We had to upgrade our Ubuntu version for our EC2 instance where we run R and achilles.
After the upgrade we had to upgrade install R latest binaries as Ubuntu upgrade removed older version of R.
Because we upgrade R to the current available version, the SqlRender currently on the instance is not compatible and asking us to upgrade to the latest version of SqlRender.
Below is the log. Anyone faced similar issues before and any help is greatly appreciated.
R --version 19:09.51 Tue Dec 12 2023 >>>
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under the terms of the
GNU General Public License versions 2 or 3.
For more information about these matters see
Licenses - GNU Project - Free Software Foundation.
<<<
<<< ohdsi@ip-10-1-2-161~
Rscript achilles.R 19:09.54 Tue Dec 12 2023 >>>
Loading required package: SqlRender
Error: package or namespace load failed for ‘SqlRender’:
package ‘SqlRender’ was installed before R 4.0.0: please re-install it
Error: package ‘SqlRender’ could not be loaded
Execution halted
<<<
When I try to update SqlRender packages, its stuck here.
<< ohdsi@ip-10-1-2-161~
R 19:10.04 Tue Dec 12 2023 >>>
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
Copyright (C) 2021 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
Natural language support but running in an English locale
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
[Previously saved workspace restored]
install.packages("SqlRender",INSTALL_opts = "--no-multiarch")
Installing package into ‘/home/ohdsi/R/x86_64-pc-linux-gnu-library/4.1’
(as ‘lib’ is unspecified)
trying URL 'https://cloud.r-project.org/src/contrib/SqlRender_1.16.1.tar.gz'
Content type 'application/x-gzip' length 453062 bytes (442 KB)
==================================================
downloaded 442 KB
- installing source package ‘SqlRender’ ...
** package ‘SqlRender’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
converting help for package ‘SqlRender’
finding HTML links ... done
SqlRender-package html
camelCaseToSnakeCase html
camelCaseToSnakeCaseNames html
camelCaseToTitleCase html
createRWrapperForSql html
getTempTablePrefix html
launchSqlRenderDeveloper html
listSupportedDialects html
loadRenderTranslateSql html
readSql html
render html
renderSql html
renderSqlFile html
snakeCaseToCamelCase html
snakeCaseToCamelCaseNames html
sparkHandleInsert html
splitSql html
supportsJava8 html
translate html
translateSingleStatement html
translateSql html
translateSqlFile html
writeSql html
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location