kevinushey
commented
5 months ago It looks like you're using an older version of renv. Can you please try updating to renv 1.0.3?
Open maxlindmark opened 5 months ago
kevinushey
commented
5 months ago It looks like you're using an older version of renv. Can you please try updating to renv 1.0.3?
maxlindmark
commented
5 months ago Ah, I thought I had done that, sorry. Ok trying again results in this:
> library(renv)
Attaching package: ‘renv’
The following objects are masked from ‘package:stats’:
embed, update
The following objects are masked from ‘package:utils’:
history, upgrade
The following objects are masked from ‘package:base’:
autoload, load, remove
> packageVersion("renv")
[1] ‘1.0.3’
> renv::init()
- Linking packages into the project library ... Done!
The following package(s) were installed from an unknown source:
- INLA [24.01.14]
renv may be unable to restore these packages in the future.
Consider reinstalling these packages from a known source (e.g. CRAN).
Error in renv_snapshot_validate_report(valid, prompt, force) :
aborting snapshot due to pre-flight validation failureNo lock file so I'm running renv::snapshot:
> renv::snapshot()
It looks like you've called renv::snapshot() in a project that hasn't been activated yet.
How would you like to proceed?
1: Activate the project and use the project library.
2: Do not activate the project and use the current library paths.
3: Cancel and resolve the situation another way.
Selection: 1
Restarting R session...
- Project '~/Dropbox/Max work/R/cod-interactions' loaded. [renv 1.0.3]
- The project is out-of-sync -- use `renv::status()` for details.Still no lockfile, doing renv::status() followed by new snapshot:
> renv::status()
This project does not contain a lockfile.
Use `renv::snapshot()` to create a lockfile.
> renv::snapshot()
The following package(s) were installed from an unknown source:
- INLA [24.01.14]
renv may be unable to restore these packages in the future.
Consider reinstalling these packages from a known source (e.g. CRAN).
Do you want to proceed? [Y/n]: Y
The following package(s) will be updated in the lockfile:
# CRAN -----------------------------------------------------------------------
- alabama [* -> 2023.1.0]
- ape [* -> 5.7-1]
- askpass [* -> 1.1]
- assertthat [* -> 0.2.1]
- backports [* -> 1.4.1]
- base64enc [* -> 0.1-3]
- BH [* -> 1.81.0-1]
- bit [* -> 4.0.5]
- bit64 [* -> 4.0.5]
- blob [* -> 1.2.4]
- boot [* -> 1.3-28.1]
- brew [* -> 1.0-8]
- brio [* -> 1.1.3]
- broom [* -> 1.0.4]
- broom.helpers [* -> 1.14.0]
- bslib [* -> 0.4.2]
- cachem [* -> 1.0.7]
- callr [* -> 3.7.3]
- cellranger [* -> 1.1.0]
- checkmate [* -> 2.1.0]
- chron [* -> 2.3-60]
- class [* -> 7.3-21]
- classInt [* -> 0.4-9]
- cli [* -> 3.6.1]
- clipr [* -> 0.8.0]
- clisymbols [* -> 1.2.0]
- cluster [* -> 2.1.4]
- codetools [* -> 0.2-19]
- colorspace [* -> 2.1-0]
- commonmark [* -> 1.9.0]
- conflicted [* -> 1.2.0]
