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renv still unstable #2103
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The fact that installation is failing because 'zoo' could not be found, even though it was installed in the previous step, makes me think that your R installation has been customized in some way that's manipulating the library paths in a way that Can you also share the output of |
You might also want to try using options(renv.config.pak.enabled = TRUE)
renv::install("colorspace", dependencies = TRUE) since |
Thanks so much for the response. I've since wiped out the renv, started again and it ran. It ran fine with a minimal install of colorspace in a test folder. The only potentially unexpected thing re libraries is that I use the r2u system for package installs. What seems most likely is that an incomplete installation of something happened randomly, making it look like an install occured when it didn't and renv couldn't detect it and couldn't recover from it? I'm happy to still share diagnostics when I'm back at a computer. |
Here you go - after removing my renv setup for the project and starting it again it worked. However, the NAs for the packages that ship with R still might be a clue. > renv::status()
No issues found -- the project is in a consistent state.
> renv::diagnostics()
Diagnostics Report [renv 1.1.2]
===============================
# /etc/lsb-release -----------------------------------------------------------
DISTRIB_ID=Ubuntu
DISTRIB_RELEASE=22.04
DISTRIB_CODENAME=jammy
DISTRIB_DESCRIPTION="Ubuntu 22.04.5 LTS"
# /etc/os-release ------------------------------------------------------------
PRETTY_NAME="Ubuntu 22.04.5 LTS"
NAME="Ubuntu"
VERSION_ID="22.04"
VERSION="22.04.5 LTS (Jammy Jellyfish)"
VERSION_CODENAME=jammy
ID=ubuntu
ID_LIKE=debian
HOME_URL="https://www.ubuntu.com/"
SUPPORT_URL="https://help.ubuntu.com/"
BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
UBUNTU_CODENAME=jammy
# Session Info ---------------------------------------------------------------
R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.5 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
locale:
[1] LC_CTYPE=C.UTF-8 LC_NUMERIC=C LC_TIME=C.UTF-8
[4] LC_COLLATE=C.UTF-8 LC_MONETARY=C.UTF-8 LC_MESSAGES=C.UTF-8
[7] LC_PAPER=C.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C
time zone: Pacific/Auckland
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices datasets utils methods base
loaded via a namespace (and not attached):
[1] compiler_4.4.2 tools_4.4.2 bspm_0.5.7 renv_1.1.2
# Project --------------------------------------------------------------------
Project path: "~/projects_bitbucketlinux/climate-data"
# Status ---------------------------------------------------------------------
No issues found -- the project is in a consistent state.
# Packages -------------------------------------------------------------------
Library Source Lockfile Source Path Dependency
DBI 1.2.3 CRAN 1.2.3 CRAN [1] indirect
KernSmooth 2.23-26 CRAN 2.23-26 CRAN [1] indirect
MASS 7.3-65 CRAN 7.3-65 CRAN [1] indirect
Matrix 1.7-2 CRAN 1.7-2 CRAN [1] indirect
R6 2.6.1 CRAN 2.6.1 CRAN [1] indirect
RColorBrewer 1.1-3 CRAN 1.1-3 CRAN [1] indirect
Rcpp 1.0.14 CRAN 1.0.14 CRAN [1] indirect
arrow 19.0.1 CRAN 19.0.1 CRAN [1] direct
assertthat 0.2.1 CRAN 0.2.1 CRAN [1] indirect
backports 1.5.0 CRAN 1.5.0 CRAN [1] indirect
base64url 1.4 CRAN 1.4 CRAN [1] indirect
bit 4.5.0.1 CRAN 4.5.0.1 CRAN [1] indirect
bit64 4.6.0-1 CRAN 4.6.0-1 CRAN [1] indirect
callr 3.7.6 CRAN 3.7.6 CRAN [1] indirect
class 7.3-23 CRAN 7.3-23 CRAN [1] indirect
classInt 0.4-11 CRAN 0.4-11 CRAN [1] indirect
cli 3.6.4 CRAN 3.6.4 CRAN [1] indirect
codetools 0.2-20 CRAN 0.2-20 CRAN [1] indirect
colorspace 2.1-1 CRAN 2.1-1 CRAN [1] indirect
compiler <NA> <NA> <NA> <NA> [2] indirect
cpp11 0.5.1 CRAN 0.5.1 CRAN [1] indirect
data.table 1.17.0 CRAN 1.17.0 CRAN [1] indirect
devtools <NA> <NA> <NA> <NA> <NA> direct
digest 0.6.37 CRAN 0.6.37 CRAN [1] direct
dplyr 1.1.4 CRAN 1.1.4 CRAN [1] direct
e1071 1.7-16 CRAN 1.7-16 CRAN [1] indirect
evaluate 1.0.3 CRAN 1.0.3 CRAN [1] indirect
fansi 1.0.6 CRAN 1.0.6 CRAN [1] indirect
farver 2.1.2 CRAN 2.1.2 CRAN [1] indirect
formatR 1.14 CRAN 1.14 CRAN [1] indirect
fs 1.6.5 CRAN 1.6.5 CRAN [1] indirect
futile.logger 1.4.3 CRAN 1.4.3 CRAN [1] direct
futile.options 1.0.1 CRAN 1.0.1 CRAN [1] indirect
future 1.34.0 CRAN 1.34.0 CRAN [1] direct
future.apply 1.11.3 CRAN 1.11.3 CRAN [1] direct
generics 0.1.3 CRAN 0.1.3 CRAN [1] indirect
geoarrow 0.2.1 CRAN 0.2.1 CRAN [1] direct
ggplot2 3.5.1 CRAN 3.5.1 CRAN [1] direct
globals 0.16.3 CRAN 0.16.3 CRAN [1] indirect
glue 1.8.0 CRAN 1.8.0 CRAN [1] indirect
grDevices <NA> <NA> <NA> <NA> [2] indirect
graphics <NA> <NA> <NA> <NA> [2] indirect
grid <NA> <NA> <NA> <NA> [2] indirect
gtable 0.3.6 CRAN 0.3.6 CRAN [1] indirect
highr 0.11 CRAN 0.11 CRAN [1] indirect
igraph 2.1.4 CRAN 2.1.4 CRAN [1] indirect
isoband 0.2.7 CRAN 0.2.7 CRAN [1] indirect
knitr 1.49 CRAN 1.49 CRAN [1] indirect
labeling 0.4.3 CRAN 0.4.3 CRAN [1] indirect
lambda.r 1.2.4 CRAN 1.2.4 CRAN [1] indirect
lattice 0.22-6 CRAN 0.22-6 CRAN [1] indirect
lifecycle 1.0.4 CRAN 1.0.4 CRAN [1] indirect
listenv 0.9.1 CRAN 0.9.1 CRAN [1] indirect
magrittr 2.0.3 CRAN 2.0.3 CRAN [1] indirect
methods <NA> <NA> <NA> <NA> [2] indirect
mgcv 1.9-1 CRAN 1.9-1 CRAN [1] indirect
munsell 0.5.1 CRAN 0.5.1 CRAN [1] indirect
nanoarrow 0.6.0 CRAN 0.6.0 CRAN [1] indirect
nlme 3.1-167 CRAN 3.1-167 CRAN [1] indirect
parallel <NA> <NA> <NA> <NA> [2] indirect
parallelly 1.42.0 CRAN 1.42.0 CRAN [1] indirect
pillar 1.10.1 CRAN 1.10.1 CRAN [1] indirect
pkgconfig 2.0.3 CRAN 2.0.3 CRAN [1] indirect
processx 3.8.6 CRAN 3.8.6 CRAN [1] indirect
proxy 0.4-27 CRAN 0.4-27 CRAN [1] indirect
ps 1.9.0 CRAN 1.9.0 CRAN [1] indirect
purrr 1.0.4 CRAN 1.0.4 CRAN [1] indirect
renv 1.1.2 RSPM 1.1.2 RSPM [1] direct
rlang 1.1.5 CRAN 1.1.5 CRAN [1] indirect
roxygen2 <NA> <NA> <NA> <NA> <NA> direct
s2 1.1.7 CRAN 1.1.7 CRAN [1] indirect
scales 1.3.0 CRAN 1.3.0 CRAN [1] indirect
secretbase 1.0.4 CRAN 1.0.4 CRAN [1] indirect
sf 1.0-19 CRAN 1.0-19 CRAN [1] direct
splines <NA> <NA> <NA> <NA> [2] indirect
stats <NA> <NA> <NA> <NA> [2] direct
tarchetypes 0.12.0 CRAN 0.12.0 CRAN [1] direct
targets 1.10.1 CRAN 1.10.1 CRAN [1] direct
terra 1.8-29 CRAN 1.8-29 CRAN [1] direct
