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virtualstaticvoid/.a-heroku-buildpack-r-issue-142

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heroku-buildpack-r issue #142
Raw
README.md

Replicating Issue #142

virtualstaticvoid/heroku-buildpack-r#142

Description

From issue description:

I'm currently using this build-pack to host a shiny application on Heroku. I need this app to have some basic authentication, so I found a library called "shinymanager" which works exactly like I want it too. This library is hosted on the CRAN and can be found here.

I first tried to install shiny manager through the recommended init.R file using the helpers.installPackages() command. This did not work, so I then tried to install shiny manager locally by including the tar.gz file in my build. I tried putting it in the main directory, as well as creating a folder called localpckgs, neither of these worked. I also made sure to include "/app" in front of the path of the file, this also did not work.

I'm not sure why this package won't install, every time I build I get the error "there is no library called shinymanager". I think it works with the R version being used, so not sure what other issues there could be.

Usage

Create and configure the application:

heroku create --stack heroku-18
heroku buildpacks:add https://github.com/virtualstaticvoid/heroku-buildpack-r.git

Optionally, enable debugging:

heroku config:set BUILDPACK_DEBUG=1

Deploy the application:

git push heroku main

Check application logs:

heroku logs

View application in web browser:

heroku open

License

MIT License. Copyright (c) 2021 Chris Stefano. See LICENSE for details.

Raw
Aptfile
libsqlite3-0
libsqlite3-dev
libssl-dev
Raw
init.R
# install additional packages, using helper function
# helpers.installPackages("shiny", "shinymanager")
# install RSQLite but don't test load so we can inspect the outputs
install.packages("RSQLite", INSTALL_opts=c("--no-test-load"))
Raw
LICENSE
MIT License
Copyright (c) 2021 Chris Stefano
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
Raw
run.R
library(shiny)
port <- Sys.getenv('PORT')
shiny::runApp(
appDir = getwd(),
host = '0.0.0.0',
port = as.numeric(port)
)
Raw
server.R
library(shiny)
library(shinymanager)
# example from http://shiny.rstudio.com/gallery/kmeans-example.html
# combined with https://datastorm-open.github.io/shinymanager/
# **** FOR EXAMPLE PURPOSES ONLY ****
# define admin credentials
# See https://datastorm-open.github.io/shinymanager/#secure-database
credentials <- data.frame(
user = c("admin", "user"),
password = c("p@ssw0rd", "p@ssw0rd"),
admin = c(TRUE, FALSE)
)
palette(c("#E41A1C", "#377EB8", "#4DAF4A", "#984EA3", "#FF7F00", "#FFFF33", "#A65628", "#F781BF", "#999999"))
# Define server logic required to generate and plot a random distribution
server <- shinyServer(function(input, output, session) {
# check_credentials returns a function to authenticate users
res_auth <- secure_server(
check_credentials = check_credentials(credentials)
)
output$auth_output <- renderPrint({
reactiveValuesToList(res_auth)
})
# Combine the selected variables into a new data frame
selectedData <- reactive({
iris[, c(input$xcol, input$ycol)]
})
clusters <- reactive({
kmeans(selectedData(), input$clusters)
})
output$plot1 <- renderPlot({
par(mar = c(5.1, 4.1, 0, 1))
plot(selectedData(),
col = clusters()$cluster,
pch = 20, cex = 3)
points(clusters()$centers, pch = 4, cex = 4, lwd = 4)
})
})
Raw
TROUBLESHOOTING.md

Troubleshooting

R builds RSQLite package succesfully, but unable to load during test stage.

Error: package or namespace load failed for ‘RSQLite’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/app/R/site-library/00LOCK-RSQLite/00new/RSQLite/libs/RSQLite.so':
  /app/R/site-library/00LOCK-RSQLite/00new/RSQLite/libs/RSQLite.so: undefined symbol: stat64
Error: loading failed

Error is undefined symbol: stat64 which means RSQLite.so is referencing a non-exported symbol, possibly from libc.

