... I cannot publish to RSConnect even the most basic app. I used to publish with ease. The problem happens during the Deploying Bundle step. RSConnect starts to installed required packages, then it blocks when it tries to install the later package.
This is the error message:
[Connect] 2021/04/23 13:04:41.909670026 Installing later (1.1.0.1) ...
[Connect] 2021/04/23 13:04:42.424743205 curl: HTTP 200 https://stat.ethz.ch/CRAN/src/contrib/PACKAGES.rds
[Connect] 2021/04/23 13:04:43.184476060 curl: HTTP 200 http://cedar.gene.com/gran/tst/src/contrib/PACKAGES.rds
[Connect] 2021/04/23 13:04:44.809901588 curl: HTTP 200 https://stat.ethz.ch/CRAN/src/contrib/later_1.1.0.1.tar.gz
[Connect] 2021/04/23 13:04:51.586132860 [1] "Command failed (1)\n\nFailed to run system command:\n\n\t'/opt/bee_tools/R/3.6.3/lib64/R/bin/R' --vanilla CMD INSTALL --preclean '/opt/rstudio-connect/mnt/tmp/Rtmp7SJ6rB/packrat-install-ca7240a6f20/later' --library='/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3' --install-tests --no-docs --no-multiarch --no-demo \n\nThe command failed with output:\n* installing *source* package ‘later’ ...\n** package ‘later’ successfully unpacked and MD5 sums checked\n** using staged installation\nRunning configure script\n-latomic linker flag not needed.\n** libs\ng++ -std=gnu++11 -I\"/opt/bee_tools/R/3.6.3/lib64/R/include\" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I\"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/Rcpp/include\" -I\"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/BH/include\" -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o\ng++ -std=gnu++11 -I\"/opt/bee_tools/R/3.6.3/lib64/R/include\"
[Connect] -DNDEBUG -pthread -DSTRICT_R_HEADERS -I\"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/Rcpp/include\" -I\"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/BH/include\" -I/usr/local/include -fpic -g -O2 -c callback_registry.cpp -o callback_registry.o\ng++ -std=gnu++11 -I\"/opt/bee_tools/R/3.6.3/lib64/R/include\" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I\"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/Rcpp/include\" -I\"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/BH/include\" -I/usr/local/include -fpic -g -O2 -c debug.cpp -o debug.o\ngcc -std=gnu99 -I\"/opt/bee_tools/R/3.6.3/lib64/R/include\" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I\"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/Rcpp/include\" -I\"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/BH/include\" -I/usr/local/include -fpic -g -O2 -c init.c -o init.o\ng++ -std=gnu++11 -I\"/opt/bee_tools/R/3.6.3/lib64/R/include\" -DNDEBUG -pt
[Connect] hread -DSTRICT_R_HEADERS -I\"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/Rcpp/include\" -I\"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/BH/include\" -I/usr/local/include -fpic -g -O2 -c later.cpp -o later.o\ng++ -std=gnu++11 -I\"/opt/bee_tools/R/3.6.3/lib64/R/include\" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I\"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/Rcpp/include\" -I\"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/BH/include\" -I/usr/local/include -fpic -g -O2 -c later_posix.cpp -o later_posix.o\ng++ -std=gnu++11 -I\"/opt/bee_tools/R/3.6.3/lib64/R/include\" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I\"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/Rcpp/include\" -I\"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/BH/include\" -I/usr/local/include -fpic -g -O2 -c later_win32.cpp -o later_win32.o\ng++ -std=gnu++11 -I\"/opt/bee_tools/R/3.6.3/lib64/R/include\" -DNDEBUG -pthread -
[Connect] DSTRICT_R_HEADERS -I\"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/Rcpp/include\" -I\"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/BH/include\" -I/usr/local/include -fpic -g -O2 -c timer_posix.cpp -o timer_posix.o\ng++ -std=gnu++11 -I\"/opt/bee_tools/R/3.6.3/lib64/R/include\" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I\"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/Rcpp/include\" -I\"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/BH/include\" -I/usr/local/include -fpic -g -O2 -c timestamp_unix.cpp -o timestamp_unix.o\ng++ -std=gnu++11 -I\"/opt/bee_tools/R/3.6.3/lib64/R/include\" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I\"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/Rcpp/include\" -I\"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/BH/include\" -I/usr/local/include -fpic -g -O2 -c timestamp_win32.cpp -o timestamp_win32.o\ngcc -std=gnu99 -I\"/opt/bee_tools/R/3.6.3/lib64/R/include\" -D
[Connect] NDEBUG -pthread -DSTRICT_R_HEADERS -I\"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/Rcpp/include\" -I\"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/BH/include\" -I/usr/local/include -fpic -g -O2 -c tinycthread.c -o tinycthread.o\ng++ -std=gnu++11 -shared -L/opt/bee_tools/R/3.6.3/lib64/R/lib -L/usr/local/lib64 -o later.so RcppExports.o callback_registry.o debug.o init.o later.o later_posix.o later_win32.o timer_posix.o timestamp_unix.o timestamp_win32.o tinycthread.o -pthread -L/opt/bee_tools/R/3.6.3/lib64/R/lib -lR\ninstalling to /opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/00LOCK-later/00new/later/libs\n** R\n** inst\n** tests\n** byte-compile and prepare package for lazy loading\nError in dyn.load(file, DLLpath = DLLpath, ...) : \n unable to load shared object '/opt/rstudio-connect/mnt/packrat/3.6.3/v2/library/Rcpp/d891b607ea796cf30abfe4795380423f/Rcpp/libs/Rcpp.so':\n /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required b
[Connect] y /opt/rstudio-connect/mnt/packrat/3.6.3/v2/library/Rcpp/d891b607ea796cf30abfe4795380423f/Rcpp/libs/Rcpp.so)\nCalls: <Anonymous> ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load\nExecution halted\nERROR: lazy loading failed for package ‘later’\n* removing ‘/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/later’"
[Connect] 2021/04/23 13:04:51.589245067 Error: Command failed (1)
[Connect] 2021/04/23 13:04:51.589251088
[Connect] 2021/04/23 13:04:51.589273749 Failed to run system command:
[Connect] 2021/04/23 13:04:51.589274767
[Connect] 2021/04/23 13:04:51.589284132 '/opt/bee_tools/R/3.6.3/lib64/R/bin/R' --vanilla CMD INSTALL --preclean '/opt/rstudio-connect/mnt/tmp/Rtmp7SJ6rB/packrat-install-ca7240a6f20/later' --library='/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3' --install-tests --no-docs --no-multiarch --no-demo
[Connect] 2021/04/23 13:04:51.589296294
[Connect] 2021/04/23 13:04:51.589328777 The command failed with output:
[Connect] 2021/04/23 13:04:51.589331705 * installing *source* package ‘later’ ...
[Connect] 2021/04/23 13:04:51.589354598 ** package ‘later’ successfully unpacked and MD5 sums checked
[Connect] 2021/04/23 13:04:51.589356317 ** using staged installation
[Connect] 2021/04/23 13:04:51.589373309 Running configure script
[Connect] 2021/04/23 13:04:51.589374145 -latomic linker flag not needed.
[Connect] 2021/04/23 13:04:51.589393590 ** libs
[Connect] 2021/04/23 13:04:51.589444717 g++ -std=gnu++11 -I"/opt/bee_tools/R/3.6.3/lib64/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/Rcpp/include" -I"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/BH/include" -I/usr/local/include -fpic -g -O2 -c RcppExports.cpp -o RcppExports.o
[Connect] 2021/04/23 13:04:51.589495560 g++ -std=gnu++11 -I"/opt/bee_tools/R/3.6.3/lib64/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/Rcpp/include" -I"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/BH/include" -I/usr/local/include -fpic -g -O2 -c callback_registry.cpp -o callback_registry.o
[Connect] 2021/04/23 13:04:51.589514696 g++ -std=gnu++11 -I"/opt/bee_tools/R/3.6.3/lib64/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/Rcpp/include" -I"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/BH/include" -I/usr/local/include -fpic -g -O2 -c debug.cpp -o debug.o
[Connect] 2021/04/23 13:04:51.589531709 gcc -std=gnu99 -I"/opt/bee_tools/R/3.6.3/lib64/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/Rcpp/include" -I"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/BH/include" -I/usr/local/include -fpic -g -O2 -c init.c -o init.o
[Connect] 2021/04/23 13:04:51.589537407 g++ -std=gnu++11 -I"/opt/bee_tools/R/3.6.3/lib64/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/Rcpp/include" -I"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/BH/include" -I/usr/local/include -fpic -g -O2 -c later.cpp -o later.o
[Connect] 2021/04/23 13:04:51.589547332 g++ -std=gnu++11 -I"/opt/bee_tools/R/3.6.3/lib64/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/Rcpp/include" -I"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/BH/include" -I/usr/local/include -fpic -g -O2 -c later_posix.cpp -o later_posix.o
[Connect] 2021/04/23 13:04:51.589547998 g++ -std=gnu++11 -I"/opt/bee_tools/R/3.6.3/lib64/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/Rcpp/include" -I"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/BH/include" -I/usr/local/include -fpic -g -O2 -c later_win32.cpp -o later_win32.o
[Connect] 2021/04/23 13:04:51.589557411 g++ -std=gnu++11 -I"/opt/bee_tools/R/3.6.3/lib64/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/Rcpp/include" -I"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/BH/include" -I/usr/local/include -fpic -g -O2 -c timer_posix.cpp -o timer_posix.o
[Connect] 2021/04/23 13:04:51.589558037 g++ -std=gnu++11 -I"/opt/bee_tools/R/3.6.3/lib64/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/Rcpp/include" -I"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/BH/include" -I/usr/local/include -fpic -g -O2 -c timestamp_unix.cpp -o timestamp_unix.o
[Connect] 2021/04/23 13:04:51.589567324 g++ -std=gnu++11 -I"/opt/bee_tools/R/3.6.3/lib64/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/Rcpp/include" -I"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/BH/include" -I/usr/local/include -fpic -g -O2 -c timestamp_win32.cpp -o timestamp_win32.o
[Connect] 2021/04/23 13:04:51.589577030 gcc -std=gnu99 -I"/opt/bee_tools/R/3.6.3/lib64/R/include" -DNDEBUG -pthread -DSTRICT_R_HEADERS -I"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/Rcpp/include" -I"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/BH/include" -I/usr/local/include -fpic -g -O2 -c tinycthread.c -o tinycthread.o
[Connect] 2021/04/23 13:04:51.589587301 g++ -std=gnu++11 -shared -L/opt/bee_tools/R/3.6.3/lib64/R/lib -L/usr/local/lib64 -o later.so RcppExports.o callback_registry.o debug.o init.o later.o later_posix.o later_win32.o timer_posix.o timestamp_unix.o timestamp_win32.o tinycthread.o -pthread -L/opt/bee_tools/R/3.6.3/lib64/R/lib -lR
[Connect] 2021/04/23 13:04:51.589587983 installing to /opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/00LOCK-later/00new/later/libs
[Connect] 2021/04/23 13:04:51.589605765 ** R
[Connect] 2021/04/23 13:04:51.589606991 ** inst
[Connect] 2021/04/23 13:04:51.589616544 ** tests
[Connect] 2021/04/23 13:04:51.589617253 ** byte-compile and prepare package for lazy loading
[Connect] 2021/04/23 13:04:51.589626904 Error in dyn.load(file, DLLpath = DLLpath, ...) :
[Connect] 2021/04/23 13:04:51.589628189 unable to load shared object '/opt/rstudio-connect/mnt/packrat/3.6.3/v2/library/Rcpp/d891b607ea796cf30abfe4795380423f/Rcpp/libs/Rcpp.so':
[Connect] 2021/04/23 13:04:51.589641660 /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /opt/rstudio-connect/mnt/packrat/3.6.3/v2/library/Rcpp/d891b607ea796cf30abfe4795380423f/Rcpp/libs/Rcpp.so)
[Connect] 2021/04/23 13:04:51.589651144 Calls: <Anonymous> ... namespaceImport -> loadNamespace -> library.dynam -> dyn.load
[Connect] 2021/04/23 13:04:51.589661367 Execution halted
[Connect] 2021/04/23 13:04:51.589662089 ERROR: lazy loading failed for package ‘later’
[Connect] 2021/04/23 13:04:51.589671402 * removing ‘/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/later’
[Connect] 2021/04/23 13:04:51.589672106
[Connect] 2021/04/23 13:04:51.589681007 Unable to fully restore the R packages associated with this deployment.
[Connect] 2021/04/23 13:04:51.589682007 Please review the preceding messages to determine which package
[Connect] 2021/04/23 13:04:51.589691299 encountered installation difficulty and the cause of the failure.
[Connect] 2021/04/23 13:04:51.587160529 Error code: r-missing-system-library
[Connect] An R package cannot be installed because a required system-level dependency is missing.
[Connect] Possible causes:
[Connect] * An R package requires a system-level dependency, such as a library or executable, which is not installed on the Connect server.
[Connect]
[Connect] Possible solutions:
[Connect] * Install the required package using your system package manager (such as apt or yum).
[Connect] * If you have RStudio Package Manager, open the information page for the affected R package. Installation instructions for the package's system-level dependencies are included under the Install System Prerequisites heading
[Connect] * Otherwise, use the messages in the deployment log to identify which system package you need to install.
[Connect]
[Connect] References:
[Connect] * https://docs.rstudio.com/connect/admin/getting-started/#redhat-package-dependencies
[Connect] * https://docs.rstudio.com/connect/admin/getting-started/#suse-package-dependencies
[Connect] * https://docs.rstudio.com/connect/admin/getting-started/#ubuntu-package-dependencies
[Connect]
[Connect] 2021/04/23 13:04:51.587160529 Additional data:
[Connect] PackageVersion: '1.1.0.1'
[Connect] RequiredFile: '/opt/rstudio-connect/mnt/packrat/3.6.3/v2/library/Rcpp/d891b607ea796cf30abfe4795380423f/Rcpp/libs/Rcpp.so'
[Connect] Package: 'later'
[Connect] Found in the following log entry:
[Connect] NDEBUG -pthread -DSTRICT_R_HEADERS -I\"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/Rcpp/include\" -I\"/opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/BH/include\" -I/usr/local/include -fpic -g -O2 -c tinycthread.c -o tinycthread.o\ng++ -std=gnu++11 -shared -L/opt/bee_tools/R/3.6.3/lib64/R/lib -L/usr/local/lib64 -o later.so RcppExports.o callback_registry.o debug.o init.o later.o later_posix.o later_win32.o timer_posix.o timestamp_unix.o timestamp_win32.o tinycthread.o -pthread -L/opt/bee_tools/R/3.6.3/lib64/R/lib -lR\ninstalling to /opt/rstudio-connect/mnt/app/packrat/lib/x86_64-pc-linux-gnu/3.6.3/00LOCK-later/00new/later/libs\n** R\n** inst\n** tests\n** byte-compile and prepare package for lazy loading\nError in dyn.load(file, DLLpath = DLLpath, ...) : \n unable to load shared object '/opt/rstudio-connect/mnt/packrat/3.6.3/v2/library/Rcpp/d891b607ea796cf30abfe4795380423f/Rcpp/libs/Rcpp.so':\n /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required b
[Connect] Build error: An R package cannot be installed because a required system-level dependency is missing. (r-missing-system-library)
Application deployment failed with error: An R package cannot be installed because a required system-level dependency is missing. (r-missing-system-library)
Warning message:
invalid uid value replaced by that for user 'nobody'
and my R session info
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux
Matrix products: default
BLAS/LAPACK: /usr/lib64/libopenblas-r0.3.3.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] shiny_1.5.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 digest_0.6.27 withr_2.4.1 later_1.1.0.1 mime_0.10 R6_2.5.0 jsonlite_1.7.1 xtable_1.8-4
[9] magrittr_2.0.1 rlang_0.4.8 curl_4.3 promises_1.2.0.1 tools_3.6.3 httpuv_1.5.5 yaml_2.2.1 rsconnect_0.8.16
[17] fastmap_1.0.1 compiler_3.6.3 askpass_1.1 htmltools_0.5.1.1 openssl_1.4.3