renv::restore() doesn't use RemoteSHA recorded in the lockfile when running in Docker container
#1883
Comments
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Can you please provide a reproducible example? Also note that the field is normally called RemoteSha, in case you're generating your renv lock files by hand. |
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Hi @kevinushey, thank you for the prompt response! |
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Hi @kevinushey,
docker build -f Dockerfile -t test:arm64_latest . 2>&1 | tee build.logAnd check the Thank you in advance for looking into this! |
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Thanks -- much appreciated! I'll try to take a closer look tomorrow. |
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Sounds good, thank you @kevinushey ! |
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Thanks! I've confirmed the issue, and it's specific to usages of GitHub repositories when We're creating the remote specification using RemoteRef rather than RemoteSha, which is incorrect. For the curious: Lines 126 to 127 in 5cbf955 but we prefer using RemoteRef when available when formatting a remote: Lines 131 to 138 in 5cbf955 so we'll want to adjust how we format the remote for use by Thanks again for providing the reproducible example; it made it far easier to ascertain the root cause here! |
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@kevinushey Awesome, thank you for diagnosing the issue! So is it just a matter of switching the order of the |
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Not quite; that function is used both when trying to format a record as a remote for display (where we might want to truncate the SHA since just the first few characters are probably fine), whereas we'd want to preserve the entire SHA when using that for an actual installation request. I'm going to poke at it a bit further. |
kevinushey
added a commit
that referenced
this issue
Apr 26, 2024
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This should now be fixed up in the development version of |
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Hi @kevinushey, |
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Hi @kevinushey, Does it make sense to you that this would happen or should I try to create a reprex? It seems like it needs to resolve to whichever is the latest, unless that conflict with an explicit exact version/hash declaration that uses the Or it could just ignore all the dependency versions and install whatever the explicitly declared version is in the |
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Hey @kevinushey, |
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We just built these two utilities for overwriting the latest version that renv_gh_pkgs <- function(file = "renv.lock") {
lf <- if (!inherits(file, "renv_lockfile"))
renv::lockfile_read(file)
else
file
gh_pkgs <- purrr::keep(lf$Packages, \(.x) .x$Source == "GitHub")
}
renv_gh_pkgs_install <- function(pkgs) {
purrr::walk(pkgs, \(.x) {
remotes::install_github(
sprintf("%s/%s", .x$RemoteUsername, .x$RemoteRepo),
ref = .x$RemoteSha
)
})
}We've implemented after # Copies the renv.lock file from your local project into the Docker image.
# This lock file ensures that R packages are installed at specific versions for reproducibility.
COPY renv.lock renv.lock
# Copies the .Renviron file, which typically contains environment variables for R.
# This can include API keys or other credentials needed for your R environment.
COPY .Renviron .Renviron
# Copies the .Rprofile, which can contain R commands to run every time an R session starts.
# This can be used to set global options or load certain packages by default.
COPY .Rprofile .Rprofile
# Copies the .Rbuildignore file into the Docker image.
# This file indicates which files and directories should be ignored by R build tools.
COPY .Rbuildignore .Rbuildignore
# Copies the 'renv' directory, which contains R package caches and configuration files.
# This directory helps 'renv' manage packages more efficiently.
COPY renv renv
# Sets the RENV_PATHS_LIBRARY environment variable.
# This tells 'renv' where to store and look for installed R packages.
ENV RENV_PATHS_LIBRARY /usr/local/lib/R/site-library
# Installs the 'remotes' package, which is useful for installing R packages from sources such as GitHub.
RUN R --quiet -e "install.packages('remotes')"
# Installs the 'renv' package, a package management tool that helps isolate project-specific dependencies.
# This version includes a fix that ensures the SHA of Github packages recorded in the lockfile are installed instead of the most recent version.
RUN R --quiet -e "install.packages('renv')"
# Restores the R environment based on the renv.lock file.
# This ensures that all R package dependencies are installed.
RUN R --quiet -e "renv::diagnostics();renv::restore(library = '/usr/local/lib/R/site-library')"
# Copy functions for installing specific versions
COPY R/utils_renv.R R/utils_renv.R
# Overwrite whatever versions the `renv::restore` installed for Github Repositories with those recorded in the lockfile
RUN R --quiet -e "source('R/utils_renv.R'); renv_gh_pkgs_install(renv_gh_pkgs());"
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Could you also share the lockfile where you saw this issue, so I can try to reproduce locally and better understand the issue? |
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Hi @kevinushey, As I'm debugging this Dockerfile, it looks like We've happened upon another issue, which I can move over to another issue if need be. We re-arranged our workaround a bit in the Dockerfile: # This tells 'renv' where to store and look for installed R packages.
ENV RENV_PATHS_LIBRARY /usr/local/lib/R/site-library
# Installs the 'remotes' package, which is useful for installing R packages from sources such as GitHub.
RUN R --quiet -e "install.packages('remotes', lib = Sys.getenv('RENV_PATHS_LIBRARY'))"
# Installs the 'renv' package, a package management tool that helps isolate project-specific dependencies.
# This version includes a fix that ensures the SHA of Github packages recorded in the lockfile are installed instead of the most recent version.
RUN R --quiet -e "install.packages('renv', lib = Sys.getenv('RENV_PATHS_LIBRARY'))"
# Copy functions for installing specific versions
COPY R/utils_renv.R R/utils_renv.R
# Need purrr for subsequent calls
RUN R --quiet -e "install.packages('purrr', lib = Sys.getenv('RENV_PATHS_LIBRARY'))"
# Overwrite whatever versions the `renv::restore` installed for Github Repositories with those recorded in the lockfile
RUN R --quiet -e "source('R/utils_renv.R'); renv::deactivate(); renv_gh_pkgs_install(renv_gh_pkgs());"
# Restores the R environment based on the renv.lock file.
# This ensures that all R package dependencies are installed.
RUN R --quiet -e "renv::deactivate();source('R/utils_renv.R'); renv::restore(exclude = names(renv_gh_pkgs()))"
In order to install the Github repos first, using their specific RemoteSha values, and then exclude them from the For some reason, switching the order of operations has now produced this obtuse error when running The container is built off of this image: FROM rocker/r-ver:4.3.0@sha256:9c1703e265fca5a17963a1b255b3b2ead6dfc6d65c57e4af2f31bec15554da86 AS base-arm64And I verified that it can run
Any idea what's going on here? Seems like it can't run the Full build.log output with traceback |
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Hey @kevinushey, In the process of attempting to derive a functioning workaround we're encountering other unexpected issues, one of which I thought ought to be surfaced to the I'm interactively debugging a container built from the The container has been built with the 2.2.1 version of packageDescription("bs4Dash")
Package: bs4Dash
Type: Package
Title: A 'Bootstrap 4' Version of 'shinydashboard'
Version: 2.2.1
Authors@R: c( person("David", "Granjon", email = "dgranjon@ymail.com",
role = c("aut", "cre")), person(family = "RinteRface", role =
"cph"), person(family = "Almasaeed Studio", role = c("ctb",
"cph"), comment = "AdminLTE3 theme for Bootstrap 4"),
person("Winston", "Chang", role = c("ctb", "cph"), comment =
"Utils functions from shinydashboard"))
Maintainer: David Granjon <dgranjon@ymail.com>
Description: Make 'Bootstrap 4' Shiny dashboards. Use the full power of
'AdminLTE3', a dashboard template built on top of 'Bootstrap 4'
<https://github.com/ColorlibHQ/AdminLTE>.
URL: https://rinterface.github.io/bs4Dash/index.html,
https://github.com/RinteRface/bs4Dash
BugReports: https://github.com/RinteRface/bs4Dash/issues
License: GPL (>= 2) | file LICENSE
Imports: shiny (>= 1.6.0), htmltools (>= 0.5.1.1), jsonlite (>=
0.9.16), fresh, grDevices, waiter (>= 0.2.3), httpuv (>=
1.5.2), lifecycle, bslib (>= 0.2.4), httr, UU (>= 1.5.1)
Suggests: knitr, rmarkdown, testthat (>= 2.1.0), golem, DT, thematic
(>= 0.1.2)
Encoding: UTF-8
RoxygenNote: 7.2.3
VignetteBuilder: knitr
Collate: 'aaa_reimports.R' 'feedbacks.R' 'useful-items.R' 'tabs.R'
.....
RdMacros: lifecycle
Remotes: yogat3ch/UU
NeedsCompilation: no
Packaged: 2024-05-23 14:58:06 UTC; root
Author: David Granjon [aut, cre], RinteRface [cph], Almasaeed Studio
[ctb, cph] (AdminLTE3 theme for Bootstrap 4), Winston Chang
[ctb, cph] (Utils functions from shinydashboard)
Built: R 4.3.0; ; 2024-05-23 14:58:07 UTC; unix
RemoteType: github
RemoteHost: api.github.com
RemoteRepo: bs4Dash
RemoteUsername: yogat3ch
RemotePkgRef: yogat3ch/bs4Dash@HEAD
RemoteRef: HEAD
RemoteSha: 1d4d4618e47457067fd07e17c840e58f0213c684
GithubRepo: bs4Dash
GithubUsername: yogat3ch
GithubRef: HEAD
GithubSHA1: 1d4d4618e47457067fd07e17c840e58f0213c684
-- File: /usr/local/lib/R/site-library/bs4Dash/Meta/package.rds As part of the Dockerfile build process, one step is RUN R --quiet -e "renv::restore()"
#10 [stage-4 5/5] RUN R --quiet -e "renv::restore()"
#10 0.368 > renv::restore()
#10 4.992
#10 6.615 ✔ Updated metadata database: 1.37 MB in 1 file.
#10 6.615
#10 6.616 ℹ Updating metadata database
#10 8.851 ✔ Updating metadata database ... done
#10 8.852
#10 9.077
#10 9.078
#10 9.240 ℹ No downloads are needed
#10 9.273 ✔ 2 pkgs + 1 dep: [5.3s]
#10 9.296 >
#10 9.296 >
#10 DONE 9.8sdespite the fact that in the > rl$Packages$bs4Dash
$Package
[1] "bs4Dash"
$Version
[1] "2.3.3"
$Source
[1] "GitHub"
$Remotes
[1] "yogat3ch/UU"
$RemoteType
[1] "github"
$RemoteHost
[1] "api.github.com"
$RemoteRepo
[1] "bs4Dash"
$RemoteUsername
[1] "yogat3ch"
$RemoteRef
[1] "bc1e40f"
$RemoteSha
[1] "bc1e40f404915e566c0a70acc543288a0928989f"
$Requirements
[1] "UU" "bslib" "fresh" "grDevices" "htmltools" "httpuv"
[7] "httr" "jsonlite" "lifecycle" "shiny" "waiter"
$Hash
[1] "a707c272226b7265b5d2221f66a604c8"There's a discrepancy in version number and hash number that I've replicated this same behavior outside the Docker container on my Mac environment. .libPaths()
[1] "/Users/stephenholsenbeck/Library/Caches/org.R-project.R/R/renv/library/dmdu-4393acb2/R-4.3/aarch64-apple-darwin20"
[2] "/Users/stephenholsenbeck/Library/Caches/org.R-project.R/R/renv/sandbox/R-4.3/aarch64-apple-darwin20/ac5c2659"Am I missing something critical about how renv::diagnostics from my macrenv::diagnostics()
Diagnostics Report [renv 1.0.7]
===============================
# Session Info --------------------------------------------------------
R version 4.3.0 (2023-04-21)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS 14.5
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: America/New_York
tzcode source: internal
attached base packages:
[1] stats graphics grDevices datasets utils methods base
loaded via a namespace (and not attached):
[1] utf8_1.2.4 magrittr_2.0.3 glue_1.6.2 stringr_1.5.0
[5] tibble_3.2.1 pkgconfig_2.0.3 lifecycle_1.0.3 cli_3.6.2
[9] fansi_1.0.4 vctrs_0.6.5 renv_1.0.7 compiler_4.3.0
[13] plyr_1.8.8 tools_4.3.0 purrr_1.0.2 rstudioapi_0.15.0
[17] pillar_1.9.0 Rcpp_1.0.11 rlang_1.1.3 fs_1.6.3
[21] stringi_1.7.12
# Project -------------------------------------------------------------
Project path: "~/Documents/R/Contributor_Repos/VirgaLabs/dmdu"
# Status --------------------------------------------------------------
No issues found -- the project is in a consistent state.
# Packages ------------------------------------------------------------
Library Source Lockfile Source Path Dependency
AsioHeaders 1.22.1-2 CRAN <NA> <NA> [1] indirect
BH 1.81.0-1 CRAN 1.81.0-1 CRAN [1] indirect
BOR 0.4.0 GitHub <NA> <NA> [1] direct
DBI 1.1.3 CRAN <NA> <NA> [1] <NA>
DMDUAPI 2.9.0 GitHub 2.9.0 GitHub [1] direct
DT 0.27 CRAN 0.27 CRAN [1] direct
DTExtend 1.3.1.9000 GitHub 1.3.1.9000 GitHub [1] direct
DiagrammeR 1.0.10 CRAN 1.0.10 CRAN [1] direct
Formula 1.2-5 CRAN <NA> <NA> [1] <NA>
KernSmooth 2.23-20 CRAN <NA> <NA> [2] <NA>
MASS 7.3-60 CRAN 7.3-60 CRAN [1] direct
Matrix 1.5-4.1 CRAN 1.5-4.1 CRAN [1] indirect
OpenMCE 1.0.1 GitHub 1.0.1 GitHub [1] direct
R.cache 0.16.0 CRAN <NA> <NA> [1] <NA>
R6 2.5.1 CRAN 2.5.1 CRAN [1] direct
RColorBrewer 1.1-3 CRAN 1.1-3 CRAN [1] direct
RMySQL 0.10.25 CRAN <NA> <NA> [1] <NA>
Rcpp 1.0.12 CRAN 1.0.12 CRAN [1] indirect
RcppCCTZ 0.2.12 CRAN <NA> <NA> [1] <NA>
RcppDate 0.0.3 CRAN <NA> <NA> [1] <NA>
UU 1.54.1 GitHub 1.54.1 GitHub [1] direct
V8 4.3.3 CRAN 4.3.3 CRAN [1] indirect
airtabler 0.1.6 GitHub 0.1.6 GitHub [1] direct
anytime 0.3.9 CRAN 0.3.9 CRAN [1] indirect
askpass 1.2.0 CRAN 1.2.0 CRAN [1] indirect
assertthat 0.2.1 CRAN 0.2.1 CRAN [1] indirect
attempt 0.3.1 CRAN 0.3.1 CRAN [1] indirect
aws.iam 0.1.8 CRAN <NA> <NA> [1] <NA>
aws.s3 0.3.21 CRAN <NA> <NA> [1] direct
aws.signature 0.6.0 CRAN <NA> <NA> [1] indirect
backports 1.4.1 CRAN 1.4.1 CRAN [1] indirect
base <NA> <NA> <NA> <NA> [2] direct
base64enc 0.1-3 CRAN 0.1-3 CRAN [1] indirect
bayestestR 0.13.0 CRAN <NA> <NA> [1] <NA>
beeswarm 0.4.0 CRAN 0.4.0 CRAN [1] indirect
bit 4.0.5 CRAN 4.0.5 CRAN [1] indirect
bit64 4.0.5 CRAN 4.0.5 CRAN [1] indirect
blob 1.2.4 CRAN <NA> <NA> [1] <NA>
boot 1.3-28.1 CRAN <NA> <NA> [2] <NA>
brew 1.0-10 CRAN 1.0-10 CRAN [1] indirect
brio 1.1.3 CRAN 1.1.3 CRAN [1] indirect
broom 1.0.5 CRAN 1.0.5 CRAN [1] indirect
bs4Dash 2.2.1 GitHub 2.2.1 GitHub [1] direct
bslib 0.6.1 CRAN 0.6.1 CRAN [1] indirect
cachem 1.0.8 CRAN 1.0.8 CRAN [1] indirect
callr 3.7.3 RSPM 3.7.3 CRAN [1] indirect
capture 0.1.4 GitHub 0.1.4 GitHub [1] direct
cellranger 1.1.0 CRAN <NA> <NA> [1] indirect
checkmate 2.2.0 CRAN 2.2.0 CRAN [1] indirect
chromote 0.1.2.9000 GitHub <NA> <NA> [1] indirect
cicerone 1.0.5.9000 GitHub <NA> <NA> [1] <NA>
class 7.3-21 CRAN <NA> <NA> [2] <NA>
cli 3.6.2 CRAN 3.6.2 CRAN [1] direct
clipr 0.8.0 CRAN 0.8.0 CRAN [1] indirect
cluster 2.1.4 CRAN <NA> <NA> [2] <NA>
codetools 0.2-19 CRAN 0.2-19 CRAN [2] indirect
collections 0.3.7 CRAN <NA> <NA> [1] <NA>
colorspace 2.1-0 CRAN 2.1-0 CRAN [1] direct
commonmark 1.9.1 CRAN 1.9.1 CRAN [1] indirect
compiler <NA> <NA> <NA> <NA> [2] indirect
config 0.3.1 CRAN 0.3.1 CRAN [1] direct
correlation 0.8.3 CRAN <NA> <NA> [1] <NA>
corrplot 0.92 CRAN 0.92 CRAN [1] indirect
countrycode 1.5.0 CRAN 1.5.0 CRAN [1] indirect
covrpage <NA> <NA> <NA> <NA> <NA> direct
cpp11 0.4.7 CRAN 0.4.7 CRAN [1] indirect
crayon 1.5.2 CRAN 1.5.2 CRAN [1] indirect
credentials 2.0.1 CRAN 2.0.1 CRAN [1] indirect
crew 0.9.2 CRAN 0.9.2 CRAN [1] direct
crosstalk 1.2.1 GitHub 1.2.1 GitHub [1] direct
crssDB 1.0.0 GitHub <NA> <NA> [1] <NA>
curl 5.2.1 CRAN 5.2.1 CRAN [1] direct
cyclocomp 1.1.0 CRAN <NA> <NA> [1] <NA>
data.table 1.14.10 CRAN 1.14.10 CRAN [1] indirect
data.tree 1.0.0 CRAN 1.0.0 CRAN [1] indirect
datawizard 0.7.1 CRAN <NA> <NA> [1] <NA>
dbplyr 2.3.2 CRAN <NA> <NA> [1] <NA>
desc <NA> <NA> <NA> <NA> [1] indirect
devtools 2.4.5 CRAN 2.4.5 CRAN [1] direct
diffobj 0.3.5 CRAN 0.3.5 CRAN [1] indirect
digest 0.6.35 CRAN 0.6.35 CRAN [1] direct
dmdu 1.32.0 unknown <NA> <NA> [1] direct
downlit 0.4.3 CRAN 0.4.3 CRAN [1] indirect
downloader 0.4 CRAN 0.4 CRAN [1] indirect
dplyr 1.1.4 CRAN 1.1.4 CRAN [1] direct
echarts4r 0.4.5 CRAN 0.4.5 CRAN [1] direct
echartsUtils 0.8.0.9000 GitHub 0.8.0.9000 GitHub [1] direct
echarty 1.4.5 CRAN 1.4.5 CRAN [1] direct
effectsize 0.8.3 CRAN <NA> <NA> [1] <NA>
ellipsis 0.3.2 CRAN 0.3.2 CRAN [1] indirect
emayili 0.7.18 CRAN 0.7.18 CRAN [1] indirect
english 1.2-6 CRAN 1.2-6 CRAN [1] direct
evaluate 0.21 CRAN 0.21 CRAN [1] indirect
fansi 1.0.4 CRAN 1.0.4 CRAN [1] indirect
farver 2.1.1 CRAN 2.1.1 CRAN [1] indirect
fastmap 1.1.1 CRAN 1.1.1 CRAN [1] indirect
filelock 1.0.2 CRAN <NA> <NA> [1] <NA>
fontawesome 0.5.2 CRAN 0.5.2 CRAN [1] indirect
foreign 0.8-84 CRAN <NA> <NA> [2] <NA>
fresh 0.2.0 CRAN 0.2.0 CRAN [1] indirect
fs 1.6.3 CRAN 1.6.3 CRAN [1] direct
gargle 1.3.0 CRAN <NA> <NA> [1] direct
generics 0.1.3 CRAN 0.1.3 CRAN [1] indirect
gert 2.0.1 CRAN 2.0.1 CRAN [1] indirect
getip 0.1-4 CRAN 0.1-4 CRAN [1] indirect
ggbeeswarm 0.7.2 CRAN 0.7.2 CRAN [1] direct
ggplot2 3.4.4 CRAN 3.4.4 CRAN [1] direct
gh 1.4.0 CRAN 1.4.0 CRAN [1] indirect
gitcreds 0.1.2 CRAN 0.1.2 CRAN [1] indirect
globals 0.16.2 CRAN 0.16.2 CRAN [1] indirect
glue 1.7.0 CRAN 1.7.0 CRAN [1] direct
gmailr <NA> <NA> <NA> <NA> <NA> direct
golem 0.4.1 CRAN 0.4.1 CRAN [1] direct
googleAuthR 2.0.1 CRAN <NA> <NA> [1] <NA>
googleLanguageR 0.3.0 CRAN <NA> <NA> [1] <NA>
googledrive 2.1.0 CRAN <NA> <NA> [1] direct
googlesheets4 1.1.0 CRAN <NA> <NA> [1] direct
grDevices <NA> <NA> <NA> <NA> [2] direct
graphics <NA> <NA> <NA> <NA> [2] indirect
grid <NA> <NA> <NA> <NA> [2] indirect
gridExtra 2.3 CRAN 2.3 CRAN [1] indirect
gtable 0.3.4 CRAN 0.3.4 CRAN [1] indirect
hardhat 1.3.0 CRAN 1.3.0 CRAN [1] indirect
here 1.0.1 CRAN 1.0.1 CRAN [1] indirect
highr 0.10 CRAN 0.10 CRAN [1] indirect
hms 1.1.3 CRAN 1.1.3 CRAN [1] indirect
html2R 0.1.0 CRAN <NA> <NA> [1] <NA>
html2tags 0.0.0.9000 GitHub <NA> <NA> [1] <NA>
htmltools 0.5.8.1 CRAN 0.5.8.1 CRAN [1] direct
htmlwidgets 1.6.4 CRAN 1.6.4 CRAN [1] direct
httpuv 1.6.15 CRAN 1.6.15 CRAN [1] direct
httr 1.4.7 CRAN 1.4.7 CRAN [1] indirect
httr2 1.0.0 CRAN 1.0.0 CRAN [1] indirect
ids 1.0.1 CRAN <NA> <NA> [1] indirect
igraph 1.5.1 CRAN 1.5.1 CRAN [1] direct
ini 0.3.1 CRAN 0.3.1 CRAN [1] indirect
insight 0.19.1 CRAN <NA> <NA> [1] <NA>
inum 1.0-5 CRAN <NA> <NA> [1] <NA>
isoband 0.2.7 CRAN 0.2.7 CRAN [1] indirect
jose 1.2.0 CRAN 1.2.0 CRAN [1] indirect
jquerylib 0.1.4 CRAN 0.1.4 CRAN [1] indirect
jsonlite 1.8.8 CRAN 1.8.8 CRAN [1] direct
jsonvalidate 1.3.2 CRAN 1.3.2 CRAN [1] direct
knitr 1.44 CRAN 1.44 CRAN [1] indirect
labeling 0.4.3 CRAN 0.4.3 CRAN [1] indirect
languageserver 0.3.15 CRAN <NA> <NA> [1] <NA>
later 1.3.2 CRAN 1.3.2 CRAN [1] indirect
lattice 0.20-45 CRAN 0.20-45 CRAN [1] indirect
lazyeval 0.2.2 CRAN 0.2.2 CRAN [1] indirect
learnr 0.11.3 CRAN 0.11.3 CRAN [1] indirect
libcoin 1.0-9 CRAN <NA> <NA> [1] <NA>
lifecycle 1.0.3 CRAN 1.0.3 CRAN [1] indirect
lintr 3.1.0 CRAN <NA> <NA> [1] <NA>
listviewer 3.0.0 CRAN <NA> <NA> [1] <NA>
logger 0.2.2 CRAN 0.2.2 CRAN [1] indirect
lubridate 1.9.3 CRAN 1.9.3 CRAN [1] direct
magrittr 2.0.3 CRAN 2.0.3 CRAN [1] indirect
markdown 1.5 CRAN 1.5 CRAN [1] indirect
memoise 2.0.1 CRAN 2.0.1 CRAN [1] indirect
methods <NA> <NA> <NA> <NA> [2] indirect
mgcv 1.9-0 CRAN 1.9-0 CRAN [1] indirect
mime 0.12 CRAN 0.12 CRAN [1] indirect
miniUI 0.1.1.1 CRAN 0.1.1.1 CRAN [1] indirect
mirai 0.12.0 CRAN 0.12.0 CRAN [1] indirect
modelbased 0.8.6 CRAN <NA> <NA> [1] <NA>
munsell 0.5.0 CRAN 0.5.0 CRAN [1] indirect
mvtnorm 1.2-2 CRAN 1.2-2 CRAN [1] direct
nanonext 1.0.0 CRAN 1.0.0 CRAN [1] direct
nanotime 0.3.7 CRAN <NA> <NA> [1] <NA>
nlme 3.1-162 CRAN 3.1-162 CRAN [2] indirect
nnet 7.3-18 CRAN <NA> <NA> [2] <NA>
officer <NA> <NA> <NA> <NA> <NA> direct
openssl 2.1.1 CRAN 2.1.1 CRAN [1] indirect
packer 0.1.3 CRAN 0.1.3 CRAN [1] indirect
parallel <NA> <NA> <NA> <NA> [2] indirect
parameters 0.20.2 CRAN <NA> <NA> [1] <NA>
parsnip 1.0.4 CRAN 1.0.4 CRAN [1] direct
partykit 1.2-19 CRAN <NA> <NA> [1] <NA>
performance 0.10.2 CRAN <NA> <NA> [1] <NA>
pillar 1.9.0 CRAN 1.9.0 CRAN [1] indirect
pingr 2.0.2 CRAN <NA> <NA> [1] indirect
pkgbuild 1.4.3 CRAN 1.4.3 CRAN [1] indirect
pkgconfig 2.0.3 CRAN 2.0.3 CRAN [1] indirect
pkgdown 2.0.7 CRAN 2.0.7 CRAN [1] indirect
pkgload 1.3.4 CRAN 1.3.4 CRAN [1] direct
plotly 4.10.1 CRAN 4.10.1 CRAN [1] direct
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prettyunits 1.2.0 CRAN 1.2.0 CRAN [1] indirect
processx 3.8.3 CRAN 3.8.3 CRAN [1] indirect
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progress 1.2.2 CRAN 1.2.2 CRAN [1] indirect
promises 1.2.1 CRAN 1.2.1 CRAN [1] indirect
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purrr 1.0.2 CRAN 1.0.2 CRAN [1] direct
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rcmdcheck 1.4.0 CRAN 1.4.0 CRAN [1] indirect
readr 2.1.5 CRAN 2.1.5 CRAN [1] direct
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rex 1.2.1 RSPM <NA> <NA> [1] <NA>
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sentryR 1.1.1.9000 GitHub 1.1.1.9000 GitHub [1] direct
sessioninfo 1.2.2 CRAN 1.2.2 CRAN [1] indirect
shiny 1.8.1.1 CRAN 1.8.1.1 CRAN [1] direct
shiny.i18n 0.3.0 GitHub 0.3.0 GitHub [1] direct
shiny.tailwind 0.2.2 GitHub 0.2.2 GitHub [1] direct
shinyAce 0.4.2 CRAN <NA> <NA> [1] <NA>
shinyVirga 0.45.1 GitHub 0.45.1 GitHub [1] direct
shinyWidgets 0.8.3 GitHub 0.8.3 GitHub [1] direct
shinybrowser 1.0.0 CRAN 1.0.0 CRAN [1] direct
shinycssloaders 1.0.0.9011 GitHub 1.0.0.9011 GitHub [1] direct
shinyjqui 0.4.1 CRAN <NA> <NA> [1] <NA>
shinyjs 2.1.0 CRAN 2.1.0 CRAN [1] direct
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sortable 0.5.0 GitHub 0.5.0 GitHub [1] direct
sos <NA> <NA> <NA> <NA> [1] indirect
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splines <NA> <NA> <NA> <NA> [2] indirect
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tinytex 0.46 CRAN 0.46 CRAN [1] indirect
tippy 1.0.0 GitHub 1.0.0 GitHub [1] direct
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triebeard 0.4.1 CRAN 0.4.1 CRAN [1] indirect
tzdb 0.4.0 CRAN 0.4.0 CRAN [1] indirect
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urltools 1.7.3 CRAN 1.7.3 CRAN [1] indirect
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utils <NA> <NA> <NA> <NA> [2] direct
uuid 1.1-0 CRAN 1.1-0 CRAN [1] indirect
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vipor 0.4.5 CRAN 0.4.5 CRAN [1] indirect
virgaUtils 0.5.0 GitHub 0.5.0 GitHub [1] direct
viridis 0.6.3 CRAN 0.6.3 CRAN [1] indirect
viridisLite 0.4.2 CRAN 0.4.2 CRAN [1] indirect
visNetwork 2.1.2 CRAN 2.1.2 CRAN [1] indirect
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yaml 2.3.8 CRAN 2.3.8 CRAN [1] indirect
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[1]: /Users/stephenholsenbeck/Library/Caches/org.R-project.R/R/renv/library/dmdu-4393acb2/R-4.3/aarch64-apple-darwin20
[2]: /Users/stephenholsenbeck/Library/Caches/org.R-project.R/R/renv/sandbox/R-4.3/aarch64-apple-darwin20/ac5c2659
# ABI -----------------------------------------------------------------
- No ABI problems were detected in the set of installed packages.
# User Profile --------------------------------------------------------
Source Package Require Version Dev
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List of 13
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List of 9
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# PATH ----------------------------------------------------------------
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# Cache ---------------------------------------------------------------
There are a total of 723 packages installed in the renv cache.
Cache path: "~/Documents/R/renv_cache/cache/v5/R-4.3/aarch64-apple-darwin20"renv::diagnostics from the Docker imagerenv::diagnostics()
Diagnostics Report [renv 1.0.7]
===============================
# Session Info ---------------------------------------------------------------
R version 4.3.0 (2023-04-21)
Platform: aarch64-unknown-linux-gnu (64-bit)
Running under: Ubuntu 22.04.2 LTS
Matrix products: default
BLAS: /usr/lib/aarch64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/aarch64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.3.0 tools_4.3.0 parallel_4.3.0 renv_1.0.7
# Project --------------------------------------------------------------------
Project path: "/dmdu"
# Status ---------------------------------------------------------------------
There are no packages installed in the project library.
Use `renv::restore()` to install the packages defined in lockfile.
# Packages -------------------------------------------------------------------
The project library "/usr/local/lib/R/site-library/R-4.3/aarch64-unknown-linux-gnu" does not exist.
Library Source Lockfile Source Path Dependency
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DMDUAPI 2.9.0 GitHub 2.9.0 GitHub [1] direct
DT 0.33 CRAN 0.27 CRAN [1] direct
DTExtend 1.3.1.9000 GitHub 1.3.1.9000 GitHub [1] direct
DiagrammeR 1.0.10 CRAN 1.0.10 CRAN [1] direct
KernSmooth 2.23-20 CRAN <NA> <NA> [2] <NA>
MASS 7.3-60 CRAN 7.3-60 CRAN [1] direct
Matrix 1.5-4.1 CRAN 1.5-4.1 CRAN [1] indirect
OpenMCE 1.0.1 GitHub 1.0.1 GitHub [1] direct
R6 2.5.1 CRAN 2.5.1 CRAN [1] direct
RColorBrewer 1.1-3 CRAN 1.1-3 CRAN [1] direct
Rcpp 1.0.12 CRAN 1.0.12 CRAN [1] indirect
UU 1.54.1 GitHub 1.54.1 GitHub [1] direct
V8 4.3.3 CRAN 4.3.3 CRAN [1] indirect
airtabler 0.1.6 GitHub 0.1.6 GitHub [1] direct
anytime 0.3.9 CRAN 0.3.9 CRAN [1] indirect
askpass 1.2.0 CRAN 1.2.0 CRAN [1] indirect
assertthat 0.2.1 CRAN 0.2.1 CRAN [1] indirect
attempt 0.3.1 CRAN 0.3.1 CRAN [1] indirect
backports 1.5.0 CRAN 1.4.1 CRAN [1] indirect
base <NA> <NA> <NA> <NA> [2] direct
base64enc 0.1-3 CRAN 0.1-3 CRAN [1] indirect
beeswarm 0.4.0 CRAN 0.4.0 CRAN [1] indirect
bit 4.0.5 CRAN 4.0.5 CRAN [1] indirect
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boot 1.3-28.1 CRAN <NA> <NA> [2] <NA>
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brio 1.1.5 CRAN 1.1.3 CRAN [1] indirect
broom 1.0.6 CRAN 1.0.5 CRAN [1] indirect
bs4Dash 2.2.1 GitHub 2.3.3 GitHub [1] direct
bslib 0.7.0 CRAN 0.6.1 CRAN [1] indirect
cachem 1.1.0 CRAN 1.0.8 CRAN [1] indirect
callr 3.7.6 CRAN 3.7.3 CRAN [1] indirect
capture 0.1.4 GitHub 0.1.4 GitHub [1] direct
checkmate 2.3.1 CRAN 2.2.0 CRAN [1] indirect
class 7.3-21 CRAN <NA> <NA> [2] <NA>
cli 3.6.2 CRAN 3.6.2 CRAN [1] direct
clipr 0.8.0 CRAN 0.8.0 CRAN [1] indirect
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codetools 0.2-19 CRAN 0.2-19 CRAN [2] indirect
colorspace 2.1-0 CRAN 2.1-0 CRAN [1] direct
commonmark 1.9.1 CRAN 1.9.1 CRAN [1] indirect
compiler <NA> <NA> <NA> <NA> [2] indirect
config 0.3.2 CRAN 0.3.1 CRAN [1] direct
corrplot 0.92 CRAN 0.92 CRAN [1] indirect
countrycode 1.6.0 CRAN 1.5.0 CRAN [1] indirect
cpp11 0.4.7 CRAN 0.4.7 CRAN [1] indirect
crayon 1.5.2 CRAN 1.5.2 CRAN [1] indirect
credentials 2.0.1 CRAN 2.0.1 CRAN [1] indirect
crew 0.9.2 CRAN 0.9.2 CRAN [1] direct
crosstalk 1.2.1 GitHub 1.2.1 GitHub [1] direct
curl 5.2.1 CRAN 5.2.1 CRAN [1] direct
data.table 1.14.10 CRAN 1.14.10 CRAN [1] indirect
data.tree 1.0.0 CRAN 1.0.0 CRAN [1] indirect
desc <NA> <NA> <NA> <NA> [1] indirect
devtools 2.4.5 CRAN 2.4.5 CRAN [1] direct
diffobj 0.3.5 CRAN 0.3.5 CRAN [1] indirect
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dmdu <NA> <NA> <NA> <NA> <NA> direct
docopt 0.7.1 RSPM <NA> <NA> [1] <NA>
downlit 0.4.3 CRAN 0.4.3 CRAN [1] indirect
downloader 0.4 CRAN 0.4 CRAN [1] indirect
dplyr 1.1.4 CRAN 1.1.4 CRAN [1] direct
echarts4r 0.4.5 CRAN 0.4.5 CRAN [1] direct
echartsUtils 0.8.0.9000 GitHub 0.8.0.9000 GitHub [1] direct
echarty 1.4.5 CRAN 1.4.5 CRAN [1] direct
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emayili 0.8.0 CRAN 0.7.18 CRAN [1] indirect
english 1.2-6 CRAN 1.2-6 CRAN [1] direct
evaluate 0.23 CRAN 0.21 CRAN [1] indirect
fansi 1.0.6 CRAN 1.0.4 CRAN [1] indirect
farver 2.1.2 CRAN 2.1.1 CRAN [1] indirect
fastmap 1.2.0 CRAN 1.1.1 CRAN [1] indirect
fontawesome 0.5.2 CRAN 0.5.2 CRAN [1] indirect
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fresh 0.2.0 CRAN 0.2.0 CRAN [1] indirect
fs 1.6.4 CRAN 1.6.3 CRAN [1] direct
generics 0.1.3 CRAN 0.1.3 CRAN [1] indirect
gert 2.0.1 CRAN 2.0.1 CRAN [1] indirect
getip 0.1-4 CRAN 0.1-4 CRAN [1] indirect
ggbeeswarm 0.7.2 CRAN 0.7.2 CRAN [1] direct
ggplot2 3.4.4 CRAN 3.4.4 CRAN [1] direct
gh 1.4.1 CRAN 1.4.0 CRAN [1] indirect
gitcreds 0.1.2 CRAN 0.1.2 CRAN [1] indirect
globals 0.16.2 CRAN 0.16.2 CRAN [1] indirect
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golem 0.4.1 CRAN 0.4.1 CRAN [1] direct
googlesheets4 <NA> <NA> <NA> <NA> <NA> direct
grDevices <NA> <NA> <NA> <NA> [2] direct
graphics <NA> <NA> <NA> <NA> [2] indirect
grid <NA> <NA> <NA> <NA> [2] indirect
gridExtra 2.3 CRAN 2.3 CRAN [1] indirect
gtable 0.3.4 CRAN 0.3.4 CRAN [1] indirect
hardhat 1.3.0 CRAN 1.3.0 CRAN [1] indirect
here 1.0.1 CRAN 1.0.1 CRAN [1] indirect
highr 0.10 CRAN 0.10 CRAN [1] indirect
hms 1.1.3 CRAN 1.1.3 CRAN [1] indirect
htmltools 0.5.8.1 CRAN 0.5.8.1 CRAN [1] direct
htmlwidgets 1.6.4 CRAN 1.6.4 CRAN [1] direct
httpuv 1.6.15 CRAN 1.6.15 CRAN [1] direct
httr 1.4.7 CRAN 1.4.7 CRAN [1] indirect
httr2 1.0.1 CRAN 1.0.0 CRAN [1] indirect
igraph 1.5.1 CRAN 1.5.1 CRAN [1] direct
ini 0.3.1 CRAN 0.3.1 CRAN [1] indirect
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jose 1.2.0 CRAN 1.2.0 CRAN [1] indirect
jquerylib 0.1.4 CRAN 0.1.4 CRAN [1] indirect
jsonlite 1.8.8 CRAN 1.8.8 CRAN [1] direct
jsonvalidate 1.3.2 CRAN 1.3.2 CRAN [1] direct
knitr 1.46 CRAN 1.44 CRAN [1] indirect
labeling 0.4.3 CRAN 0.4.3 CRAN [1] indirect
later 1.3.2 CRAN 1.3.2 CRAN [1] indirect
lattice 0.20-45 CRAN 0.20-45 CRAN [1] indirect
lazyeval 0.2.2 CRAN 0.2.2 CRAN [1] indirect
learnr 0.11.5 CRAN 0.11.3 CRAN [1] indirect
lifecycle 1.0.4 CRAN 1.0.3 CRAN [1] indirect
littler 0.3.18 RSPM <NA> <NA> [1] <NA>
logger 0.3.0 CRAN 0.2.2 CRAN [1] indirect
lubridate 1.9.3 CRAN 1.9.3 CRAN [1] direct
magrittr 2.0.3 CRAN 2.0.3 CRAN [1] indirect
markdown 1.12 CRAN 1.5 CRAN [1] indirect
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nanonext 1.0.0 CRAN 1.0.0 CRAN [1] direct
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packer 0.1.3 CRAN 0.1.3 CRAN [1] indirect
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pillar 1.9.0 CRAN 1.9.0 CRAN [1] indirect
pkgbuild 1.4.4 CRAN 1.4.3 CRAN [1] indirect
pkgconfig 2.0.3 CRAN 2.0.3 CRAN [1] indirect
pkgdown 2.0.9 CRAN 2.0.7 CRAN [1] indirect
pkgload 1.3.4 CRAN 1.3.4 CRAN [1] direct
plotly 4.10.1 CRAN 4.10.1 CRAN [1] direct
plyr 1.8.9 CRAN 1.8.9 CRAN [1] direct
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profvis 0.3.8 CRAN 0.3.8 CRAN [1] indirect
progress 1.2.2 CRAN 1.2.2 CRAN [1] indirect
promises 1.3.0 CRAN 1.2.1 CRAN [1] indirect
ps 1.7.6 CRAN 1.7.6 CRAN [1] indirect
purrr 1.0.2 CRAN 1.0.2 CRAN [1] direct
ragg 1.3.2 CRAN 1.2.5 CRAN [1] indirect
rappdirs 0.3.3 CRAN 0.3.3 CRAN [1] indirect
rcmdcheck 1.4.0 CRAN 1.4.0 CRAN [1] indirect
readr 2.1.5 CRAN 2.1.5 CRAN [1] direct
rematch2 2.1.2 CRAN 2.1.2 CRAN [1] indirect
remotes 2.5.0 CRAN 2.5.0 CRAN [1] direct
renv 1.0.7 CRAN 1.0.7 CRAN [1] direct
rlang 1.1.3 CRAN 1.1.3 CRAN [1] direct
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rpart 4.1.19 CRAN <NA> <NA> [2] <NA>
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rversions 2.1.2 CRAN 2.1.2 CRAN [1] indirect
rvest 1.0.4 CRAN 1.0.3 CRAN [1] indirect
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scales 1.3.0 CRAN 1.3.0 CRAN [1] direct
selectr 0.4-2 CRAN 0.4-2 CRAN [1] indirect
sendgridr 0.6.3 GitHub 0.6.3 GitHub [1] direct
sentryR 1.1.1.9000 GitHub 1.1.1.9000 GitHub [1] direct
sessioninfo 1.2.2 CRAN 1.2.2 CRAN [1] indirect
shiny 1.8.1.1 CRAN 1.8.1.1 CRAN [1] direct
shiny.i18n 0.3.0 GitHub 0.3.0 GitHub [1] direct
shiny.tailwind 0.2.2 GitHub 0.2.2 GitHub [1] direct
shinyVirga 0.45.1 GitHub 0.45.1 GitHub [1] direct
shinyWidgets 0.8.3 GitHub 0.8.3 GitHub [1] direct
shinybrowser 1.0.0 CRAN 1.0.0 CRAN [1] direct
shinycssloaders 1.0.0.9011 GitHub 1.0.0.9011 GitHub [1] direct
shinyjs 2.1.0 CRAN 2.1.0 CRAN [1] direct
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shinyvalidate 0.1.2 CRAN 0.1.2 CRAN [1] direct
sinew <NA> <NA> <NA> <NA> [1] indirect
snakecase 0.11.1 CRAN 0.11.1 CRAN [1] direct
sortable 0.5.0 GitHub 0.5.0 GitHub [1] direct
sos <NA> <NA> <NA> <NA> [1] indirect
sourcetools 0.1.7-1 CRAN 0.1.7-1 CRAN [1] indirect
spatial 7.3-16 CRAN <NA> <NA> [2] <NA>
splines <NA> <NA> <NA> <NA> [2] indirect
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stringi 1.8.4 CRAN 1.7.12 CRAN [1] direct
stringr 1.5.1 CRAN 1.5.1 CRAN [1] direct
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tinytex 0.51 CRAN 0.46 CRAN [1] indirect
tippy 1.0.0 GitHub 1.0.0 GitHub [1] direct
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transifex 0.0.4 GitHub 0.0.4 GitHub [1] direct
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tzdb 0.4.0 CRAN 0.4.0 CRAN [1] indirect
urlchecker 1.0.1 CRAN 1.0.1 CRAN [1] indirect
urltools 1.7.3 CRAN 1.7.3 CRAN [1] indirect
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virgaUtils 0.5.0 GitHub 0.5.0 GitHub [1] direct
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[1]: /usr/local/lib/R/site-library
[2]: /usr/local/lib/R/library
# ABI ------------------------------------------------------------------------
- No ABI problems were detected in the set of installed packages.
# User Profile ---------------------------------------------------------------
[no user profile detected]
# Settings -------------------------------------------------------------------
List of 13
$ bioconductor.version : chr(0)
$ external.libraries : chr(0)
$ ignored.packages : chr [1:12] "sinew" "desc" "sos" "todor" ...
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$ r.version : chr(0)
$ snapshot.type : chr "explicit"
$ use.cache : logi TRUE
$ vcs.ignore.cellar : logi TRUE
$ vcs.ignore.library : logi TRUE
$ vcs.ignore.local : logi TRUE
$ vcs.manage.ignores : logi TRUE
# Options --------------------------------------------------------------------
List of 9
$ defaultPackages : chr [1:6] "datasets" "utils" "grDevices" "graphics" ...
$ download.file.method : chr "libcurl"
$ download.file.extra : NULL
$ install.packages.compile.from.source: NULL
$ pkgType : chr "source"
$ repos : Named chr "https://cran.rstudio.com/"
..- attr(*, "names")= chr "CRAN"
$ renv.config.pak.enabled : logi TRUE
$ renv.config.auto.snapshot : logi TRUE
$ renv.verbose : logi TRUE
# Environment Variables ------------------------------------------------------
HOME = /root
LANG = en_US.UTF-8
MAKE = make
R_LIBS = /usr/local/lib/R/site-library:/usr/local/lib/R/library
R_LIBS_SITE = /usr/local/lib/R/site-library
R_LIBS_USER = /root/R/aarch64-unknown-linux-gnu-library/4.3
RENV_PATHS_LIBRARY = /usr/local/lib/R/site-library
# PATH -----------------------------------------------------------------------
- /usr/local/sbin
- /usr/local/bin
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- /usr/bin
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# Cache ----------------------------------------------------------------------
There are a total of 203 packages installed in the renv cache.
Cache path: "~/.cache/R/renv/cache/v5/R-4.3/aarch64-unknown-linux-gnu"UPDATE: I'm still unsure what's going on with the Docker container. I'm intuiting it might be using different library paths between calls as the dockerfile builds. UPDATE renv::diagnostics();packageDescription('bs4Dash');renv::restore()
Full build.log#10 [stage-4 5/17] RUN R --quiet -e "renv::diagnostics();packageDescription('bs4Dash');renv::restore()"
#10 0.389 > renv::diagnostics();packageDescription('bs4Dash');renv::restore()
#10 0.477 Diagnostics Report [renv 1.0.7]
#10 0.477 ===============================
#10 0.477
#10 0.477 # Session Info ---------------------------------------------------------------
#10 0.483 R version 4.3.0 (2023-04-21)
#10 0.483 Platform: aarch64-unknown-linux-gnu (64-bit)
#10 0.483 Running under: Ubuntu 22.04.2 LTS
#10 0.483
#10 0.483 Matrix products: default
#10 0.483 BLAS: /usr/lib/aarch64-linux-gnu/openblas-pthread/libblas.so.3
#10 0.483 LAPACK: /usr/lib/aarch64-linux-gnu/openblas-pthread/libopenblasp-r0.3.20.so; LAPACK version 3.10.0
#10 0.483
#10 0.483 locale:
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#10 0.483 [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
#10 0.483 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
#10 0.483 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
#10 0.483 [9] LC_ADDRESS=C LC_TELEPHONE=C
#10 0.483 [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
#10 0.483
#10 0.483 time zone: Etc/UTC
#10 0.483 tzcode source: system (glibc)
#10 0.483
#10 0.483 attached base packages:
#10 0.483 [1] stats graphics grDevices utils datasets methods base
#10 0.483
#10 0.483 loaded via a namespace (and not attached):
#10 0.483 [1] compiler_4.3.0 tools_4.3.0 parallel_4.3.0 renv_1.0.7
#10 0.483
#10 0.483 # Project --------------------------------------------------------------------
#10 0.484 Project path: "/dmdu"
#10 0.484
#10 0.484 # Status ---------------------------------------------------------------------
#10 0.487 There are no packages installed in the project library.
#10 0.487 Use `renv::restore()` to install the packages defined in lockfile.
#10 0.487
#10 0.487 # Packages -------------------------------------------------------------------
#10 0.516 The project library "/usr/local/lib/R/site-library/R-4.3/aarch64-unknown-linux-gnu" does not exist.
#10 4.826 Library Source Lockfile Source Path Dependency
#10 4.826 BH 1.81.0-1 CRAN 1.81.0-1 CRAN [1] indirect
#10 4.826 DMDUAPI 2.9.0 GitHub 2.9.0 GitHub [1] direct
#10 4.826 DT 0.33 CRAN 0.27 CRAN [1] direct
#10 4.826 DTExtend 1.3.1.9000 GitHub 1.3.1.9000 GitHub [1] direct
#10 4.826 DiagrammeR 1.0.10 CRAN 1.0.10 CRAN [1] direct
#10 4.826 KernSmooth 2.23-20 CRAN <NA> <NA> [2] <NA>
#10 4.826 MASS 7.3-60 CRAN 7.3-60 CRAN [1] direct
#10 4.826 Matrix 1.5-4.1 CRAN 1.5-4.1 CRAN [1] indirect
#10 4.826 OpenMCE 1.0.1 GitHub 1.0.1 GitHub [1] direct
#10 4.826 R6 2.5.1 CRAN 2.5.1 CRAN [1] direct
#10 4.826 RColorBrewer 1.1-3 CRAN 1.1-3 CRAN [1] direct
#10 4.826 Rcpp 1.0.12 CRAN 1.0.12 CRAN [1] indirect
#10 4.826 UU 1.54.1 GitHub 1.54.1 GitHub [1] direct
#10 4.826 V8 4.3.3 CRAN 4.3.3 CRAN [1] indirect
#10 4.827 airtabler 0.1.6 GitHub 0.1.6 GitHub [1] direct
#10 4.827 anytime 0.3.9 CRAN 0.3.9 CRAN [1] indirect
#10 4.827 askpass 1.2.0 CRAN 1.2.0 CRAN [1] indirect
#10 4.827 assertthat 0.2.1 CRAN 0.2.1 CRAN [1] indirect
#10 4.827 attempt 0.3.1 CRAN 0.3.1 CRAN [1] indirect
#10 4.827 backports 1.5.0 CRAN 1.4.1 CRAN [1] indirect
#10 4.827 base <NA> <NA> <NA> <NA> [2] direct
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#10 4.827 beeswarm 0.4.0 CRAN 0.4.0 CRAN [1] indirect
#10 4.827 bit 4.0.5 CRAN 4.0.5 CRAN [1] indirect
#10 4.827 bit64 4.0.5 CRAN 4.0.5 CRAN [1] indirect
#10 4.827 boot 1.3-28.1 CRAN <NA> <NA> [2] <NA>
#10 4.827 brew 1.0-10 CRAN 1.0-10 CRAN [1] indirect
#10 4.827 brio 1.1.5 CRAN 1.1.3 CRAN [1] indirect
#10 4.827 broom 1.0.6 CRAN 1.0.5 CRAN [1] indirect
#10 4.827 bs4Dash 2.2.1 GitHub 2.3.3 GitHub [1] direct
#10 4.827 bslib 0.7.0 CRAN 0.6.1 CRAN [1] indirect
#10 4.827 cachem 1.1.0 CRAN 1.0.8 CRAN [1] indirect
#10 4.827 callr 3.7.6 CRAN 3.7.3 CRAN [1] indirect
#10 4.827 capture 0.1.4 GitHub 0.1.4 GitHub [1] direct
#10 4.827 checkmate 2.3.1 CRAN 2.2.0 CRAN [1] indirect
#10 4.827 class 7.3-21 CRAN <NA> <NA> [2] <NA>
#10 4.827 cli 3.6.2 CRAN 3.6.2 CRAN [1] direct
#10 4.827 clipr 0.8.0 CRAN 0.8.0 CRAN [1] indirect
#10 4.827 cluster 2.1.4 CRAN <NA> <NA> [2] <NA>
#10 4.827 codetools 0.2-19 CRAN 0.2-19 CRAN [2] indirect
#10 4.827 colorspace 2.1-0 CRAN 2.1-0 CRAN [1] direct
#10 4.827 commonmark 1.9.1 CRAN 1.9.1 CRAN [1] indirect
#10 4.827 compiler <NA> <NA> <NA> <NA> [2] indirect
#10 4.827 config 0.3.2 CRAN 0.3.1 CRAN [1] direct
#10 4.828 corrplot 0.92 CRAN 0.92 CRAN [1] indirect
#10 4.828 countrycode 1.6.0 CRAN 1.5.0 CRAN [1] indirect
#10 4.828 cpp11 0.4.7 CRAN 0.4.7 CRAN [1] indirect
#10 4.828 crayon 1.5.2 CRAN 1.5.2 CRAN [1] indirect
#10 4.828 credentials 2.0.1 CRAN 2.0.1 CRAN [1] indirect
#10 4.828 crew 0.9.2 CRAN 0.9.2 CRAN [1] direct
#10 4.828 crosstalk 1.2.1 GitHub 1.2.1 GitHub [1] direct
#10 4.828 curl 5.2.1 CRAN 5.2.1 CRAN [1] direct
#10 4.828 data.table 1.14.10 CRAN 1.14.10 CRAN [1] indirect
#10 4.828 data.tree 1.0.0 CRAN 1.0.0 CRAN [1] indirect
#10 4.828 desc <NA> <NA> <NA> <NA> [1] indirect
#10 4.828 devtools 2.4.5 CRAN 2.4.5 CRAN [1] direct
#10 4.828 diffobj 0.3.5 CRAN 0.3.5 CRAN [1] indirect
#10 4.828 digest 0.6.35 CRAN 0.6.35 CRAN [1] direct
#10 4.828 dmdu <NA> <NA> <NA> <NA> <NA> direct
#10 4.828 docopt 0.7.1 RSPM <NA> <NA> [1] <NA>
#10 4.828 downlit 0.4.3 CRAN 0.4.3 CRAN [1] indirect
#10 4.828 downloader 0.4 CRAN 0.4 CRAN [1] indirect
#10 4.828 dplyr 1.1.4 CRAN 1.1.4 CRAN [1] direct
#10 4.828 echarts4r 0.4.5 CRAN 0.4.5 CRAN [1] direct
#10 4.828 echartsUtils 0.8.0.9000 GitHub 0.8.0.9000 GitHub [1] direct
#10 4.828 echarty 1.4.5 CRAN 1.4.5 CRAN [1] direct
#10 4.828 ellipsis 0.3.2 CRAN 0.3.2 CRAN [1] indirect
#10 4.828 emayili 0.8.0 CRAN 0.7.18 CRAN [1] indirect
#10 4.828 english 1.2-6 CRAN 1.2-6 CRAN [1] direct
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#10 4.828 foreign 0.8-84 CRAN <NA> <NA> [2] <NA>
#10 4.828 fresh 0.2.0 CRAN 0.2.0 CRAN [1] indirect
#10 4.828 fs 1.6.4 CRAN 1.6.3 CRAN [1] direct
#10 4.828 generics 0.1.3 CRAN 0.1.3 CRAN [1] indirect
#10 4.828 gert 2.0.1 CRAN 2.0.1 CRAN [1] indirect
#10 4.828 getip 0.1-4 CRAN 0.1-4 CRAN [1] indirect
#10 4.828 ggbeeswarm 0.7.2 CRAN 0.7.2 CRAN [1] direct
#10 4.830 ggplot2 3.4.4 CRAN 3.4.4 CRAN [1] direct
#10 4.830 gh 1.4.1 CRAN 1.4.0 CRAN [1] indirect
#10 4.830 gitcreds 0.1.2 CRAN 0.1.2 CRAN [1] indirect
#10 4.830 globals 0.16.2 CRAN 0.16.2 CRAN [1] indirect
#10 4.830 glue 1.7.0 CRAN 1.7.0 CRAN [1] direct
#10 4.830 golem 0.4.1 CRAN 0.4.1 CRAN [1] direct
#10 4.830 googlesheets4 <NA> <NA> <NA> <NA> <NA> direct
#10 4.830 grDevices <NA> <NA> <NA> <NA> [2] direct
#10 4.830 graphics <NA> <NA> <NA> <NA> [2] indirect
#10 4.830 grid <NA> <NA> <NA> <NA> [2] indirect
#10 4.830 gridExtra 2.3 CRAN 2.3 CRAN [1] indirect
#10 4.830 gtable 0.3.4 CRAN 0.3.4 CRAN [1] indirect
#10 4.830 hardhat 1.3.0 CRAN 1.3.0 CRAN [1] indirect
#10 4.830 here 1.0.1 CRAN 1.0.1 CRAN [1] indirect
#10 4.830 highr 0.10 CRAN 0.10 CRAN [1] indirect
#10 4.830 hms 1.1.3 CRAN 1.1.3 CRAN [1] indirect
#10 4.830 htmltools 0.5.8.1 CRAN 0.5.8.1 CRAN [1] direct
#10 4.830 htmlwidgets 1.6.4 CRAN 1.6.4 CRAN [1] direct
#10 4.830 httpuv 1.6.15 CRAN 1.6.15 CRAN [1] direct
#10 4.830 httr 1.4.7 CRAN 1.4.7 CRAN [1] indirect
#10 4.830 httr2 1.0.1 CRAN 1.0.0 CRAN [1] indirect
#10 4.830 igraph 1.5.1 CRAN 1.5.1 CRAN [1] direct
#10 4.830 ini 0.3.1 CRAN 0.3.1 CRAN [1] indirect
#10 4.830 isoband 0.2.7 CRAN 0.2.7 CRAN [1] indirect
#10 4.830 jose 1.2.0 CRAN 1.2.0 CRAN [1] indirect
#10 4.830 jquerylib 0.1.4 CRAN 0.1.4 CRAN [1] indirect
#10 4.830 jsonlite 1.8.8 CRAN 1.8.8 CRAN [1] direct
#10 4.830 jsonvalidate 1.3.2 CRAN 1.3.2 CRAN [1] direct
#10 4.830 knitr 1.46 CRAN 1.44 CRAN [1] indirect
#10 4.830 labeling 0.4.3 CRAN 0.4.3 CRAN [1] indirect
#10 4.830 later 1.3.2 CRAN 1.3.2 CRAN [1] indirect
#10 4.830 lattice 0.20-45 CRAN 0.20-45 CRAN [1] indirect
#10 4.830 lazyeval 0.2.2 CRAN 0.2.2 CRAN [1] indirect
#10 4.830 learnr 0.11.5 CRAN 0.11.3 CRAN [1] indirect
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#10 4.830 littler 0.3.18 RSPM <NA> <NA> [1] <NA>
#10 4.830 logger 0.3.0 CRAN 0.2.2 CRAN [1] indirect
#10 4.830 lubridate 1.9.3 CRAN 1.9.3 CRAN [1] direct
#10 4.830 magrittr 2.0.3 CRAN 2.0.3 CRAN [1] indirect
#10 4.830 markdown 1.12 CRAN 1.5 CRAN [1] indirect
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#10 4.830 methods <NA> <NA> <NA> <NA> [2] indirect
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#10 4.830 mime 0.12 CRAN 0.12 CRAN [1] indirect
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#10 4.830 mirai 0.12.0 CRAN 0.12.0 CRAN [1] indirect
#10 4.830 munsell 0.5.1 CRAN 0.5.0 CRAN [1] indirect
#10 4.830 mvtnorm 1.2-2 CRAN 1.2-2 CRAN [1] direct
#10 4.830 nanonext 1.0.0 CRAN 1.0.0 CRAN [1] direct
#10 4.830 nlme 3.1-162 CRAN 3.1-162 CRAN [2] indirect
#10 4.830 nnet 7.3-18 CRAN <NA> <NA> [2] <NA>
#10 4.830 openssl 2.2.0 CRAN 2.1.1 CRAN [1] indirect
#10 4.830 packer 0.1.3 CRAN 0.1.3 CRAN [1] indirect
#10 4.830 pak 0.7.2 https://r-lib.github.io/p/pak/stable/source/linux-gnu/aarch64 <NA> <NA> [1] <NA>
#10 4.830 parallel <NA> <NA> <NA> <NA> [2] indirect
#10 4.830 parsnip 1.0.4 CRAN 1.0.4 CRAN [1] direct
#10 4.830 pillar 1.9.0 CRAN 1.9.0 CRAN [1] indirect
#10 4.830 pkgbuild 1.4.4 CRAN 1.4.3 CRAN [1] indirect
#10 4.830 pkgconfig 2.0.3 CRAN 2.0.3 CRAN [1] indirect
#10 4.830 pkgdown 2.0.9 CRAN 2.0.7 CRAN [1] indirect
#10 4.830 pkgload 1.3.4 CRAN 1.3.4 CRAN [1] direct
#10 4.830 plotly 4.10.1 CRAN 4.10.1 CRAN [1] direct
#10 4.830 plyr 1.8.9 CRAN 1.8.9 CRAN [1] direct
#10 4.830 praise 1.0.0 CRAN 1.0.0 CRAN [1] indirect
#10 4.830 prettyunits 1.2.0 CRAN 1.2.0 CRAN [1] indirect
#10 4.830 processx 3.8.4 CRAN 3.8.3 CRAN [1] indirect
#10 4.830 profvis 0.3.8 CRAN 0.3.8 CRAN [1] indirect
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#10 4.830 promises 1.3.0 CRAN 1.2.1 CRAN [1] indirect
#10 4.830 ps 1.7.6 CRAN 1.7.6 CRAN [1] indirect
#10 4.830 purrr 1.0.2 CRAN 1.0.2 CRAN [1] direct
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#10 4.830 rversions 2.1.2 CRAN 2.1.2 CRAN [1] indirect
#10 4.830 rvest 1.0.4 CRAN 1.0.3 CRAN [1] indirect
#10 4.830 sass 0.4.9 CRAN 0.4.9 CRAN [1] direct
#10 4.830 scales 1.3.0 CRAN 1.3.0 CRAN [1] direct
#10 4.830 selectr 0.4-2 CRAN 0.4-2 CRAN [1] indirect
#10 4.830 sendgridr 0.6.3 GitHub 0.6.3 GitHub [1] direct
#10 4.830 sentryR 1.1.1.9000 GitHub 1.1.1.9000 GitHub [1] direct
#10 4.830 sessioninfo 1.2.2 CRAN 1.2.2 CRAN [1] indirect
#10 4.830 shiny 1.8.1.1 CRAN 1.8.1.1 CRAN [1] direct
#10 4.830 shiny.i18n 0.3.0 GitHub 0.3.0 GitHub [1] direct
#10 4.830 shiny.tailwind 0.2.2 GitHub 0.2.2 GitHub [1] direct
#10 4.830 shinyVirga 0.45.1 GitHub 0.45.1 GitHub [1] direct
#10 4.830 shinyWidgets 0.8.3 GitHub 0.8.3 GitHub [1] direct
#10 4.830 shinybrowser 1.0.0 CRAN 1.0.0 CRAN [1] direct
#10 4.830 shinycssloaders 1.0.0.9011 GitHub 1.0.0.9011 GitHub [1] direct
#10 4.830 shinyjs 2.1.0 CRAN 2.1.0 CRAN [1] direct
#10 4.830 shinytest2 <NA> <NA> <NA> <NA> <NA> direct
#10 4.830 shinyvalidate 0.1.2 CRAN 0.1.2 CRAN [1] direct
#10 4.830 sinew <NA> <NA> <NA> <NA> [1] indirect
#10 4.830 snakecase 0.11.1 CRAN 0.11.1 CRAN [1] direct
#10 4.830 sortable 0.5.0 GitHub 0.5.0 GitHub [1] direct
#10 4.830 sos <NA> <NA> <NA> <NA> [1] indirect
#10 4.830 sourcetools 0.1.7-1 CRAN 0.1.7-1 CRAN [1] indirect
#10 4.830 spatial 7.3-16 CRAN <NA> <NA> [2] <NA>
#10 4.830 splines <NA> <NA> <NA> <NA> [2] indirect
#10 4.830 stats <NA> <NA> <NA> <NA> [2] indirect
#10 4.830 stringi 1.8.4 CRAN 1.7.12 CRAN [1] direct
#10 4.830 stringr 1.5.1 CRAN 1.5.1 CRAN [1] direct
#10 4.830 survival 3.5-5 CRAN <NA> <NA> [2] <NA>
#10 4.830 svglite 2.1.1 CRAN 2.1.1 CRAN [1] direct
#10 4.830 sys 3.4.2 CRAN 3.4.2 CRAN [1] indirect
#10 4.830 systemfonts 1.1.0 CRAN 1.0.4 CRAN [1] indirect
#10 4.830 testthat 3.2.1.1 CRAN 3.2.1 CRAN [1] direct
#10 4.830 textshaping 0.3.7 CRAN 0.3.6 CRAN [1] indirect
#10 4.830 tibble 3.2.1 CRAN 3.2.1 CRAN [1] direct
#10 4.830 tidyr 1.3.1 CRAN 1.3.1 CRAN [1] direct
#10 4.830 tidyselect 1.2.1 CRAN 1.2.1 CRAN [1] direct
#10 4.830 timechange 0.3.0 CRAN 0.3.0 CRAN [1] indirect
#10 4.830 tinytex 0.51 CRAN 0.46 CRAN [1] indirect
#10 4.830 tippy 1.0.0 GitHub 1.0.0 GitHub [1] direct
#10 4.830 tools <NA> <NA> <NA> <NA> [2] indirect
#10 4.830 transifex 0.0.4 GitHub 0.0.4 GitHub [1] direct
#10 4.830 triebeard 0.4.1 CRAN 0.4.1 CRAN [1] indirect
#10 4.830 tzdb 0.4.0 CRAN 0.4.0 CRAN [1] indirect
#10 4.830 urlchecker 1.0.1 CRAN 1.0.1 CRAN [1] indirect
#10 4.830 urltools 1.7.3 CRAN 1.7.3 CRAN [1] indirect
#10 4.830 usethis 2.2.3 CRAN 2.2.2 CRAN [1] indirect
#10 4.830 utf8 1.2.4 CRAN 1.2.4 CRAN [1] direct
#10 4.830 utils <NA> <NA> <NA> <NA> [2] direct
#10 4.830 uuid 1.2-0 CRAN 1.1-0 CRAN [1] indirect
#10 4.830 vctrs 0.6.5 CRAN 0.6.5 CRAN [1] direct
#10 4.830 vipor 0.4.5 CRAN 0.4.5 CRAN [1] indirect
#10 4.830 virgaUtils 0.5.0 GitHub 0.5.0 GitHub [1] direct
#10 4.830 viridis 0.6.3 CRAN 0.6.3 CRAN [1] indirect
#10 4.830 viridisLite 0.4.2 CRAN 0.4.2 CRAN [1] indirect
#10 4.830 visNetwork 2.1.2 CRAN 2.1.2 CRAN [1] indirect
#10 4.830 vroom 1.6.1 CRAN 1.6.1 CRAN [1] indirect
#10 4.830 waiter 0.2.5 CRAN 0.2.5 CRAN [1] indirect
#10 4.830 waldo 0.5.2 CRAN 0.5.1 CRAN [1] indirect
#10 4.830 whisker 0.4.1 CRAN 0.4.1 CRAN [1] indirect
#10 4.830 withr 3.0.0 CRAN 3.0.0 CRAN [1] indirect
#10 4.830 xfun 0.44 CRAN 0.40 CRAN [1] indirect
#10 4.830 xgboost 1.7.5.1 CRAN 1.7.5.1 CRAN [1] direct
#10 4.830 xml2 1.3.6 CRAN 1.3.5 CRAN [1] indirect
#10 4.830 xopen 1.0.1 CRAN 1.0.0 CRAN [1] indirect
#10 4.830 xtable 1.8-4 CRAN 1.8-4 CRAN [1] indirect
#10 4.830 yaml 2.3.8 CRAN 2.3.8 CRAN [1] indirect
#10 4.830 yardstick 1.1.0 CRAN 1.1.0 CRAN [1] direct
#10 4.830 zip 2.3.1 CRAN 2.3.1 CRAN [1] indirect
#10 4.830
#10 4.830 [1]: /usr/local/lib/R/site-library
#10 4.830 [2]: /usr/local/lib/R/library
#10 4.830
#10 4.830 # ABI ------------------------------------------------------------------------
#10 6.700 - No ABI problems were detected in the set of installed packages.
#10 6.700
#10 6.700 # User Profile ---------------------------------------------------------------
#10 6.700 [no user profile detected]
#10 6.700
#10 6.700 # Settings -------------------------------------------------------------------
#10 6.702 List of 13
#10 6.702 $ bioconductor.version : chr(0)
#10 6.702 $ external.libraries : chr(0)
#10 6.703 $ ignored.packages : chr [1:12] "sinew" "desc" "sos" "todor" ...
#10 6.703 $ package.dependency.fields: chr [1:3] "Imports" "Depends" "LinkingTo"
#10 6.703 $ ppm.enabled : NULL
#10 6.704 $ ppm.ignored.urls : NULL
#10 6.704 $ r.version : chr(0)
#10 6.705 $ snapshot.type : chr "explicit"
#10 6.705 $ use.cache : logi TRUE
#10 6.706 $ vcs.ignore.cellar : logi TRUE
#10 6.706 $ vcs.ignore.library : logi TRUE
#10 6.706 $ vcs.ignore.local : logi TRUE
#10 6.707 $ vcs.manage.ignores : logi TRUE
#10 6.707
#10 6.707 # Options --------------------------------------------------------------------
#10 6.708 List of 9
#10 6.708 $ defaultPackages : chr [1:6] "datasets" "utils" "grDevices" "graphics" ...
#10 6.708 $ download.file.method : chr "libcurl"
#10 6.709 $ download.file.extra : NULL
#10 6.709 $ install.packages.compile.from.source: NULL
#10 6.709 $ pkgType : chr "source"
#10 6.710 $ repos : Named chr "https://cran.rstudio.com/"
#10 6.710 ..- attr(*, "names")= chr "CRAN"
#10 6.710 $ renv.config.pak.enabled : logi TRUE
#10 6.711 $ renv.config.auto.snapshot : logi TRUE
#10 6.711 $ renv.verbose : logi TRUE
#10 6.711
#10 6.711 # Environment Variables ------------------------------------------------------
#10 6.712 HOME = /root
#10 6.712 LANG = en_US.UTF-8
#10 6.712 MAKE = make
#10 6.712 R_LIBS = /usr/local/lib/R/site-library:/usr/local/lib/R/library
#10 6.712 R_LIBS_SITE = /usr/local/lib/R/site-library
#10 6.712 R_LIBS_USER = /root/R/aarch64-unknown-linux-gnu-library/4.3
#10 6.712 RENV_PATHS_LIBRARY = /usr/local/lib/R/site-library
#10 6.712
#10 6.712 # PATH -----------------------------------------------------------------------
#10 6.712 - /usr/local/sbin
#10 6.712 - /usr/local/bin
#10 6.712 - /usr/sbin
#10 6.712 - /usr/bin
#10 6.712 - /sbin
#10 6.712 - /bin
#10 6.712
#10 6.712 # Cache ----------------------------------------------------------------------
#10 6.714 There are a total of 2 packages installed in the renv cache.
#10 6.715 Cache path: "~/.cache/R/renv/cache/v5/R-4.3/aarch64-unknown-linux-gnu"
#10 6.715
#10 6.720 Package: bs4Dash
#10 6.720 Type: Package
#10 6.720 Title: A 'Bootstrap 4' Version of 'shinydashboard'
#10 6.720 Version: 2.2.1
#10 6.720 Authors@R: c( person("David", "Granjon", email = "dgranjon@ymail.com",
#10 6.720 role = c("aut", "cre")), person(family = "RinteRface", role =
#10 6.720 "cph"), person(family = "Almasaeed Studio", role = c("ctb",
#10 6.720 "cph"), comment = "AdminLTE3 theme for Bootstrap 4"),
#10 6.720 person("Winston", "Chang", role = c("ctb", "cph"), comment =
#10 6.720 "Utils functions from shinydashboard"))
#10 6.720 Maintainer: David Granjon <dgranjon@ymail.com>
#10 6.720 Description: Make 'Bootstrap 4' Shiny dashboards. Use the full power of
#10 6.720 'AdminLTE3', a dashboard template built on top of 'Bootstrap 4'
#10 6.720 <https://github.com/ColorlibHQ/AdminLTE>.
#10 6.720 URL: https://rinterface.github.io/bs4Dash/index.html,
#10 6.720 https://github.com/RinteRface/bs4Dash
#10 6.720 BugReports: https://github.com/RinteRface/bs4Dash/issues
#10 6.720 License: GPL (>= 2) | file LICENSE
#10 6.720 Imports: shiny (>= 1.6.0), htmltools (>= 0.5.1.1), jsonlite (>=
#10 6.720 0.9.16), fresh, grDevices, waiter (>= 0.2.3), httpuv (>=
#10 6.720 1.5.2), lifecycle, bslib (>= 0.2.4), httr, UU (>= 1.5.1)
#10 6.720 Suggests: knitr, rmarkdown, testthat (>= 2.1.0), golem, DT, thematic
#10 6.720 (>= 0.1.2)
#10 6.720 Encoding: UTF-8
#10 6.720 RoxygenNote: 7.2.3
#10 6.720 VignetteBuilder: knitr
#10 6.720 Collate: 'aaa_reimports.R' 'feedbacks.R' 'useful-items.R' 'tabs.R'
#10 6.720 .....
#10 6.720 RdMacros: lifecycle
#10 6.720 Remotes: yogat3ch/UU
#10 6.720 NeedsCompilation: no
#10 6.720 Packaged: 2024-05-23 14:58:06 UTC; root
#10 6.720 Author: David Granjon [aut, cre], RinteRface [cph], Almasaeed Studio
#10 6.720 [ctb, cph] (AdminLTE3 theme for Bootstrap 4), Winston Chang
#10 6.720 [ctb, cph] (Utils functions from shinydashboard)
#10 6.720 Built: R 4.3.0; ; 2024-05-23 14:58:07 UTC; unix
#10 6.720 RemoteType: github
#10 6.720 RemoteHost: api.github.com
#10 6.720 RemoteRepo: bs4Dash
#10 6.720 RemoteUsername: yogat3ch
#10 6.720 RemotePkgRef: yogat3ch/bs4Dash@HEAD
#10 6.720 RemoteRef: HEAD
#10 6.720 RemoteSha: 1d4d4618e47457067fd07e17c840e58f0213c684
#10 6.720 GithubRepo: bs4Dash
#10 6.720 GithubUsername: yogat3ch
#10 6.720 GithubRef: HEAD
#10 6.720 GithubSHA1: 1d4d4618e47457067fd07e17c840e58f0213c684
#10 6.720
#10 6.720 -- File: /usr/local/lib/R/site-library/bs4Dash/Meta/package.rds
#10 16.37
#10 17.32 ✔ Updated metadata database: 1.37 MB in 1 file.