Debugging

Turn off package load test:

install.packages("RSQLite", INSTALL_opts=c("--no-test-load"))

git push heroku main

Build log excerpt:

...
remote:
remote:        * installing *source* package ‘RSQLite’ ...
remote:        ** package ‘RSQLite’ successfully unpacked and MD5 sums checked
remote:        ** using staged installation
remote:        ** libs
remote:        g++ -std=gnu++11 -I"/app/R/lib/R/include" -DNDEBUG -I. -Ivendor -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/app/R/site-library/plogr/include' -I'/app/R/site-library/Rcpp/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c DbColumn.cpp -o DbColumn.o
remote:        g++ -std=gnu++11 -I"/app/R/lib/R/include" -DNDEBUG -I. -Ivendor -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/app/R/site-library/plogr/include' -I'/app/R/site-library/Rcpp/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c DbColumnDataSource.cpp -o DbColumnDataSource.o
remote:        g++ -std=gnu++11 -I"/app/R/lib/R/include" -DNDEBUG -I. -Ivendor -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/app/R/site-library/plogr/include' -I'/app/R/site-library/Rcpp/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c DbColumnDataSourceFactory.cpp -o DbColumnDataSourceFactory.o
remote:        g++ -std=gnu++11 -I"/app/R/lib/R/include" -DNDEBUG -I. -Ivendor -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/app/R/site-library/plogr/include' -I'/app/R/site-library/Rcpp/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c DbColumnStorage.cpp -o DbColumnStorage.o
remote:        g++ -std=gnu++11 -I"/app/R/lib/R/include" -DNDEBUG -I. -Ivendor -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/app/R/site-library/plogr/include' -I'/app/R/site-library/Rcpp/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c DbConnection.cpp -o DbConnection.o
remote:        g++ -std=gnu++11 -I"/app/R/lib/R/include" -DNDEBUG -I. -Ivendor -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/app/R/site-library/plogr/include' -I'/app/R/site-library/Rcpp/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c DbDataFrame.cpp -o DbDataFrame.o
remote:        In file included from DbDataFrame.cpp:7:0:
remote:        vendor/boost/bind.hpp:41:1: note: #pragma message: The practice of declaring the Bind placeholders (_1, _2, ...) in the global namespace is deprecated. Please use <boost/bind/bind.hpp> + using namespace boost::placeholders, or define BOOST_BIND_GLOBAL_PLACEHOLDERS to retain the current behavior.
remote:         )
remote:         ^
remote:        g++ -std=gnu++11 -I"/app/R/lib/R/include" -DNDEBUG -I. -Ivendor -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/app/R/site-library/plogr/include' -I'/app/R/site-library/Rcpp/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c DbResult.cpp -o DbResult.o
remote:        g++ -std=gnu++11 -I"/app/R/lib/R/include" -DNDEBUG -I. -Ivendor -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/app/R/site-library/plogr/include' -I'/app/R/site-library/Rcpp/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c RcppExports.cpp -o RcppExports.o
remote:        g++ -std=gnu++11 -I"/app/R/lib/R/include" -DNDEBUG -I. -Ivendor -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/app/R/site-library/plogr/include' -I'/app/R/site-library/Rcpp/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c SqliteColumnDataSource.cpp -o SqliteColumnDataSource.o
remote:        g++ -std=gnu++11 -I"/app/R/lib/R/include" -DNDEBUG -I. -Ivendor -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/app/R/site-library/plogr/include' -I'/app/R/site-library/Rcpp/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c SqliteColumnDataSourceFactory.cpp -o SqliteColumnDataSourceFactory.o
remote:        g++ -std=gnu++11 -I"/app/R/lib/R/include" -DNDEBUG -I. -Ivendor -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/app/R/site-library/plogr/include' -I'/app/R/site-library/Rcpp/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c SqliteDataFrame.cpp -o SqliteDataFrame.o
remote:        g++ -std=gnu++11 -I"/app/R/lib/R/include" -DNDEBUG -I. -Ivendor -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/app/R/site-library/plogr/include' -I'/app/R/site-library/Rcpp/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c SqliteResult.cpp -o SqliteResult.o
remote:        g++ -std=gnu++11 -I"/app/R/lib/R/include" -DNDEBUG -I. -Ivendor -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/app/R/site-library/plogr/include' -I'/app/R/site-library/Rcpp/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c SqliteResultImpl.cpp -o SqliteResultImpl.o
remote:        gcc -I"/app/R/lib/R/include" -DNDEBUG -I. -Ivendor -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/app/R/site-library/plogr/include' -I'/app/R/site-library/Rcpp/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c affinity.c -o affinity.o
remote:        g++ -std=gnu++11 -I"/app/R/lib/R/include" -DNDEBUG -I. -Ivendor -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/app/R/site-library/plogr/include' -I'/app/R/site-library/Rcpp/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c connection.cpp -o connection.o
remote:        gcc -I"/app/R/lib/R/include" -DNDEBUG -I. -Ivendor -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/app/R/site-library/plogr/include' -I'/app/R/site-library/Rcpp/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c extension-functions.c -o extension-functions.o
remote:        g++ -std=gnu++11 -I"/app/R/lib/R/include" -DNDEBUG -I. -Ivendor -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/app/R/site-library/plogr/include' -I'/app/R/site-library/Rcpp/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c extensions.cpp -o extensions.o
remote:        gcc -I"/app/R/lib/R/include" -DNDEBUG -I. -Ivendor -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/app/R/site-library/plogr/include' -I'/app/R/site-library/Rcpp/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c import-file.c -o import-file.o
remote:        gcc -I"/app/R/lib/R/include" -DNDEBUG -I. -Ivendor -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/app/R/site-library/plogr/include' -I'/app/R/site-library/Rcpp/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c regexp.c -o regexp.o
remote:        g++ -std=gnu++11 -I"/app/R/lib/R/include" -DNDEBUG -I. -Ivendor -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/app/R/site-library/plogr/include' -I'/app/R/site-library/Rcpp/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c result.cpp -o result.o
remote:        g++ -std=gnu++11 -I"/app/R/lib/R/include" -DNDEBUG -I. -Ivendor -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/app/R/site-library/plogr/include' -I'/app/R/site-library/Rcpp/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c rsqlite.cpp -o rsqlite.o
remote:        gcc -I"/app/R/lib/R/include" -DNDEBUG -I. -Ivendor -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -DSQLITE_MAX_LENGTH=2147483647 -DHAVE_USLEEP=1 -I'/app/R/site-library/plogr/include' -I'/app/R/site-library/Rcpp/include' -I/usr/local/include  -fvisibility=hidden -fpic  -g -O2  -c vendor/sqlite3/sqlite3.c -o vendor/sqlite3/sqlite3.o
remote:        g++ -std=gnu++11 -shared -L/app/R/lib/R/lib -L/usr/local/lib -o RSQLite.so DbColumn.o DbColumnDataSource.o DbColumnDataSourceFactory.o DbColumnStorage.o DbConnection.o DbDataFrame.o DbResult.o RcppExports.o SqliteColumnDataSource.o SqliteColumnDataSourceFactory.o SqliteDataFrame.o SqliteResult.o SqliteResultImpl.o affinity.o connection.o extension-functions.o extensions.o import-file.o regexp.o result.o rsqlite.o vendor/sqlite3/sqlite3.o -L/app/R/lib/R/lib -lR
remote:        installing to /app/R/site-library/00LOCK-RSQLite/00new/RSQLite/libs
remote:        ** R
remote:        ** inst
remote:        ** byte-compile and prepare package for lazy loading
remote:        ** help
remote:        *** installing help indices
remote:        ** building package indices
remote:        ** installing vignettes
remote:        ** checking absolute paths in shared objects and dynamic libraries
remote:        * DONE (RSQLite)
...

Now get a console to inspect the slug:

heroku run /bin/bash

Check package outputs:

ls -ahl R/site-library/RSQLite/libs

Inspect RSQLite.so shared library:

ldd R/site-library/RSQLite/libs/RSQLite.so

      linux-vdso.so.1 (0x00007ffdef853000)
      libR.so => /app/R/lib/R/lib/libR.so (0x00007fc5fc095000)
      libstdc++.so.6 => /app/R/lib/R/lib/libstdc++.so.6 (0x00007fc5fbd0c000)
      libm.so.6 => /app/R/lib/R/lib/libm.so.6 (0x00007fc5fb96e000)
      libgcc_s.so.1 => /app/R/lib/R/lib/libgcc_s.so.1 (0x00007fc5fb756000)
      libc.so.6 => /app/R/lib/R/lib/libc.so.6 (0x00007fc5fb365000)
      libblas.so.3 => /app/R/lib/R/lib/libblas.so.3 (0x00007fc5fb10a000)
      libreadline.so.7 => /app/R/lib/R/lib/libreadline.so.7 (0x00007fc5faec1000)
      libpcre2-8.so.0 => /app/R/lib/R/lib/libpcre2-8.so.0 (0x00007fc5fac3f000)
      liblzma.so.5 => /app/R/lib/R/lib/liblzma.so.5 (0x00007fc5faa19000)
      libbz2.so.1.0 => /app/R/lib/R/lib/libbz2.so.1.0 (0x00007fc5fa809000)
      libz.so.1 => /app/R/lib/R/lib/libz.so.1 (0x00007fc5fa5ec000)
      librt.so.1 => /app/R/lib/R/lib/librt.so.1 (0x00007fc5fa3e4000)
      libdl.so.2 => /app/R/lib/R/lib/libdl.so.2 (0x00007fc5fa1e0000)
      libicuuc.so.60 => /app/R/lib/R/lib/libicuuc.so.60 (0x00007fc5f9e28000)
      libicui18n.so.60 => /app/R/lib/R/lib/libicui18n.so.60 (0x00007fc5f9987000)
      libgomp.so.1 => /app/R/lib/R/lib/libgomp.so.1 (0x00007fc5f9758000)
      libpthread.so.0 => /app/R/lib/R/lib/libpthread.so.0 (0x00007fc5f9539000)
      /lib64/ld-linux-x86-64.so.2 (0x00007fc5fcaa7000)
      libopenblas.so.0 => /app/R/lib/R/lib/libopenblas.so.0 (0x00007fc5f7293000)
      libtinfo.so.5 => /app/R/lib/R/lib/libtinfo.so.5 (0x00007fc5f7069000)
      libicudata.so.60 => /app/R/lib/R/lib/libicudata.so.60 (0x00007fc5f54c0000)
      libgfortran.so.4 => /app/R/lib/R/lib/libgfortran.so.4 (0x00007fc5f50e1000)
      libquadmath.so.0 => /app/R/lib/R/lib/libquadmath.so.0 (0x00007fc5f4ea1000)

readelf -d R/site-library/RSQLite/libs/RSQLite.so

Dynamic section at offset 0x16ac68 contains 28 entries:
  Tag        Type                         Name/Value
 0x0000000000000001 (NEEDED)             Shared library: [libR.so]
 0x0000000000000001 (NEEDED)             Shared library: [libstdc++.so.6]
 0x0000000000000001 (NEEDED)             Shared library: [libm.so.6]
 0x0000000000000001 (NEEDED)             Shared library: [libgcc_s.so.1]
 0x0000000000000001 (NEEDED)             Shared library: [libc.so.6]

 ...

nm -D R/site-library/RSQLite/libs/RSQLite.so | grep stat

...

      U _ZNSt15basic_streambufIcSt11char_traitsIcEE7seekposESt4fposI11__mbstate_tESt13_Ios_Openmode
      U _ZNSt9basic_iosIcSt11char_traitsIcEE5clearESt12_Ios_Iostate
      U fstat64
      U lstat64
      U stat64

...

LD_DEBUG=symbols R --no-save -e "library(RSQLite)" 2> symbols.log

cat symbols.log | grep stat64

       133: symbol=__xstat64;  lookup in file=sh [0]
       133: symbol=__xstat64;  lookup in file=/app/R/lib/R/lib/libc.so.6 [0]
       133: symbol=__fxstat64;  lookup in file=sh [0]
       133: symbol=__fxstat64;  lookup in file=/app/R/lib/R/lib/libc.so.6 [0]
       133: symbol=__lxstat64;  lookup in file=sh [0]
       133: symbol=__lxstat64;  lookup in file=/app/R/lib/R/lib/libc.so.6 [0]
       135: symbol=__xstat64;  lookup in file=sh [0]
       135: symbol=__xstat64;  lookup in file=/app/R/lib/R/lib/libc.so.6 [0]
       135: symbol=__fxstat64;  lookup in file=sh [0]
       135: symbol=__fxstat64;  lookup in file=/app/R/lib/R/lib/libc.so.6 [0]
       135: symbol=__lxstat64;  lookup in file=sh [0]
       135: symbol=__lxstat64;  lookup in file=/app/R/lib/R/lib/libc.so.6 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/bin/exec/R [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libR.so [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libc.so.6 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libblas.so.3 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libm.so.6 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libreadline.so.7 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libpcre2-8.so.0 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/liblzma.so.5 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libbz2.so.1.0 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libz.so.1 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/librt.so.1 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libdl.so.2 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libicuuc.so.60 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libicui18n.so.60 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libgomp.so.1 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libpthread.so.0 [0]
       117: symbol=stat64;  lookup in file=/lib64/ld-linux-x86-64.so.2 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libopenblas.so.0 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libtinfo.so.5 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libicudata.so.60 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libstdc++.so.6 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libgcc_s.so.1 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libgfortran.so.4 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libquadmath.so.0 [0]
       117: symbol=stat64;  lookup in file=/app/R/site-library/RSQLite/libs/RSQLite.so [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libR.so [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libstdc++.so.6 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libm.so.6 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libgcc_s.so.1 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libc.so.6 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libblas.so.3 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libreadline.so.7 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libpcre2-8.so.0 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/liblzma.so.5 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libbz2.so.1.0 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libz.so.1 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/librt.so.1 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libdl.so.2 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libicuuc.so.60 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libicui18n.so.60 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libgomp.so.1 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libpthread.so.0 [0]
       117: symbol=stat64;  lookup in file=/lib64/ld-linux-x86-64.so.2 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libopenblas.so.0 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libtinfo.so.5 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libicudata.so.60 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libgfortran.so.4 [0]
       117: symbol=stat64;  lookup in file=/app/R/lib/R/lib/libquadmath.so.0 [0]
       117: /app/R/site-library/RSQLite/libs/RSQLite.so: error: symbol lookup error: undefined symbol: stat64 (fatal)
  /app/R/site-library/RSQLite/libs/RSQLite.so: undefined symbol: stat64
       137: symbol=__xstat64;  lookup in file=sh [0]
       137: symbol=__xstat64;  lookup in file=/app/R/lib/R/lib/libc.so.6 [0]
       137: symbol=__fxstat64;  lookup in file=sh [0]
       137: symbol=__fxstat64;  lookup in file=/app/R/lib/R/lib/libc.so.6 [0]
       137: symbol=__lxstat64;  lookup in file=sh [0]
       137: symbol=__lxstat64;  lookup in file=/app/R/lib/R/lib/libc.so.6 [0]
...

