search

ncihtan / HTAN-data-curator

HTAN Data Ingest Shiny App
https://sagebio.shinyapps.io/HTAN-data-curator/
Apache License 2.0
1 stars 0 forks source link

shiny-deploy fails #41

Closed adamjtaylor closed 1 year ago

adamjtaylor commented 1 year ago

Manual activation of the shiny-deploy workflow fails with the error:

* Application depends on package "stringr" but it is not installed.

https://github.com/ncihtan/HTAN-data-curator/actions/runs/3488295771/jobs/5837162891#step:12:41

adamjtaylor commented 1 year ago

stringr is being installed it seems: https://github.com/ncihtan/HTAN-data-curator/actions/runs/3488295771/jobs/5837162891#step:7:36

adamjtaylor commented 1 year ago

Although it looks like that installation fails

Downloading package from url: https://packagemanager.rstudio.com/all/__linux__/bionic/latest/src/contrib/Archive/stringr/stringr_1.4.0.tar.gz
Installing 1 packages: stringi
stringi (NA -> 1.7.8) [CRAN]
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://packagemanager.rstudio.com/all/__linux__/bionic/latest/src/contrib/stringi_1.7.8.tar.gz'
Content type 'binary/octet-stream' length 2741522 bytes (2.6 MB)
==================================================
downloaded 2.6 MB

* installing *binary* package ‘stringi’ ...
* DONE (stringi)

The downloaded source packages are in
    ‘/tmp/RtmpuWPR7J/downloaded_packages’
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
* installing *source* package ‘stringr’ ...
** package ‘stringr’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/usr/local/lib/R/site-library/stringi/libs/stringi.so':
  libicui18n.so.60: cannot open shared object file: No such file or directory
Calls: <Anonymous> ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
Execution halted
ERROR: lazy loading failed for package ‘stringr’
* removing ‘/usr/local/lib/R/site-library/stringr’
adamjtaylor commented 1 year ago

Triggering from a commit rather than the manual deployment also leads to job faliure. https://github.com/ncihtan/HTAN-data-curator/actions/runs/3488651126/jobs/5837738999

adamjtaylor commented 1 year ago

Note that the action was running successfully as of 2 days ago For example: https://github.com/ncihtan/HTAN-data-curator/actions/runs/3470945037/jobs/5800318318#step:7:493

Downloading package from url: https://packagemanager.rstudio.com/all/__linux__/bionic/latest/src/contrib/Archive/stringr/stringr_1.4.0.tar.gz
Installing 1 packages: stringi
stringi (NA -> 1.7.8) [CRAN]
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'https://packagemanager.rstudio.com/all/__linux__/bionic/latest/src/contrib/stringi_1.7.8.tar.gz'
Content type 'binary/octet-stream' length 2741522 bytes (2.6 MB)
==================================================
downloaded 2.6 MB

* installing *binary* package ‘stringi’ ...
* DONE (stringi)

The downloaded source packages are in
    ‘/tmp/RtmpVDp661/downloaded_packages’
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
* installing *binary* package ‘stringr’ ...
* DONE (stringr)
adamjtaylor commented 1 year ago

FYI @aclayton555, @elv-sb and @milen-sage. I am going to open a FAIR service desk ticket on this as it is blocking https://github.com/ncihtan/data-release-tracker/issues/486 for data release 3 which needs https://github.com/ncihtan/data-models/pull/128 to be used in staging.

adamjtaylor commented 1 year ago

D&T service desk Work Request for FAIR data opened for this: IBCSPRT-107

adamjtaylor commented 1 year ago

A fix was deployed in https://github.com/Sage-Bionetworks/data_curator/releases/tag/v22.11.2 and this is now in staging. Thank you @milen-sage and @afwillia!