKit-DNF got state loading-cache with hint (null)
13:14:27 PackageKit-DNF repo rpmfusion-nonfree-updates not okay [repodata rpmfusion-nonfree-updates was not complete: Cannot open /var/cache/PackageKit/32/metadata/rpmfusion-nonfree-updates-32-x86_64/repodata/repomd.xml: File o directory non esistente], refreshing
13:14:27 PackageKit-DNF got state download-repository with hint (null)
Status: download-repository
Done: 16%
13:14:28 PackageKit-DNF got state loading-cache with hint (null)
Status: loading-cache
Done: 17%
13:14:30 PackageKit-DNF got state loading-cache with hint (null)
13:14:30 PackageKit-DNF Done: 18%
Deleting contents of copr:copr.fedorainfracloud.org:gnumdk:eolie as forced
13:14:30 PackageKit-DNF got state loading-cache with hint (null)
13:14:30 PackageKit-DNF repo copr:copr.fedorainfracloud.org:gnumdk:eolie not okay [repodata copr:copr.fedorainfracloud.org:gnumdk:eolie was not complete: Cannot open /var/cache/PackageKit/32/metadata/copr:copr.fedorainfracloud.org:gnumdk:eolie-32-x86_64/repodata/repomd.xml: File o directory non esistente], refreshing
13:14:30 PackageKit-DNF got state download-repository with hint (null)
Status: download-repository
13:14:31 PackageKit-DNF got state loading-cache with hint (null)
Status: loading-cache
Done: 25%
13:14:32 PackageKit-DNF got state loading-cache with hint (null)
Done: 26%
13:14:32 PackageKit-DNF Deleting contents of rpmfusion-nonfree as forced
13:14:32 PackageKit-DNF got state loading-cache with hint (null)
13:14:32 PackageKit-DNF repo rpmfusion-nonfree not okay [repodata rpmfusion-nonfree was not complete: Cannot open /var/cache/PackageKit/32/metadata/rpmfusion-nonfree-32-x86_64/repodata/repomd.xml: File o directory non esistente], refreshing
13:14:32 PackageKit-DNF got state download-repository with hint (null)
Status: download-repository
Done: 32%
13:14:32 PackageKit-DNF got state loading-cache with hint (null)
Status: loading-cache
Done: 34%
13:14:33 PackageKit-DNF got state loading-cache with hint (null)
13:14:33 PackageKit-DNF Deleting contents of copr:copr.fedorainfracloud.org:gnumdk:lollypop as forced
Done: 35%
13:14:33 PackageKit-DNF got state loading-cache with hint (null)
13:14:33 PackageKit-DNF repo copr:copr.fedorainfracloud.org:gnumdk:lollypop not okay [repodata copr:copr.fedorainfracloud.org:gnumdk:lollypop was not complete: Cannot open /var/cache/PackageKit/32/metadata/copr:copr.fedorainfracloud.org:gnumdk:lollypop-32-x86_64/repodata/repomd.xml: File o directory non esistente], refreshing
13:14:33 PackageKit-DNF got state download-repository with hint (null)
Status: download-repository
13:14:34 PackageKit-DNF got state loading-cache with hint (null)
Status: loading-cache
Done: 43%
13:14:34 PackageKit-DNF got state loading-cache with hint (null)
13:14:34 PackageKit-DNF Deleting contents of rpmfusion-free-updates as forced
13:14:34 PackageKit-DNF got state loading-cache with hint (null)
13:14:34 PackageKit-DNF repo rpmfusion-free-updates not okay [repodata rpmfusion-free-updates was not complete: Cannot open /var/cache/PackageKit/32/metadata/rpmfusion-free-updates-32-x86_64/repodata/repomd.xml: File o directory non esistente], refreshing
13:14:34 PackageKit-DNF got state download-repository with hint (null)
Status: download-repository
Done: 50%
13:14:35 PackageKit-DNF got state loading-cache with hint (null)
Status: loading-cache
Done: 52%
13:14:36 PackageKit-DNF got state loading-cache with hint (null)
13:14:36 PackageKit-DNF Deleting contents of phracek-PyCharm as forced
13:14:36 PackageKit-DNF got state loading-cache with hint (null)
13:14:36 PackageKit-DNF repo phracek-PyCharm not okay [repodata phracek-PyCharm was not complete: Cannot open /var/cache/PackageKit/32/metadata/phracek-PyCharm-32-x86_64/repodata/repomd.xml: File o directory non esistente], refreshing
13:14:36 PackageKit-DNF got state download-repository with hint (null)
Status: download-repository
13:14:37 PackageKit-DNF got state loading-cache with hint (null)
Status: loading-cache
Done: 60%
13:14:38 PackageKit-DNF got state loading-cache with hint (null)
13:14:38 PackageKit-DNF Deleting contents of google-chrome as forced
13:14:38 PackageKit-DNF got state loading-cache with hint (null)
13:14:38 PackageKit-DNF repo google-chrome not okay [repodata google-chrome was not complete: Cannot open /var/cache/PackageKit/32/metadata/google-chrome-32-x86_64/repodata/repomd.xml: File o directory non esistente], refreshing
13:14:38 PackageKit-DNF got state download-repository with hint (null)
Status: download-repository
13:14:38 PackageKit-DNF got state loading-cache with hint (null)
Status: loading-cache
Done: 69%
13:14:38 PackageKit-DNF got state loading-cache with hint (null)
13:14:38 PackageKit-DNF Deleting contents of fedora as forced
13:14:38 PackageKit-DNF got state loading-cache with hint (null)
13:14:38 PackageKit-DNF repo fedora not okay [repodata fedora was not complete: Cannot open /var/cache/PackageKit/32/metadata/fedora-32-x86_64/repodata/repomd.xml: File o directory non esistente], refreshing
13:14:38 PackageKit-DNF got state download-repository with hint (null)
Status: download-repository
Done: 70%
Done: 71%
Done: 72%
Done: 73%
Done: 74%
Done: 75%
Done: 76%
Done: 77%
13:14:39 PackageKit-DNF got state loading-cache with hint (null)
Status: loading-cache
13:16:08 PackageKit-DNF Skipping refresh of fedora: cannot update repo ‘fedora’: Yum repo downloading error: Downloading error(s): repodata/b7e1566c87075299c4a199737b341e7d15fbf1a4d49c4c2cbe43368437b02c47-comps-Everything.x86_64.xml.zck - Download failed: Curl error (23): Failed writing received data to disk/application for http://fedora.mirror.garr.it/fedora/linux/releases/32/Everything/x86_64/os/repodata/b7e1566c87075299c4a199737b341e7d15fbf1a4d49c4c2cbe43368437b02c47-comps-Everything.x86_64.xml.zck [Failed writing body (0 != 2776)]; Last error: Curl error (23): Failed writing received data to disk/application for http://fedora.mirror.garr.it/fedora/linux/releases/32/Everything/x86_64/os/repodata/b7e1566c87075299c4a199737b341e7d15fbf1a4d49c4c2cbe43368437b02c47-comps-Everything.x86_64.xml.zck [Failed writing body (0 != 2776)]
13:16:08 PackageKit-DNF Deleting contents of rpmfusion-nonfree-nvidia-driver as forced
13:16:08 PackageKit-DNF got state loading-cache with hint (null)
13:16:08 PackageKit-DNF repo rpmfusion-nonfree-nvidia-driver not okay [repodata rpmfusion-nonfree-nvidia-driver was not complete: Cannot open /var/cache/PackageKit/32/metadata/rpmfusion-nonfree-nvidia-driver-32-x86_64/repodata/repomd.xml: File o directory non esistente], refreshing
Done: 78%
13:16:08 PackageKit-DNF got state download-repository with hint (null)
Status: download-repository
Done: 84%
13:16:09 PackageKit-DNF got state loading-cache with hint (null)
Status: loading-cache
Done: 86%
13:16:10 PackageKit-DNF got state loading-cache with hint (null)
13:16:10 PackageKit-DNF Deleting contents of updates as forced
13:16:10 PackageKit-DNF got state loading-cache with hint (null)
13:16:10 PackageKit-DNF repo updates not okay [repodata updates was not complete: Cannot open /var/cache/PackageKit/32/metadata/updates-32-x86_64/repodata/repomd.xml: File o directory non esistente], refreshing
Done: 87%
13:16:10 PackageKit-DNF got state download-repository with hint (null)
Status: download-repository
Done: 89%
Done: 92%
Done: 93%
Done: 94%
13:16:11 PackageKit-DNF got state loading-cache with hint (null)
Status: loading-cache
Done: 95%
13:16:43 PackageKit-DNF got state loading-cache with hint (null)
Done: 96%
13:16:43 PackageKit-DNF got state query with hint (null)
Status: query
13:16:43 PackageKit-DNF got state loading-cache with hint (null)
Status: loading-cache
13:16:43 PackageKit-DNF got state download-repository with hint (null)
Status: download-repository
13:16:44 PackageKit-DNF got state loading-cache with hint (null)
Status: loading-cache
Error: cannot-fetch-sources cannot update repo ‘fedora’: Yum repo downloading error: Downloading error(s): repodata/b7e1566c87075299c4a199737b341e7d15fbf1a4d49c4c2cbe43368437b02c47-comps-Everything.x86_64.xml.zck - Download failed: Curl error (23): Failed writing received data to disk/application for http://fedora.mirror.garr.it/fedora/linux/releases/32/Everything/x86_64/os/repodata/b7e1566c87075299c4a199737b341e7d15fbf1a4d49c4c2cbe43368437b02c47-comps-Everything.x86_64.xml.zck [Failed writing body (0 != 659)]; Last error: Curl error (23): Failed writing received data to disk/application for http://fedora.mirror.garr.it/fedora/linux/releases/32/Everything/x86_64/os/repodata/b7e1566c87075299c4a199737b341e7d15fbf1a4d49c4c2cbe43368437b02c47-comps-Everything.x86_64.xml.zck [Failed writing body (0 != 659)]
Status: finished
Exit code: failed

1 Like

I think that it could be interesting to add the packagekit-direct result to the bug report.

done, hope someone will have a look at it…

Again out of curiosity, if you perform the download with curl

cd ~/Downloads
curl -O http://fedora.mirror.garr.it/fedora/linux/releases/32/Everything/x86_64/os/repodata/b7e1566c87075299c4a199737b341e7d15fbf1a4d49c4c2cbe43368437b02c47-comps-Everything.x86_64.xml.zck

Does it work? (I bet yes)

yes does it work without problem

I have another, maybe stupid, question: what about disk space?
df -h

plenty…well sort of

File system Dim. Usati Dispon. Uso% Montato su
devtmpfs 1,9G 0 1,9G 0% /dev
tmpfs 2,0G 36M 1,9G 2% /dev/shm
tmpfs 2,0G 1,6M 1,9G 1% /run
/dev/sda2 108G 9,9G 93G 10% /
tmpfs 2,0G 100K 2,0G 1% /tmp
/dev/sdb2 145G 78G 61G 57% /home
/dev/sda1 976M 275M 635M 31% /boot
tmpfs 390M 124K 390M 1% /run/user/1000

I was performing some test.
I used my mobile phone via usb tethering in order to connect my PC to the internet.
I don’t get the loading of MD_TYPE_PRIMARY has failed error. But when I issue the pkcon refresh force command, after a lot of time, I get an already mentioned error:

Fatal error: cannot update repo 'fedora': Yum repo downloading error: Downloading error(s): repodata/b7e1566c87075299c4a199737b341e7d15fbf1a4d49c4c2cbe43368437b02c47-comps-Everything.x86_64.xml.zck - Download failed: Curl error (23): Failed writing received data ...

If I reconnect the PC to the WiFi network, all works as expected.

Wait!

I was using an outdated system. I upgraded it with dnf.
Now if I perform the same command pkcon refresh force as before, using the mobile line, now I get
Fatal error: loading of MD_TYPE_PRIMARY has failed

Yay! :partying_face:

1 Like

@247, I mean that probably a fresh installation of Fedora will not solve your issue.

well that means that something changed in fedora, because was not having this issue weeks ago

i do think at this point, there’s not much we can do…

Hey @247, I have another test for you :sweat_smile:

Could you please edit again these two files?
/etc/yum.repos.d/fedora.repo
/etc/yum.repos.d/fedora-updates.repo

In /etc/yum.repos.d/fedora.repo, in the [fedora] repo-id stanza, comment all the metalink and baseurl lines. Then add this line:
baseurl=https://dl.fedoraproject.org/pub/fedora/linux/releases/$releasever/Everything/$basearch/os/

In /etc/yum.repos.d/fedora-updates.repo, in the [updates] repo-id stanza, also comment all the metalink and baseurl lines. Then add this line:
baseurl=https://dl.fedoraproject.org/pub/fedora/linux/updates/$releasever/Everything/$basearch/

/etc/yum.repos.d/fedora.repo
[fedora]
name=Fedora $releasever - $basearch
baseurl=https://dl.fedoraproject.org/pub/fedora/linux/releases/$releasever/Everything/$basearch/os/
# metalink=https://mirrors.fedoraproject.org/metalink?repo=fedora-$releasever&arch=$basearch
enabled=1
countme=1
metadata_expire=7d
repo_gpgcheck=0
type=rpm
gpgcheck=1
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-fedora-$releasever-$basearch
skip_if_unavailable=False
/etc/yum.repos.d/fedora-updates.repo
[updates]
name=Fedora $releasever - $basearch - Updates
baseurl=https://dl.fedoraproject.org/pub/fedora/linux/updates/$releasever/Everything/$basearch/
# metalink=https://mirrors.fedoraproject.org/metalink?repo=updates-released-f$releasever&arch=$basearch
enabled=1
countme=1
repo_gpgcheck=0
type=rpm
gpgcheck=1
metadata_expire=6h
gpgkey=file:///etc/pki/rpm-gpg/RPM-GPG-KEY-fedora-$releasever-$basearch
skip_if_unavailable=False

Then, maybe it is pointless, issue this command
sudo rm -rf /var/cache/PackageKit/32/
and reboot.

Afterwards, open a terminal, and again, issue this command:
pkcon -v refresh force

done, things hasn’t changed by a single bit…

Weird things.
As said, this issue happens to me as well using tethering with the mobile phone. Using dl.fedoraproject.org instead of a mirror seemed to work.

what can i say, i’m special…

For current and future people interested in this topic, it seems that on some network connections (like mobile 4G) there are issues while downloading zchunk files, at least using librepo, dnf, libdnf, packagekit and so on (I’m not sure what is the actual component involved).

While dnf respect the zchunk=False option specified in the dnf.conf file (in other word, dnf will download the gz or xz version of repodata files), packagekit (and/or the underlying libraries/modules) continue to download the zchunk compressed repository metadata (or the like).

Just to track this issue, these are the relevant discussions on bugzilla: