I'm trying to deploy my shiny app using rsconnect:
rsconnect::deployApp(appName = "iatlas-v2-staging")
This seems to have stopped working today. I've deployed this app many times before.
Is this an renv issue?
> rsconnect::deployApp(appName = "iatlas-v2-staging")
The following potential problems were identified in the project files:
The following lines contain paths to files not matching in case sensitivity:
19: "Description", ['Description' -> 'DESCRIPTION']
Filepaths are case-sensitive on deployment server.
Do you want to proceed with deployment? [Y/n]: y
Preparing to deploy application...
Update application currently deployed at
https://isb-cgc.shinyapps.io/iatlas-v2-staging/? [Y/n] y
DONE
Uploading bundle for application: 1861837...DONE
Deploying bundle: 3940100 for application: 1861837 ...
Waiting for task: 834470743
building: Parsing manifest
building: Building image: 4489618
building: Fetching packages
building: Building package: iatlas.modules
################################ Begin Task Log ################################
R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
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.
> install.packages("BiocInstaller", repos="http://www.bioconductor.org/packages/3.12/bioc")
Warning message:
package ‘BiocInstaller’ is not available for this version of R
A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages
>
>
[2020-12-03T21:35:21.062000283+0000] Installing R package: rlang (0.4.9)
* installing to library ‘/opt/R/4.0.3/lib/R/library’
* installing *binary* package ‘rlang’ ...
* DONE (rlang)
[2020-12-03T21:35:21.320700089+0000] Installing R package: viridisLite (0.3.0)
* installing to library ‘/opt/R/4.0.3/lib/R/library’
* installing *binary* package ‘viridisLite’ ...
* DONE (viridisLite)
[2020-12-03T21:35:21.515379369+0000] Installing R package: brew (1.0-6)
* installing to library ‘/opt/R/4.0.3/lib/R/library’
* installing *binary* package ‘brew’ ...
* DONE (brew)
<cut out a lot fo packages to save space>
[2020-12-03T21:36:19.446152250+0000] Installing R package: httpuv (1.5.4)
* installing to library ‘/opt/R/4.0.3/lib/R/library’
* installing *binary* package ‘httpuv’ ...
* DONE (httpuv)
[2020-12-03T21:36:19.999520433+0000] Installing R package: shiny (1.5.0)
* installing to library ‘/opt/R/4.0.3/lib/R/library’
* installing *binary* package ‘shiny’ ...
* DONE (shiny)
[2020-12-03T21:36:20.683068229+0000] Installing R package: shinydashboard (0.7.1)
* installing to library ‘/opt/R/4.0.3/lib/R/library’
* installing *binary* package ‘shinydashboard’ ...
* DONE (shinydashboard)
[2020-12-03T21:36:20.932558580+0000] Installing R package: plotROC (2.2.1)
* installing to library ‘/opt/R/4.0.3/lib/R/library’
* installing *binary* package ‘plotROC’ ...
* DONE (plotROC)
[2020-12-03T21:36:21.243002666+0000] Installing R package: ImmuneSubtypeClassifier (0.1.0)
* installing to library ‘/opt/R/4.0.3/lib/R/library’
* installing *binary* package ‘ImmuneSubtypeClassifier’ ...
* DONE (ImmuneSubtypeClassifier)
[2020-12-03T21:36:21.841298462+0000] Installing R package: shinycssloaders (1.0.0)
* installing to library ‘/opt/R/4.0.3/lib/R/library’
* installing *binary* package ‘shinycssloaders’ ...
* DONE (shinycssloaders)
[2020-12-03T21:36:22.057188958+0000] Installing R package: cyjShiny (1.0.17)
* installing to library ‘/opt/R/4.0.3/lib/R/library’
* installing *binary* package ‘cyjShiny’ ...
* DONE (cyjShiny)
[2020-12-03T21:36:22.505774669+0000] Installing R package: crosstalk (1.1.0.1)
* installing to library ‘/opt/R/4.0.3/lib/R/library’
* installing *binary* package ‘crosstalk’ ...
* DONE (crosstalk)
[2020-12-03T21:36:22.817281036+0000] Installing R package: DT (0.16)
* installing to library ‘/opt/R/4.0.3/lib/R/library’
* installing *binary* package ‘DT’ ...
* DONE (DT)
[2020-12-03T21:36:23.334208372+0000] Installing R package: rsconnect (0.8.16-9002)
* installing to library ‘/opt/R/4.0.3/lib/R/library’
* installing *binary* package ‘rsconnect’ ...
* DONE (rsconnect)
[2020-12-03T21:36:23.562976859+0000] Installing R package: hexbin (1.28.1)
* installing to library ‘/opt/R/4.0.3/lib/R/library’
* installing *binary* package ‘hexbin’ ...
* DONE (hexbin)
[2020-12-03T21:36:23.804522566+0000] Installing R package: plotly (4.9.2.1)
* installing to library ‘/opt/R/4.0.3/lib/R/library’
* installing *binary* package ‘plotly’ ...
* DONE (plotly)
[2020-12-03T21:36:24.325711249+0000] Building R package: iatlas.modules (0.3.1)
/mnt/packages/build /mnt
Warning in untar2(tarfile, files, list, exdir, restore_times) :
skipping pax global extended headers
* installing to library ‘/opt/R/4.0.3/lib/R/library’
* installing *source* package ‘iatlas.modules’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
# Bootstrapping renv 0.12.3 --------------------------------------------------
* Downloading renv 0.12.3 from CRAN ... OK
* Installing renv 0.12.3 ... Done!
Error installing renv:
======================
* installing *source* package ‘renv’ ...
** package ‘renv’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
ERROR: hard-coded installation path: please report to the package maintainer and use ‘--no-staged-install’
* removing ‘/tmp/Rtmp9xU7lu/R.INSTALLaf74de011e7/CRI-iAtlas-iatlas.modules-29e0631/renv/library/R-4.0/x86_64-pc-linux-gnu/renv’
Warning messages:
1: In system2(r, args, stdout = TRUE, stderr = TRUE) :
running command ''/opt/R/4.0.3/lib/R/bin/R' --vanilla CMD INSTALL -l '/tmp/Rtmp9xU7lu/R.INSTALLaf74de011e7/CRI-iAtlas-iatlas.modules-29e0631/renv/library/R-4.0/x86_64-pc-linux-gnu' '/tmp/Rtmpel3LsK/renv_0.12.3.tar.gz' 2>&1' had status 1
2: Failed to find an renv installation: the project will not be loaded.
Use `renv::activate()` to re-initialize the project.
** help
*** installing help indices
** building package indices
# Bootstrapping renv 0.12.3 --------------------------------------------------
* Downloading renv 0.12.3 from CRAN ... OK
* Installing renv 0.12.3 ... Done!
Error installing renv:
======================
* installing *source* package ‘renv’ ...
** package ‘renv’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
ERROR: hard-coded installation path: please report to the package maintainer and use ‘--no-staged-install’
* removing ‘/tmp/Rtmp9xU7lu/R.INSTALLaf74de011e7/CRI-iAtlas-iatlas.modules-29e0631/renv/library/R-4.0/x86_64-pc-linux-gnu/renv’
Warning messages:
1: In system2(r, args, stdout = TRUE, stderr = TRUE) :
running command ''/opt/R/4.0.3/lib/R/bin/R' --vanilla CMD INSTALL -l '/tmp/Rtmp9xU7lu/R.INSTALLaf74de011e7/CRI-iAtlas-iatlas.modules-29e0631/renv/library/R-4.0/x86_64-pc-linux-gnu' '/tmp/RtmpThMj3L/renv_0.12.3.tar.gz' 2>&1' had status 1
2: Failed to find an renv installation: the project will not be loaded.
Use `renv::activate()` to re-initialize the project.
** testing if installed package can be loaded from temporary location
# Bootstrapping renv 0.12.3 --------------------------------------------------
* Downloading renv 0.12.3 from CRAN ... OK
* Installing renv 0.12.3 ... Done!
Error installing renv:
======================
* installing *source* package ‘renv’ ...
** package ‘renv’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
ERROR: hard-coded installation path: please report to the package maintainer and use ‘--no-staged-install’
* removing ‘/tmp/Rtmp9xU7lu/R.INSTALLaf74de011e7/CRI-iAtlas-iatlas.modules-29e0631/renv/library/R-4.0/x86_64-pc-linux-gnu/renv’
Warning messages:
1: In system2(r, args, stdout = TRUE, stderr = TRUE) :
running command ''/opt/R/4.0.3/lib/R/bin/R' --vanilla CMD INSTALL -l '/tmp/Rtmp9xU7lu/R.INSTALLaf74de011e7/CRI-iAtlas-iatlas.modules-29e0631/renv/library/R-4.0/x86_64-pc-linux-gnu' '/tmp/RtmpRJYKG2/renv_0.12.3.tar.gz' 2>&1' had status 1
2: Failed to find an renv installation: the project will not be loaded.
Use `renv::activate()` to re-initialize the project.
** testing if installed package can be loaded from final location
# Bootstrapping renv 0.12.3 --------------------------------------------------
* Downloading renv 0.12.3 from CRAN ... OK
* Installing renv 0.12.3 ... Done!
* Successfully installed and loaded renv 0.12.3.
Error: package or namespace load failed for ‘iatlas.modules’:
.onLoad failed in loadNamespace() for 'pillar', details:
call: loadNamespace(name)
error: there is no package called ‘crayon’
Error: loading failed
Execution halted
ERROR: loading failed
* removing ‘/opt/R/4.0.3/lib/R/library/iatlas.modules’
################################# End Task Log #################################
Error: Unhandled Exception: Child Task 834470744 failed: Error building image: Error building iatlas.modules (0.3.1). Build exited with non-zero status: 1