tibble 3.2.1 CRAN 3.2.1 CRAN [1] direct
tidyselect 1.2.1 CRAN 1.2.1 CRAN [1] indirect
tools <NA> <NA> <NA> <NA> [2] direct
units 0.8-5 CRAN 0.8-5 CRAN [1] indirect
utf8 1.2.4 CRAN 1.2.4 CRAN [1] indirect
utils <NA> <NA> <NA> <NA> [2] direct
uuid 1.2-1 CRAN 1.2-1 CRAN [1] direct
vctrs 0.6.5 CRAN 0.6.5 CRAN [1] indirect
viridisLite 0.4.2 CRAN 0.4.2 CRAN [1] indirect
withr 3.0.2 CRAN 3.0.2 CRAN [1] indirect
wk 0.9.4 CRAN 0.9.4 CRAN [1] indirect
xfun 0.51 CRAN 0.51 CRAN [1] indirect
yaml 2.3.10 CRAN 2.3.10 CRAN [1] direct
[1]: /home/kendonb/.cache/R/renv/library/climate-data-cfdf3c55/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu
[2]: /home/kendonb/.cache/R/renv/sandbox/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu/9a444a72
# R System Requirements ------------------------------------------------------
The following required system packages are not installed:
- cmake [required by arrow]
The R packages depending on these system packages may fail to install.
An administrator can install these packages with:
- sudo apt install cmake
# ABI ------------------------------------------------------------------------
- No ABI problems were detected in the set of installed packages.
# User Profile ---------------------------------------------------------------
[no user profile detected]
# Settings -------------------------------------------------------------------
List of 13
$ bioconductor.version : NULL
$ external.libraries : chr(0)
$ ignored.packages : chr(0)
$ package.dependency.fields: chr [1:3] "Imports" "Depends" "LinkingTo"
$ ppm.enabled : NULL
$ ppm.ignored.urls : chr(0)
$ r.version : NULL
$ 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 : NULL
$ download.file.extra : NULL
$ install.packages.compile.from.source: NULL
$ pkgType : chr "both"
$ repos : Named chr "https://cloud.r-project.org"
..- attr(*, "names")= chr "CRAN"
$ renv.consent : logi TRUE
$ renv.project.path : chr "/home/kendonb/projects_bitbucketlinux/climate-data"
$ renv.verbose : logi TRUE
# Environment Variables ------------------------------------------------------
HOME = /home/kendonb
LANG = C.UTF-8
MAKE = make
R_LIBS = <NA>
R_LIBS_SITE = /usr/local/lib/R/site-library/:/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library
R_LIBS_USER = /home/kendonb/.cache/R/renv/library/climate-data-cfdf3c55/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu
RENV_DEFAULT_R_ENVIRON = <NA>
RENV_DEFAULT_R_ENVIRON_USER = <NA>
RENV_DEFAULT_R_LIBS = <NA>
RENV_DEFAULT_R_LIBS_SITE = /usr/local/lib/R/site-library/:/usr/local/lib/R/site-library:/usr/lib/R/site-library:/usr/lib/R/library
RENV_DEFAULT_R_LIBS_USER = /home/kendonb/R/x86_64-pc-linux-gnu-library/4.4
RENV_DEFAULT_R_PROFILE = <NA>
RENV_DEFAULT_R_PROFILE_USER = <NA>
RENV_PROJECT = /home/kendonb/projects_bitbucketlinux/climate-data
# PATH -----------------------------------------------------------------------
- /home/kendonb/.cursor-server/bin/be4f0962469499f009005e66867c8402202ff0b0/bin/remote-cli
- /home/kendonb/.local/bin
- /home/kendonb/miniconda3/bin
- /home/kendonb/miniconda3/condabin
- /home/kendonb/.cargo/bin
- /usr/local/sbin
- /usr/local/bin
- /usr/sbin
- /usr/bin
- /sbin
- /bin
- /usr/games
- /usr/local/games
- /usr/lib/wsl/lib
- /mnt/c/Users/KennyBell/miniconda3
- /mnt/c/Users/KennyBell/miniconda3/Library/mingw-w64/bin
- /mnt/c/Users/KennyBell/miniconda3/Library/usr/bin
- /mnt/c/Users/KennyBell/miniconda3/Library/bin
- /mnt/c/Users/KennyBell/miniconda3/Scripts
- /mnt/c/Users/KennyBell/miniconda3/bin
- /mnt/c/Program Files/PowerShell/7
- /mnt/c/Program Files (x86)/Common Files/Oracle/Java/javapath
- /mnt/c/Windows/system32
- /mnt/c/Windows
- /mnt/c/Windows/System32/Wbem
- /mnt/c/Windows/System32/WindowsPowerShell/v1.0
- /mnt/c/Windows/System32/OpenSSH
- /mnt/c/Program Files/dotnet
- /mnt/c/Users/KennyBell/AppData/Roaming/nvm
- /mnt/c/Program Files/nodejs
- /mnt/c/Program Files (x86)/Lua/5.1
- /mnt/c/Program Files (x86)/Lua/5.1/clibs
- /mnt/c/Program Files/Git/cmd
- /mnt/c/ProgramData/chocolatey/bin
- /mnt/c/Users/KennyBell/AppData/Local/Programs/cursor/resources/app/bin
- /mnt/c/WINDOWS/system32
- /mnt/c/WINDOWS
- /mnt/c/WINDOWS/System32/Wbem
- /mnt/c/WINDOWS/System32/WindowsPowerShell/v1.0
- /mnt/c/WINDOWS/System32/OpenSSH
- /mnt/c/Program Files/Docker/Docker/resources/bin
- /mnt/c/Program Files/Amazon/AWSCLIV2
- /mnt/c/Program Files/PowerShell/7
- /mnt/c/Users/KennyBell/.local/bin
- /mnt/c/Users/KennyBell/AppData/Local/Programs/Quarto/bin
- /mnt/c/Users/KennyBell/AppData/Roaming/TinyTeX/bin/windows
- /mnt/c/Users/KennyBell/AppData/Local/Microsoft/WindowsApps
- /mnt/c/Users/KennyBell/AppData/Local/Programs/Microsoft VS Code/bin
- /mnt/c/Users/KennyBell/AppData/Local/Programs/MiKTeX/miktex/bin/x64
- /mnt/c/Users/KennyBell/AppData/Roaming/nvm
- /mnt/c/Program Files/nodejs
- /mnt/c/Users/KennyBell/AppData/Roaming/nvm/v19.9.0
- /mnt/c/Program Files/R/R-4.4.1/bin/x64
- /mnt/c/Program Files (x86)/Lua/5.1
- /mnt/c/Users/KennyBell/AppData/Local/Programs/Microsoft VS Code Insiders/bin
- /mnt/c/Users/KennyBell/.dotnet/tools
- /mnt/c/rakudo/bin
- /mnt/c/rakudo/share/perl6/site/bin
- /mnt/c/RBuildTools/4.4/usr/bin
- /mnt/c/RBuildTools/4.4/mingw64/bin
- /mnt/c/Users/KennyBell/AppData/Local/Pandoc
- /mnt/c/Users/KennyBell/AppData/Local/Microsoft/WindowsApps
- /mnt/c/Users/KennyBell/AppData/Local/Programs/Julia-1.9.1/bin
- /mnt/c/Users/KennyBell/miniconda3/condabin
- /mnt/c/Users/KennyBell/AppData/Local/Programs/cursor/resources/app/bin
- /mnt/c/Users/KennyBell/AppData/Local/Muse Hub/lib
- /mnt/c/Users/KennyBell/miniconda3/Library/bin
- /mnt/c/Users/KennyBell/miniconda3/Scripts
- /mnt/c/Users/KennyBell/miniconda3/condabin
- /snap/bin
- /home/kendonb/julia-1.9.0/bin
- /home/kendonb/julia-1.9.0/bin
# Cache ----------------------------------------------------------------------
There are a total of 152 packages installed in the renv cache.
Cache path: "~/.cache/R/renv/cache/v5/linux-ubuntu-jammy/R-4.4/x86_64-pc-linux-gnu"
|
I am trying out renv after about 6 years of not really using it. I have found it is still quite buggy and unstable, with packages failing to install, needing to start again to get renv working. I don't have much to offer other than this vague feedback and that I've been struggling to install
colorspace
andlmtest
on WSL.The text was updated successfully, but these errors were encountered: