Error parsing manifest: Unknown repository for package source: local, while deploying

Dear all,

I am trying to deploy my R shiny applicationto shinyapp.io.
But when I publish, I have this error message:

── Deploying to server ─────────────────────────────────────────────────────────
Waiting for task: 1404566911
building: Processing bundle: 8481173
error: Parsing manifest

Begin Task Log

End Task Log

Erreur : Unhandled Exception: child_task=1404566914 child_task_status=failed: Error parsing manifest: Unknown repository for package source: local
Exécution arrêtée

After some research, it seems that the problem comes from one of my installed package; but I am not able to know which one creates the issue.
Here is my seesion info:

I hope that you can help me.
Kind Regards,
Prin

Hi all,

I have now reinstalled all the libraries from scratch and I am able to publish eventually.
However, I don't see my application running.
Indeed, when I run the app, the page stays in the loading page and does not progress.

Coukd you please provide help?

Kind Regards,

Prin

I suggest you add the shinyappsio tag, to increase the chances that the right people see your post.

Hi Gabor,

Thanks a lot for your suggestion.
I will add some tags in the post!

KInd Regards,

Prin

I think we would need to see your app's logs so we can try to troubleshoot

Dear Andresrcs,

Many thanks for your feedback!
I made progress this time and was ale to publish. I had initiall an oom issue; but managed to solved it.

However, this time, I have a very weird error message when I try to publish. Indeed, it seems that during the deployment at the step "building Image", the deployment fails.

I have this message:

── Preparing for deployment ────────────────────────────────────────────────────
:heavy_check_mark: Re-deploying "nepal-dengue-dashboard" to "server: shinyapps.io / username: searo-cds-dashboard"
:information_source: Looking up application with id "11730252"...
:heavy_check_mark: Found application https://searo-cds-dashboard.shinyapps.io/nepal-dengue-dashboard/
:information_source: Bundling 114 files: '.RData', '.Renviron', '.Rprofile', '.rsconnect_profile', 'app.R', 'global.R', 'Install_package.R', 'README.md', 'utils/chart.R', 'utils/utils.R', 'components/.DS_Store', 'components/country_profile/dynamic_ui/country_profile.R', 'components/country_profile/dynamic_ui/country_profile_toast.R', 'components/country_profile/layout/main.R', 'components/overview/data/indicator_map_in_overview_data.R', 'components/overview/dynamic_ui/map_year_picker_in_overview.R', 'components/overview/dynamic_ui/value_box.new.R', 'components/overview/dynamic_ui/value_box.ori.R', …, 'www/WHO-WPRO-Logo-PMS-2925.png', and 'www/WHO_SEARO_Square.jpg'
:information_source: Capturing R dependencies with renv
:heavy_check_mark: Found 146 dependencies
:heavy_check_mark: Created 9,903,657b bundle
:information_source: Uploading bundle...
:heavy_check_mark: Uploaded bundle with id 8500618
── Deploying to server ─────────────────────────────────────────────────────────
Waiting for task: 1406283700
building: Processing bundle: 8500618
building: Parsing manifest
building: Building image: 10333822
building: Installing system dependencies

Begin Task Log

Quarto not found.
[2024-04-16T13:23:40.130934030+0000] Execute script: packages/build/rJava.sh

  • set -e
  • apt-get update -qq
    W: http://cran.rstudio.com/bin/linux/ubuntu/jammy-cran40/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
  • apt-get install bzip2 libbz2-dev
    Reading package lists...
    Building dependency tree...
    Reading state information...
    bzip2 is already the newest version (1.0.8-5build1).
    bzip2 set to manually installed.
    libbz2-dev is already the newest version (1.0.8-5build1).
    libbz2-dev set to manually installed.
    0 upgraded, 0 newly installed, 0 to remove and 117 not upgraded.
    [2024-04-16T13:23:43.620976785+0000] Execute script: packages/build/units.sh
  • set -e
  • apt-get update -qq
    W: http://cran.rstudio.com/bin/linux/ubuntu/jammy-cran40/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
  • apt-get install -y libudunits2-dev
    Reading package lists...
    Building dependency tree...
    Reading state information...
    The following additional packages will be installed:
    libudunits2-0 libudunits2-data
    The following NEW packages will be installed:
    libudunits2-0 libudunits2-data libudunits2-dev
    0 upgraded, 3 newly installed, 0 to remove and 117 not upgraded.
    Need to get 433 kB of archives.
    After this operation, 1064 kB of additional disk space will be used.
    Get:1 Index of /ubuntu jammy/universe amd64 libudunits2-data all 2.2.28-3 [19.0 kB]
    Get:2 Index of /ubuntu jammy/universe amd64 libudunits2-0 amd64 2.2.28-3 [50.3 kB]
    Get:3 Index of /ubuntu jammy/universe amd64 libudunits2-dev amd64 2.2.28-3 [364 kB]
    debconf: delaying package configuration, since apt-utils is not installed
    Fetched 433 kB in 0s (16.7 MB/s)
    Selecting previously unselected package libudunits2-data.
    (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 289120 files and directories currently installed.)
    Preparing to unpack .../libudunits2-data_2.2.28-3_all.deb ...
    Unpacking libudunits2-data (2.2.28-3) ...
    Selecting previously unselected package libudunits2-0.
    Preparing to unpack .../libudunits2-0_2.2.28-3_amd64.deb ...
    Unpacking libudunits2-0 (2.2.28-3) ...
    Selecting previously unselected package libudunits2-dev.
    Preparing to unpack .../libudunits2-dev_2.2.28-3_amd64.deb ...
    Unpacking libudunits2-dev (2.2.28-3) ...
    Setting up libudunits2-data (2.2.28-3) ...
    Setting up libudunits2-0 (2.2.28-3) ...
    Setting up libudunits2-dev (2.2.28-3) ...
    Processing triggers for install-info (6.8-4build1) ...
    Processing triggers for libc-bin (2.35-0ubuntu3.4) ...
    [2024-04-16T13:23:47.137337527+0000] Execute script: packages/build/V8.sh
    W: http://cran.rstudio.com/bin/linux/ubuntu/jammy-cran40/InRelease: Key is stored in legacy trusted.gpg keyring (/etc/apt/trusted.gpg), see the DEPRECATION section in apt-key(8) for details.
    Reading package lists...
    Building dependency tree...
    Reading state information...
    The following additional packages will be installed:
    libc-ares2 libnode72 libuv1 libuv1-dev
    The following NEW packages will be installed:
    libc-ares2 libnode-dev libnode72 libuv1-dev
    The following packages will be upgraded:
    libuv1
    1 upgraded, 4 newly installed, 0 to remove and 116 not upgraded.
    Need to get 11.7 MB of archives.
    After this operation, 48.1 MB of additional disk space will be used.
    Get:1 Index of /ubuntu jammy-updates/main amd64 libuv1 amd64 1.43.0-1ubuntu0.1 [92.7 kB]
    Get:2 Index of /ubuntu jammy-updates/main amd64 libuv1-dev amd64 1.43.0-1ubuntu0.1 [130 kB]
    Get:3 Index of /ubuntu jammy-updates/main amd64 libc-ares2 amd64 1.18.1-1ubuntu0.22.04.3 [45.1 kB]
    Err:4 Index of /ubuntu jammy-security/universe amd64 libnode72 amd64 12.22.9~dfsg-1ubuntu3.5
    404 Not Found [IP: 91.189.91.81 80]
    Err:5 Index of /ubuntu jammy-security/universe amd64 libnode-dev amd64 12.22.9~dfsg-1ubuntu3.5
    404 Not Found [IP: 91.189.91.81 80]
    Fetched 268 kB in 0s (5187 kB/s)
    E: Failed to fetch http://security.ubuntu.com/ubuntu/pool/universe/n/nodejs/libnode72_12.22.9~dfsg-1ubuntu3.5_amd64.deb 404 Not Found [IP: 91.189.91.81 80]
    E: Failed to fetch http://security.ubuntu.com/ubuntu/pool/universe/n/nodejs/libnode-dev_12.22.9~dfsg-1ubuntu3.5_amd64.deb 404 Not Found [IP: 91.189.91.81 80]
    E: Unable to fetch some archives, maybe run apt-get update or try with --fix-missing?## End Task Log ################################################################
    Erreur : Unhandled Exception: child_task=1406283701 child_task_status=failed: Error building image: Build exited with non-zero status: 100
    Exécution arrêtée

I am not sure why I have this issue!

Kind Regards,

Nirmal

It seems to me like a temporary unavailability of Ubuntu system libraries. If that is the case there is nothing for you to do at the user level other than wait until the server malfunction gets fixed