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h836472 / ContScout

ContScout sequence contamination filter tool
GNU General Public License v3.0
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Error updateDB : package or namespace load failed #4

Closed odethier-ulb closed 5 months ago

odethier-ulb commented 5 months ago

Hello,

I have an issue while trying to install a database (uniref90) using a singularity image built from the latest docker image, it also appears with a simple updateDB -i.

Here are the commands I typed:

i. singularity build contscout_latest.sif docker://h836472/contscout:latest (downloaded and built this 05/21/2024) ii. singularity exec contscout_latest.sif updateDB -i

And for the output I have: During startup - Warning messages: 1: Setting LC_TIME failed, using "C" 2: Setting LC_MONETARY failed, using "C" 3: Setting LC_PAPER failed, using "C" 4: Setting LC_MEASUREMENT failed, using "C" This is the database updater component of ContScout. Loading R libraries. Error: package or namespace load failed for ‘googlesheets4’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): namespace ‘glue’ 1.4.1 is already loaded, but >= 1.4.2 is required Execution halted

Is it possible to update the docker image or provide a workaround to install a database?

Regards

h836472 commented 5 months ago

Hi There,

This is a quick e-mail with an unconfirmed hint assuming you wish to proceed with the troubleshooting fast. (I will have the chance to deal with the request more thoroughly only by the end of the week)

I assume that Singularity mounts up your host /home directory where glue 1.4.1 is installed. The bug is caused by your host "local" library version overriding the one that is installed within the container.

You might wish to mount your singularity home manually, to an external empty folder, away from your host R libraries singularity -B /my_empty_directory:/home exec contscout_latest.sif updateDB -i

Also, please do not forget to mount a write-able temp folder too, when starting singularity

Hope the hint fits and solves your issue. Please let me know if it helps and then I add a description to the portal too, so that this error will be covered for all users.

Balazs

On Tue, 21 May 2024 at 09:59, odethier-ulb @.***> wrote:

Hello,

I have an issue while trying to install a database (uniref90) using a singularity image built from the latest docker image, it also appears with a simple updateDB -i.

Here are the commands I typed:

i. singularity build contscout_latest.sif docker://h836472/contscout:latest (downloaded and built this 05/21/2024) ii. singularity exec contscout_latest.sif updateDB -i

And the output I have:

During startup - Warning messages: 1: Setting LC_TIME failed, using "C" 2: Setting LC_MONETARY failed, using "C" 3: Setting LC_PAPER failed, using "C" 4: Setting LC_MEASUREMENT failed, using "C" This is the database updater component of ContScout. Loading R libraries. Error: package or namespace load failed for ‘googlesheets4’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): namespace ‘glue’ 1.4.1 is already loaded, but >= 1.4.2 is required Execution halted

Is it possible to update the docker image or provide a workaround to install a database?

Regards

— Reply to this email directly, view it on GitHub https://github.com/h836472/ContScout/issues/4, or unsubscribe https://github.com/notifications/unsubscribe-auth/AL2BSTHWWERBTHA4I54ECLTZDL5ENAVCNFSM6AAAAABIBC4WEKVHI2DSMVQWIX3LMV43ASLTON2WKOZSGMYDONRQHEYDCMY . You are receiving this because you are subscribed to this thread.Message ID: @.***>

odethier-ulb commented 5 months ago

Thank you, indeed by mounting a new home it seems to be running now.