LD_DEBUG=bindings R --no-save -e "library(RSQLite)" 2> bindings.log

cat bindings.log | grep stat64

        23: binding file sh [0] to /app/R/lib/R/lib/libc.so.6 [0]: normal symbol `__xstat64' [GLIBC_2.2.5]
        23: binding file sh [0] to /app/R/lib/R/lib/libc.so.6 [0]: normal symbol `__fxstat64' [GLIBC_2.2.5]
        23: binding file sh [0] to /app/R/lib/R/lib/libc.so.6 [0]: normal symbol `__lxstat64' [GLIBC_2.2.5]
        25: binding file sh [0] to /app/R/lib/R/lib/libc.so.6 [0]: normal symbol `__xstat64' [GLIBC_2.2.5]
        25: binding file sh [0] to /app/R/lib/R/lib/libc.so.6 [0]: normal symbol `__fxstat64' [GLIBC_2.2.5]
        25: binding file sh [0] to /app/R/lib/R/lib/libc.so.6 [0]: normal symbol `__lxstat64' [GLIBC_2.2.5]
         7: /app/R/site-library/RSQLite/libs/RSQLite.so: error: symbol lookup error: undefined symbol: stat64 (fatal)
  /app/R/site-library/RSQLite/libs/RSQLite.so: undefined symbol: stat64
        27: binding file sh [0] to /app/R/lib/R/lib/libc.so.6 [0]: normal symbol `__xstat64' [GLIBC_2.2.5]
        27: binding file sh [0] to /app/R/lib/R/lib/libc.so.6 [0]: normal symbol `__fxstat64' [GLIBC_2.2.5]
        27: binding file sh [0] to /app/R/lib/R/lib/libc.so.6 [0]: normal symbol `__lxstat64' [GLIBC_2.2.5]

Inspect libc.so.6:

nm -D R/lib/R/lib/libc.so.6 | grep stat64

000000000010f8c0 T __fxstat64
000000000010f910 T __lxstat64
000000000010f870 T __xstat64

Inspecting RSQLite.so on a working setup:

docker run -it r-base:4.0.0 /bin/bash

R --no-save -e 'install.packages("RSQLite")'

nm -D /usr/local/lib/R/site-library/RSQLite/libs/RSQLite.so | grep stat

     U __fxstat64
     U __lxstat64
     U __xstat64
     U _ZNSt15basic_streambufIcSt11char_traitsIcEE7seekposESt4fposI11__mbstate_tESt13_Ios_Openmode
     U _ZNSt9basic_iosIcSt11char_traitsIcEE5clearESt12_Ios_Iostate

Why isn't RSQLite.so importing __xstat64 instead of stat64?

stat64(2) - Linux man page vs xstat64 - Large file support

Need to debug the build process, when RSQLite.so is created.

Raw
ui.R
library(shiny)
library(shinymanager)
# example from http://shiny.rstudio.com/gallery/kmeans-example.html
# combined with https://datastorm-open.github.io/shinymanager/
# Define UI for application that plots random distributions
page <- pageWithSidebar(
headerPanel('Iris k-means clustering'),
sidebarPanel(
selectInput('xcol', 'X Variable', names(iris)),
selectInput('ycol', 'Y Variable', names(iris),
selected=names(iris)[[2]]),
numericInput('clusters', 'Cluster count', 3,
min = 1, max = 9)
),
mainPanel(
plotOutput('plot1')
)
)
# Wrap your UI with secure_app
ui <- secure_app(page, enable_admin = TRUE)
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