- cpp11 [* -> 0.4.3]
- crayon [* -> 1.5.2]
- credentials [* -> 1.3.2]
- crosstalk [* -> 1.2.0]
- curl [* -> 5.0.0]
- data.table [* -> 1.14.8]
- DBI [* -> 1.1.3]
- dbplyr [* -> 2.3.2]
- desc [* -> 1.4.2]
- devtools [* -> 2.4.5]
- DHARMa [* -> 0.4.6]
- diffobj [* -> 0.3.5]
- digest [* -> 0.6.31]
- doParallel [* -> 1.0.17]
- downlit [* -> 0.4.2]
- dplyr [* -> 1.1.2]
- dtplyr [* -> 1.3.1]
- e1071 [* -> 1.7-13]
- ellipsis [* -> 0.3.2]
- evaluate [* -> 0.20]
- fansi [* -> 1.0.4]
- farver [* -> 2.1.1]
- fastmap [* -> 1.1.1]
- fishMod [* -> 0.29]
- fmesher [* -> 0.1.5]
- fontawesome [* -> 0.5.1]
- forcats [* -> 1.0.0]
- foreach [* -> 1.5.2]
- fs [* -> 1.6.2]
- gap [* -> 1.5-1]
- gap.datasets [* -> 0.0.5]
- gargle [* -> 1.4.0]
- generics [* -> 0.1.3]
- geojsonsf [* -> 2.0.3]
- geometries [* -> 0.2.3]
- gert [* -> 1.9.2]
- ggh4x [* -> 0.2.4]
- ggplot2 [* -> 3.4.2]
- ggrepel [* -> 0.9.3]
- ggridges [* -> 0.5.4]
- gh [* -> 1.4.0]
- gitcreds [* -> 0.1.2]
- gllvm [* -> 1.4.3]
- glue [* -> 1.6.2]
- googledrive [* -> 2.1.0]
- googlesheets4 [* -> 1.1.0]
- gridExtra [* -> 2.3]
- gtable [* -> 0.3.3]
- haven [* -> 2.5.2]
- here [* -> 1.0.1]
- highr [* -> 0.10]
- hms [* -> 1.1.3]
- htmltools [* -> 0.5.5]
- htmlwidgets [* -> 1.6.2]
- httpuv [* -> 1.6.9]
- httr [* -> 1.4.5]
- httr2 [* -> 0.2.2]
- icesDatras [* -> 1.4.0]
- ids [* -> 1.0.1]
- ini [* -> 0.3.1]
- inlabru [* -> 2.7.0]
- inline [* -> 0.3.19]
- isoband [* -> 0.2.7]
- iterators [* -> 1.0.14]
- janitor [* -> 2.2.0]
- jquerylib [* -> 0.1.4]
- jsonify [* -> 1.2.2]
- jsonlite [* -> 1.8.4]
- KernSmooth [* -> 2.23-20]
- knitr [* -> 1.42]
- labeling [* -> 0.4.3]
- labelled [* -> 2.12.0]
- later [* -> 1.3.0]
- lattice [* -> 0.20-45]
- lazyeval [* -> 0.2.2]
- leafem [* -> 0.2.3]
- leaflet [* -> 2.1.2]
- leaflet.providers [* -> 1.9.0]
- leafpop [* -> 0.1.0]
- lifecycle [* -> 1.0.3]
- lme4 [* -> 1.1-33]
- lmtest [* -> 0.9-40]
- loo [* -> 2.6.0]
- lubridate [* -> 1.9.2]
- magrittr [* -> 2.0.3]
- mapplots [* -> 1.5.1]
- mapview [* -> 2.11.2]
- markdown [* -> 1.6]
- MASS [* -> 7.3-58.2]
- Matrix [* -> 1.5-3]
- MatrixModels [* -> 0.5-1]
- matrixStats [* -> 0.63.0]
- memoise [* -> 2.0.1]
- mgcv [* -> 1.8-42]
- mime [* -> 0.12]
- minqa [* -> 1.2.5]
- modelr [* -> 0.1.11]
- munsell [* -> 0.5.0]
- mvabund [* -> 4.2.1]
- mvtnorm [* -> 1.1-3]
- nabor [* -> 0.5.0]
- ncdf4 [* -> 1.22]
- nlme [* -> 3.1-162]
- nloptr [* -> 2.0.3]
- nngeo [* -> 0.4.7]
- numDeriv [* -> 2016.8-1.1]
- openssl [* -> 2.1.1]
- permute [* -> 0.9-7]
- pillar [* -> 1.9.0]
- pkgbuild [* -> 1.4.0]
- pkgconfig [* -> 2.0.3]
- pkgdown [* -> 2.0.7]
- pkgload [* -> 1.3.2]
- plotly [* -> 4.10.1]
- plyr [* -> 1.8.8]
- png [* -> 0.1-8]
- praise [* -> 1.0.0]
- prettyunits [* -> 1.1.1]
- processx [* -> 3.8.1]
- profvis [* -> 0.3.7]
- progress [* -> 1.2.2]
- promises [* -> 1.2.0.1]
- proxy [* -> 0.4-27]
- ps [* -> 1.7.5]
- purrr [* -> 1.0.1]
- qgam [* -> 1.3.4]
- QuickJSR [* -> 1.0.6]
- R6 [* -> 2.5.1]
- ragg [* -> 1.2.5]
- rapidjsonr [* -> 1.2.0]
- rappdirs [* -> 0.3.3]
- raster [* -> 3.6-20]
- rcmdcheck [* -> 1.4.0]
- RColorBrewer [* -> 1.1-3]
- Rcpp [* -> 1.0.10]
- RcppEigen [* -> 0.3.3.9.3]
- RcppGSL [* -> 0.3.13]
- RcppParallel [* -> 5.1.7]
- RCurl [* -> 1.98-1.12]
- readr [* -> 2.1.4]
- readxl [* -> 1.4.2]
- rematch [* -> 1.0.1]
- rematch2 [* -> 2.1.2]
- remotes [* -> 2.4.2]
- renv [* -> 1.0.3]
- reprex [* -> 2.0.2]
- rgdal [* -> 1.6-6]
- rlang [* -> 1.1.1]
- rmarkdown [* -> 2.21]
- rnaturalearth [* -> 0.3.2]
- rnaturalearthdata [* -> 0.1.0]
- roxygen2 [* -> 7.2.3]
- rprojroot [* -> 2.0.3]
- rstan [* -> 2.32.3]
- rstudioapi [* -> 0.14]
- rversions [* -> 2.1.2]
- rvest [* -> 1.0.3]
- s2 [* -> 1.1.2]
- sass [* -> 0.4.5]
- satellite [* -> 1.0.4]
- scales [* -> 1.2.1]
- selectr [* -> 0.4-2]
- servr [* -> 0.27]
- sessioninfo [* -> 1.2.2]
- sf [* -> 1.0-12]
- sfheaders [* -> 0.4.3]
- shiny [* -> 1.7.5]
- snakecase [* -> 0.11.0]
- sourcetools [* -> 0.1.7-1]
- sp [* -> 2.1-2]
- StanHeaders [* -> 2.26.28]
- statmod [* -> 1.5.0]
- stringi [* -> 1.7.12]
- stringr [* -> 1.5.0]
- svglite [* -> 2.1.1]
- sys [* -> 3.4.1]
- systemfonts [* -> 1.0.4]
- testthat [* -> 3.1.7]
- textshaping [* -> 0.3.6]
- tibble [* -> 3.2.1]
- tidylog [* -> 1.0.2]
- tidyr [* -> 1.3.0]
- tidyselect [* -> 1.2.0]
- tidyverse [* -> 2.0.0]
- timechange [* -> 0.2.0]
- tinytex [* -> 0.45]
- TMB [* -> 1.9.3]
- tmbstan [* -> 1.0.9]
- tweedie [* -> 2.3.5]
- tzdb [* -> 0.3.0]
- units [* -> 0.8-1]
- urlchecker [* -> 1.0.1]
- usethis [* -> 2.1.6]
- utf8 [* -> 1.2.3]
- uuid [* -> 1.1-0]
- vctrs [* -> 0.6.2]
- vegan [* -> 2.6-4]
- viridis [* -> 0.6.2]
- viridisLite [* -> 0.4.2]
- vroom [* -> 1.6.1]
- waldo [* -> 0.4.0]
- whisker [* -> 0.4.1]
- withr [* -> 2.5.0]
- wk [* -> 0.7.2]
- xfun [* -> 0.39]
- xml2 [* -> 1.3.3]
- xopen [* -> 1.0.0]
- xtable [* -> 1.8-4]
- yaml [* -> 2.3.8]
- zip [* -> 2.3.0]
- zoo [* -> 1.8-12]
# GitHub ---------------------------------------------------------------------
- ggsidekick [* -> seananderson/ggsidekick@HEAD]
- ggstats [* -> larmarange/ggstats@HEAD]
- glmmTMB [* -> glmmTMB/glmmTMB:glmmTMB@HEAD]
- patchwork [* -> thomasp85/patchwork@HEAD]
- sdmTMB [* -> pbs-assess/sdmTMB@HEAD]
- sdmTMBextra [* -> pbs-assess/sdmTMBextra@HEAD]
# RSPM -----------------------------------------------------------------------
- bitops [* -> 1.0-7]
- miniUI [* -> 0.1.1.1]
# https://rspatial.r-universe.dev --------------------------------------------
- terra [* -> 1.7-30]
# (Unknown Source) -----------------------------------------------------------
- INLA [* -> 24.01.14]
The version of R recorded in the lockfile will be updated:
- R [* -> 4.2.3]
- Lockfile written to "~/Dropbox/Max work/R/cod-interactions/renv.lock".And this works, I now have the lockfile. The entry for INLA is this:
"INLA": {
"Package": "INLA",
"Version": "24.01.14",
"Source": "unknown",
"Requirements": [
"Matrix",
"R",
"fmesher",
"grDevices",
"graphics",
"lifecycle",
"methods",
"parallel",
"rlang",
"sp",
"splines",
"stats",
"utils",
"withr"
],
"Hash": "5ac0668b39fe835f190251b14394c449"
},Now, here I would have though that the Source should be inferred from the package description, but it is unknown. When I navigate to the INLA package within the project's renv folder, the DESCRIPTION file says this:
Package: INLA
Type: Package
Title: Full Bayesian Analysis of Latent Gaussian Models using
Integrated Nested Laplace Approximations
Authors@R: c(
person("Havard", "Rue", email = "hrue@r-inla.org", role = c("cre","aut")),
person("Finn", "Lindgren", email = "finn.lindgren@gmail.com", role = "aut"),
person("Elias", "Teixeira Krainski", email = "elias@r-inla.org", role = "aut"),
person("Sara", "Martino", email = "saramartino0@gmail.com", role = "ctb"),
person("Haakon", "Bakka", email = "bakka@r-inla.org", role = "ctb"),
person("Daniel", "Simpson", email = "dp.simpson@gmail.com", role = "ctb"),
person("Andrea", "Riebler", email = "andrea.riebler@math.ntnu.no", role = "ctb"),
person("Geir-Arne", "Fuglstad", email = "geirarne.fulgstad@gmail.com", role = "ctb"),
person("Martin", "Modrak", email = "modrak.m@email.cz", role = "ctb"),
person("Cristian", "Chiuchiolo", email = "cristian.chiuchiolo@kaust.edu.sa", role = "ctb"))
Description: Full Bayesian analysis of latent Gaussian models using Integrated Nested Laplace Approximaxion. It is a front-end to the inla-program.
Reposity: https://inla.r-inla-download.org/R/stable
Additional_repositories: http:://inlabru-org.r-universe.dev/
Depends: R (>= 3.5), Matrix (>= 1.3-0), sp (>= 1.6-0)
Imports: graphics, grDevices, fmesher (>= 0.0.9.9026), lifecycle,
methods, parallel, rlang, splines, stats, utils, withr
Suggests: Deriv, Ecdat, HKprocess, MatrixModels, Rgraphviz, deldir,
devtools, doParallel, dplyr, evd, fields, ggplot2, gsl, graph,
gridExtra, knitr, markdown, MASS, matrixStats, mlogit, mvtnorm,
numDeriv, pixmap, rgl, rmarkdown, sf, shiny, sn, spdep,
splancs, terra, tidyterra, testthat, tools, INLAspacetime
VignetteBuilder: knitr
BuildVignettes: true
LazyData: true
License: GPL (>= 2) + file LICENSE
RoxygenNote: 7.2.3
Encoding: UTF-8
StagedInstall: no
Collate: '00000.R' 'INLA-package.R' 'agaussian.R' 'ar.R' 'barrier.R'
'binary.R' 'binary.install.R' 'cgeneric.R' 'changelog.R'
'collect.results.R' 'compare.results.R' 'control.R' 'coxph.R'
'cpo.R' 'create.data.file.R' 'cut.R' 'debug.graph.R'
'dev.new.R' 'display.matrix.R' 'doc.R' 'dryrun.R'
'expand.dataframe.R' 'export-class.R' 'external-package.R'
'f.R' 'fgn.R' 'finn.R' 'fmesher-io.R' 'fmesher-transition.R'
'fmesher.R' 'graph.convert.R' 'graph.matrix.R' 'group.R'
'group.cv.R' 'hyper.R' 'hyperpar.R' 'idx.R' 'iidkd.R' 'inla.R'
'inla.call.R' 'inlaEnv.R' 'interpret.formula.R' 'jmarginal.R'
'jp.R' 'knmodels.R' 'knmodels.sample.R' 'lattice2node.R'
'likelihood.R' 'lincomb.R' 'link-functions.R' 'list-models.R'
'load.R' 'marginal.R' 'mdata.R' 'merge.R' 'mesh.R'
'mesh.components.R' 'meshassessment.R' 'meshbuilder.R'
'model-wrapper.R' 'models-generate.R' 'models.R'
'models_documentation.R' 'nmix.lambda.fitted.R' 'obsolete.R'
'options.R' 'os.R' 'over_sp_mesh.R' 'pardiso.R' 'pc-alphaw.R'
'pc-ar.R' 'pc-bym.R' 'pc-cor0.R' 'pc-cor1.R' 'pc-cormat.R'
'pc-gamma.R' 'pc-gammacount.R' 'pc-gev.R' 'pc-multvar.R'
'pc-prec.R' 'pc-sn.R' 'pc-t.R' 'plot.R' 'posterior.sample.R'
'print.R' 'priors.used.R' 'prune.R' 'q.R' 'qinv.R'
'qreordering.R' 'qsample.R' 'qsolve.R' 'quantile-regression.R'
'read.graph.R' 'remote.R' 'reorderings.R' 'rerun.R'
'residuals.R' 'rgeneric.R' 'rprior.R' 'sampler.R' 'sandbox.R'
'scale.model.R' 'scopy.summary.R' 'sections.R'
'set.default.arguments.R' 'sm.R' 'spde.common.R' 'spde1.R'
'spde2.R' 'spde3.R' 'spmesh.R' 'startup.R' 'summary.R' 'surv.R'
'upgrade.R' 'utils.R' 'version.R'
Roxygen: list(markdown = TRUE)
Version: 24.01.14
NeedsCompilation: no
Packaged: 2024-01-14 09:53:49 UTC; hrue
Author: Havard Rue [cre, aut],
Finn Lindgren [aut],
Elias Teixeira Krainski [aut],
Sara Martino [ctb],
Haakon Bakka [ctb],
Daniel Simpson [ctb],
Andrea Riebler [ctb],
Geir-Arne Fuglstad [ctb],
Martin Modrak [ctb],
Cristian Chiuchiolo [ctb]
Maintainer: Havard Rue <hrue@r-inla.org>
Built: R 4.3.2; ; 2024-01-14 09:55:58 UTC; unixOk, so given that I got a warning during snapshot about the package, and renv fails to retrieve information from the DESCRIPTION file, I think I need to add the source for INLA as a custom repository (if I understand the vignette correctly)
> repos <- c(CRAN = "https://cloud.r-project.org", INLA = "https://inla.r-inla-download.org/R/stable")
> options(repos = repos)
> options('repos')
$repos
CRAN INLA
"https://cloud.r-project.org" "https://inla.r-inla-download.org/R/stable"And from here I tried two things. In a new session, ensuring and that INLA was still in $repos, I did library(INLA) and tried to run a function, which didn't work. Then I tried to manually edit the lockfile and replaced the unknown source with that from the DESCRIPTION (https://inla.r-inla-download.org/R/stable). I reopened the project and got this:
> options('repos')
$repos
CRAN INLA
"https://cloud.r-project.org" "https://inla.r-inla-download.org/R/stable"
>
> renv::restore()
The following package(s) will be updated:
# https://inla.r-inla-download.org/R/stable ----------------------------------
- INLA [24.01.14: unknown -> https://inla.r-inla-download.org/R/stable]
Do you want to proceed? [Y/n]: Y
# Installing packages --------------------------------------------------------
- Installing INLA ... OK [linked from cache]
> library(INLA)
Loading required package: Matrix
Loading required package: sp
Registered S3 methods overwritten by 'fmesher':
method from
$.fm_crs inlabru
print.fm_crs inlabru
This is INLA_24.01.14 built 2024-01-14 09:55:58 UTC.
- See www.r-inla.org/contact-us for how to get help.
- List available models/likelihoods/etc with inla.list.models()
- Use inla.doc(<NAME>) to access documentation
- Save 186.4Mb of storage running 'inla.prune()'
Warning message:
package ‘INLA’ was built under R version 4.3.2 It seems to install and load correctly, and appears in the session info:
> sessionInfo()
R version 4.2.3 (2023-03-15)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS 14.2.1
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices datasets utils methods base
other attached packages:
[1] rnaturalearthdata_0.1.0 rnaturalearth_0.3.2 ggsidekick_0.0.2 sf_1.0-12
[5] sdmTMBextra_0.0.1 ggh4x_0.2.4 ggstats_0.5.1.9000 patchwork_1.2.0.9000
[9] devtools_2.4.5 usethis_2.1.6 RColorBrewer_1.1-3 sdmTMB_0.3.0.9002
[13] RCurl_1.98-1.12 tidylog_1.0.2 lubridate_1.9.2 forcats_1.0.0
[17] stringr_1.5.0 dplyr_1.1.2 purrr_1.0.1 readr_2.1.4
[21] tidyr_1.3.0 tibble_3.2.1 ggplot2_3.4.2 tidyverse_2.0.0
[25] INLA_24.01.14 sp_2.1-2 Matrix_1.5-3 But when I try to run a function from INLA I get this: Error in inla.call.builtin() : INLA installation error; no such file
I'm not sure I'm doing the custom repository right...
kevinushey
commented
5 months ago It seems to work for me...
> INLA:::inla.call.builtin()
[1] "/Users/kevin/Library/Caches/org.R-project.R/R/renv/cache/v5/R-4.3/aarch64-apple-darwin20/INLA/23.09.09/677bafc30f91ff926febf5888993aefb/INLA/bin/mac.arm64/inla.run"
> packageVersion("INLA")
[1] ‘23.9.9’But it's hard for me to debug further. You could look at the source code for INLA:::inla.call.builtin() and see what code it's trying to run, and see if you can make sense of why it's failing.
maxlindmark
commented
5 months ago I understand! I ended up re-installing R and RStudio from scratch, and then all packages again. I got the same messages when doing renv::init() and renv::snapshot(), but this time I manually replaced source unknown in the lockfile with the INLA path, like this:
"INLA": {
"Package": "INLA",
"Version": "24.01.14",
"Source": "unknown",
"INLA": {
"Package": "INLA",
"Version": "23.09.09",
"Source": "https://inla.r-inla-download.org/R/stable",And then I also added this to the .Rprofile:
repos <- c(CRAN = "https://cloud.r-project.org", INLA = "https://inla.r-inla-download.org/R/stable")
options(repos = repos)
source("renv/activate.R")And it seems to work, I can use INLA now outside and within the project, and if I clone a forked version of my repo into a new version control project and do renv::restore, it also works. Does this seem like an OK way to do it?
Hi thanks for a nice package! This might not be an issue for other people, but I'm pretty stuck.
I'm trying to run
renv::init()within an RStudio project that relies on the package INLA, which is not on CRAN.I get this:
Then I try
renv::snapshot:Next I do
renv::status()And then
renv::snapshotagain:So now I finally have a lockfile. It has INLA in it, but nothing about where to download it.
I read in the user manual about custom repositories and think I have to do something like this:
Running
renv::snapshotagain but the lockfile is not updated (no reference to the repository or anything like that). When I open the project in a fresh session, I don't see an issue when runninglibrary(INLA)and it appears as a loaded package in
sessionInfo(). But when running an INLA function I get this:Error in inla.call.builtin() : INLA installation error; no such fileThis also happens if I change the lockfile like this:
"Source": "https://inla.r-inla-download.org/R/stable",Where do I go wrong?