#10 17.32
#10 17.32 ℹ Updating metadata database
#10 20.11 ✔ Updating metadata database ... done
#10 20.11
#10 20.51
#10 20.52
#10 20.72 ℹ No downloads are needed
#10 20.76 ✔ 2 pkgs + 1 dep: [6.4s]
#10 20.78 >
#10 20.78 >
#10 DONE 21.7s
#11 [stage-4 6/17] RUN R --quiet -e "pkgload::load_all(); .libPaths();renv_gh_pkgs_install(rev(renv_gh_pkgs()));"
#11 0.349 > pkgload::load_all(); .libPaths();renv_gh_pkgs_install(rev(renv_gh_pkgs()));
#11 0.574 ℹ Loading dmdu
#11 0.791 ℹ `opts` & `toggle` functions were generated for the following options in
#11 0.791 '.Rprofile': use_db, use_crew, use_tracking, use_translation, max_policies,
#11 0.791 phase, use_local_db_API, renv.config.auto.snapshot, memoise, use_reprex,
#11 0.791 use_debug, use_intro, shiny.autoload.r, shiny.testmode
#11 0.791 This message is displayed once per session.
#11 2.254 Error in load_imports(path) :
#11 2.254 The package "bs4Dash" (>= 2.3.3) is required.
#11 2.254 Calls: <Anonymous> ... load_imports -> deps_check_installed -> check_installed
#11 2.254 Execution halted
#11 ERROR: process "/bin/sh -c R --quiet -e \"pkgload::load_all(); .libPaths();renv_gh_pkgs_install(rev(renv_gh_pkgs()));\"" did not complete successfully: exit code: 1
------
> [stage-4 6/17] RUN R --quiet -e "pkgload::load_all(); .libPaths();renv_gh_pkgs_install(rev(renv_gh_pkgs()));":
0.574 ℹ Loading dmdu
0.791 ℹ `opts` & `toggle` functions were generated for the following options in
0.791 '.Rprofile': use_db, use_crew, use_tracking, use_translation, max_policies,
0.791 phase, use_local_db_API, renv.config.auto.snapshot, memoise, use_reprex,
0.791 use_debug, use_intro, shiny.autoload.r, shiny.testmode
0.791 This message is displayed once per session.
2.254 Error in load_imports(path) :
2.254 The package "bs4Dash" (>= 2.3.3) is required.
2.254 Calls: <Anonymous> ... load_imports -> deps_check_installed -> check_installed
2.254 Execution halted
------
Dockerfile:42
--------------------
40 | RUN R --quiet -e "renv::diagnostics();packageDescription('bs4Dash');renv::restore()"
41 | # Install the versions of Github packages specified in the lockfile
42 | >>> RUN R --quiet -e "pkgload::load_all(); .libPaths();renv_gh_pkgs_install(rev(renv_gh_pkgs()));"
43 | # Creates a directory to hold deployment related files.
44 | RUN mkdir -p deploy
--------------------
ERROR: failed to solve: process "/bin/sh -c R --quiet -e \"pkgload::load_all(); .libPaths();renv_gh_pkgs_install(rev(renv_gh_pkgs()));\"" did not complete successfully: exit code: 1
|
|
Apologies for the late response; I've been out of office. I'm hoping to investigate again shortly; is your diagnosis in #1883 (comment) still current? |
|
Hi @kevinushey , I believe this is related: I am seeing that some packages in a The attached lock file generates the following build output: As you can see, bit, bit64, blob, vctrs, glue, lifecycle, and pkgconfig are all ignored. The lockfile restores properly outside of a Docker context. |
|
@kmasiello I suspect this is because those packages are already installed in another library on your library paths, or because those packages were already installed via some separate mechanism. Is that possible? Are you able to share the whole build log? |
|
<ceases pulling out hair> @kevinushey I think you're right. They are buried in our base r-session-complete image. Still haven't found exactly where, but running a clean session with just |
|
I think I have encountered the same issue @yogat3ch mentioned in this comment. Here is a reprex in case it helps. I think the important thing here is the lockfile contains a github package mkdir renv-pak-test && cd renv-pak-test
# might need to clear the pak cache first? not sure
# Rscript -e "pak::cache_clean(); pak::meta_clean(force = TRUE)"
# Install packages. ggbarf is a github package that depends on another github
# package, ggtextures. here I'm installing an older commit of ggtextures --
# that's what should make it into the lockfile
Rscript -e "remotes::install_github('rstudio/renv@5725cdee36c6d0b8c32fef4f0bd4b4e1da9e73e2'); remotes::install_github('clauswilke/ggtextures@156c0c6799b53b317d4dfc5ba284254f0fd68ed5'); remotes::install_github('karawoo/ggbarf@master')"
echo "library('ggbarf')" >> script.R
Rscript -e "renv::init()"
# succeeds
rm -rf renv/library
Rscript -e "renv::restore()"
# fails
rm -rf renv/library
Rscript -e "options('renv.config.pak.enabled'=TRUE); renv::restore()"
mkdir renv-pak-test && cd renv-pak-test
# installing an older commit of bslib
Rscript -e "remotes::install_github('rstudio/renv@5725cdee36c6d0b8c32fef4f0bd4b4e1da9e73e2'); remotes::install_github('rstudio/bslib@e862e0bdd7deafcad7b001b058995308a0b36654'); remotes::install_github('rstudio/shinyuieditor@main')"
echo "library('shinyuieditor')" >> script.R
Rscript -e "renv::init()"
# succeeds
rm -rf renv/library
Rscript -e "renv::restore()"
# also succeeds
rm -rf renv/library
Rscript -e "options('renv.config.pak.enabled'=TRUE); renv::restore()"
|
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For reference, I think the issue arises because and that implicitly means, for I think this would need to be handled in Somewhat more minimal example: |
|
It's also possible that |
|
If you are sure that you have all dependencies covered, then try passing |
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Awesome; thanks, I'll do that! |
kevinushey
added a commit
that referenced
this issue
Oct 10, 2024
|
This gets closer, but with the above example > renv::restore(exclude = "renv")
✔ Loading metadata database ... done
→ Will install 2 packages.
→ All 2 packages (0 B) are cached.
+ ggbarf 0.0.0.9000 👷🏼🔧 (GitHub: d42cc6e)
+ ggtextures 0.0.1 👷🏽🔧 (GitHub: 156c0c6)
ℹ No downloads are needed, 2 pkgs are cached
ℹ Building ggtextures 0.0.1
ℹ Building ggbarf 0.0.0.9000
✖ Failed to build ggbarf 0.0.0.9000 (128ms)
Error:
! error in pak subprocess
Caused by error in `stop_task_build(state, worker)`:
! Failed to build source package ggbarf.
Type .Last.error to see the more details.
Traceback (most recent calls last):
6: renv::restore(exclude = "renv")
5: renv_pak_restore(lockfile = lockfile, packages = packages, exclude = exclude,
prompt = prompt, project = project)
4: pak$pkg_install(pkg = remotes, ask = prompt, dependencies = FALSE)
3: remote(function(...) get("pkg_install_do_plan", asNamespace("pak"))(...),
list(proposal = NULL))
2: err$throw(res$error)
1: base::stop(cond)
> .Last.error
<callr_error/rlib_error_3_0/rlib_error/error>
Error:
! error in pak subprocess
Caused by error in `stop_task_build(state, worker)`:
! Failed to build source package ggbarf.
---
Backtrace:
1. renv::restore(exclude = "renv")
2. renv:::renv_pak_restore(lockfile = lockfile, packages = packages, exclude = exclude, …
3. pak$pkg_install(pkg = remotes, ask = prompt, dependencies = FALSE)
4. pak:::remote(function(...) get("pkg_install_do_plan", asNamespace("pak"))(...), …
5. err$throw(res$error)
---
Subprocess backtrace:
1. base::withCallingHandlers(cli_message = function(msg) { …
2. get("pkg_install_do_plan", asNamespace("pak"))(...)
3. proposal$install()
4. pkgdepends::install_package_plan(plan, lib = private$library, num_workers = nw, …
5. base::withCallingHandlers({ …
6. pkgdepends:::handle_events(state, events)
7. pkgdepends:::handle_event(state, i)
8. pkgdepends:::stop_task(state, worker)
9. pkgdepends:::stop_task_build(state, worker)
10. base::throw(pkg_error("Failed to build source package {.pkg {pkg}}.", …
11. | base::signalCondition(cond)
12. global (function (e) …Any recommendations on how I can debug / get more output on the underlying error here? The package does install successfully without |
|
I wonder if this is because # work in new library
templib <- tempfile("library-")
dir.create(templib)
.libPaths(templib)
# get pak
install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/stable/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))
# install ggbarf to prepare library
pak::pkg_install("karawoo/ggbarf")
# now, try installing those specific remote requirements
remotes <- c(
ggbarf = "karawoo/ggbarf@d42cc6ec343fa9fd37f4308eb0956c012edd342d",
ggtextures = "clauswilke/ggtextures@156c0c6799b53b317d4dfc5ba284254f0fd68ed5"
)
# remove cached packages + installed packages for testing
pak::cache_delete(package = "ggbarf")
pak::cache_delete(package = "ggtextures")
remove.packages(c("ggbarf", "ggtextures"))
# try to install
pak::pkg_install(remotes, dependencies = FALSE)That gives me: > pak::pkg_install(remotes, dependencies = FALSE)
→ Will install 2 packages.
→ Will download 2 packages with unknown size.
+ ggbarf 0.0.0.9000 👷🏻♂️🔧 ⬇ (GitHub: d42cc6e)
+ ggtextures 0.0.1 👷🏼♀️🔧 ⬇ (GitHub: 156c0c6)
ℹ Getting 2 pkgs with unknown sizes
✔ Got ggbarf 0.0.0.9000 (source) (58.29 kB)
✔ Got ggtextures 0.0.1 (source) (1.72 MB)
✔ Downloaded 2 packages (1.78 MB) in 631ms
ℹ Packaging ggbarf 0.0.0.9000
ℹ Packaging ggtextures 0.0.1
✔ Packaged ggbarf 0.0.0.9000 (379ms)
ℹ Building ggbarf 0.0.0.9000
✔ Packaged ggtextures 0.0.1 (462ms)
ℹ Building ggtextures 0.0.1
✖ Failed to build ggbarf 0.0.0.9000 (147ms)
Error:
! error in pak subprocess
Caused by error in `stop_task_build(state, worker)`:
! Failed to build source package ggbarf.
Type .Last.error to see the more details.If that's the case, I think |
|
Oh, yeah, that's a good point, then |
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Hi @kevinushey and renv dev team,
We're using
renv::restoreas part of our Docker build process and just discovered that whenrenv::restoreruns while building the Docker image it's not respecting the RemoteSHA recorded in the lockfile for github dependencies, and is rather using the most recent commit. I was under the assumption thatrenv::restoreuses the RemoteSHA specified in the renv.lock file, but that doesn't seem to be the case. Am I missing a configuration option to ensure thatrenv::restoreuses the RemoteSHA from the lock file?The text was updated successfully, but these errors were encountered: