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Error in inla.call.builtin() : INLA installation error; no such file #98

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david616007 opened this issue May 11, 2024 · 12 comments
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@david616007
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Before I reinstall my laptop, it ran just fine for the INLA package. Unfortunately, now I can't use the package. I tried several version of R (4.3.0, 4.3.1, 4.3.2, 4.3.3, 4.4.0) but still doesn't work. The latest attempt I tried, I install the package from github. I don't know why I can't install it from the r-inla website. Here is the outcome when I use inla() for my model

Error in inla.call.builtin() : INLA installation error; no such file

And here is the session information
Session info ──────────────────────────────────────────────────────────────────────────────────────────────────────────────
setting value
version R version 4.3.3 (2024-02-29 ucrt)
os Windows 11 x64 (build 22631)
system x86_64, mingw32
ui RStudio
language (EN)
collate English_Indonesia.utf8
ctype English_Indonesia.utf8
tz Asia/Jakarta
date 2024-05-11
rstudio 2024.04.0+735 Chocolate Cosmos (desktop)
pandoc NA

─ Packages ──────────────────────────────────────────────────────────────────────────────────────────────────────────────────
package * version date (UTC) lib source
cachem 1.0.8 2023-05-01 [1] CRAN (R 4.3.3)
class 7.3-22 2023-05-03 [2] CRAN (R 4.3.3)
classInt 0.4-10 2023-09-05 [1] CRAN (R 4.3.3)
cli 3.6.2 2023-12-11 [1] CRAN (R 4.3.3)
coda * 0.19-4.1 2024-01-31 [1] CRAN (R 4.3.3)
curl 5.2.1 2024-03-01 [1] CRAN (R 4.3.3)
DBI 1.2.2 2024-02-16 [1] CRAN (R 4.3.3)
devtools * 2.4.5 2022-10-11 [1] CRAN (R 4.3.3)
digest 0.6.35 2024-03-11 [1] CRAN (R 4.3.3)
e1071 1.7-14 2023-12-06 [1] CRAN (R 4.3.3)
ellipsis 0.3.2 2021-04-29 [1] CRAN (R 4.3.3)
fastmap 1.1.1 2023-02-24 [1] CRAN (R 4.3.3)
fmesher 0.1.5 2023-12-20 [1] CRAN (R 4.3.3)
fs 1.6.4 2024-04-25 [1] CRAN (R 4.3.3)
glue 1.7.0 2024-01-09 [1] CRAN (R 4.3.3)
htmltools 0.5.8.1 2024-04-04 [1] CRAN (R 4.3.3)
htmlwidgets 1.6.4 2023-12-06 [1] CRAN (R 4.3.3)
httpuv 1.6.15 2024-03-26 [1] CRAN (R 4.3.3)
INLA * 99.99.9999 2024-05-11 [1] Github (b762014)
jagsUI * 1.6.2 2024-01-30 [1] CRAN (R 4.3.3)
KernSmooth 2.23-22 2023-07-10 [2] CRAN (R 4.3.3)
later 1.3.2 2023-12-06 [1] CRAN (R 4.3.3)
lattice 0.22-5 2023-10-24 [2] CRAN (R 4.3.3)
lifecycle 1.0.4 2023-11-07 [1] CRAN (R 4.3.3)
magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.3.3)
Matrix * 1.6-5 2024-01-11 [2] CRAN (R 4.3.3)
memoise 2.0.1 2021-11-26 [1] CRAN (R 4.3.3)
mime 0.12 2021-09-28 [1] CRAN (R 4.3.1)
miniUI 0.1.1.1 2018-05-18 [1] CRAN (R 4.3.3)
pkgbuild 1.4.4 2024-03-17 [1] CRAN (R 4.3.3)
pkgload 1.3.4 2024-01-16 [1] CRAN (R 4.3.3)
profvis 0.3.8 2023-05-02 [1] CRAN (R 4.3.3)
promises 1.3.0 2024-04-05 [1] CRAN (R 4.3.3)
proxy 0.4-27 2022-06-09 [1] CRAN (R 4.3.3)
purrr 1.0.2 2023-08-10 [1] CRAN (R 4.3.3)
R6 2.5.1 2021-08-19 [1] CRAN (R 4.3.3)
Rcpp 1.0.12 2024-01-09 [1] CRAN (R 4.3.3)
remotes 2.5.0 2024-03-17 [1] CRAN (R 4.3.3)
rjags * 4-15 2023-11-30 [1] CRAN (R 4.3.3)
rlang 1.1.3 2024-01-10 [1] CRAN (R 4.3.3)
rstudioapi 0.16.0 2024-03-24 [1] CRAN (R 4.3.3)
sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.3.3)
sf 1.0-16 2024-03-24 [1] CRAN (R 4.3.3)
shiny 1.8.1.1 2024-04-02 [1] CRAN (R 4.3.3)
sp * 2.1-4 2024-04-30 [1] CRAN (R 4.3.3)
stringi 1.8.4 2024-05-06 [1] CRAN (R 4.3.3)
stringr 1.5.1 2023-11-14 [1] CRAN (R 4.3.3)
units 0.8-5 2023-11-28 [1] CRAN (R 4.3.3)
urlchecker 1.0.1 2021-11-30 [1] CRAN (R 4.3.3)
usethis * 2.2.3 2024-02-19 [1] CRAN (R 4.3.3)
vctrs 0.6.5 2023-12-01 [1] CRAN (R 4.3.3)
withr 3.0.0 2024-01-16 [1] CRAN (R 4.3.3)
xtable 1.8-4 2019-04-21 [1] CRAN (R 4.3.3)

What should I do? I need the package for my bachelor degree.
Thank you.

@hrue
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hrue commented May 11, 2024 via email

@hrue
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hrue commented May 11, 2024 via email

@david616007
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Hallo Sir, I tried the code:
options(timeout=9999)
if (!requireNamespace("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install(c("graph", "Rgraphviz"), dep=TRUE)
install.packages("INLA",repos=c(getOption("repos"),INLA="https://inla.r-inla-download.org/R/testing"), dep=TRUE)

but when it ran the last line, it failed

install.packages("INLA",repos=c(getOption("repos"),INLA="https://inla.r-inla-download.org/R/testing"), dep=TRUE)
WARNING: Rtools is required to build R packages but is not currently installed. Please download and install the appropriate version of Rtools before proceeding:

https://cran.rstudio.com/bin/windows/Rtools/
Installing package into ‘C:/Users/User/AppData/Local/R/win-library/4.4’
(as ‘lib’ is unspecified)
Warning in install.packages :
dependencies ‘Rgraphviz’, ‘graph’ are not available
trying URL 'https://inla.r-inla-download.org/R/testing/bin/windows/contrib/4.4/INLA_24.05.10.zip'
Content type 'application/zip' length 54409128 bytes (51.9 MB)
downloaded 2.0 MB

Warning in install.packages :
downloaded length 2095869 != reported length 54409128
Warning in install.packages :
URL 'https://inla.r-inla-download.org/R/testing/bin/windows/contrib/4.4/INLA_24.05.10.zip': Timeout of 60 seconds was reached
Error in download.file(url, destfile, method, mode = "wb", ...) :
download from 'https://inla.r-inla-download.org/R/testing/bin/windows/contrib/4.4/INLA_24.05.10.zip' failed
Warning in install.packages :
download of package ‘INLA’ failed

@david616007
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This is my laptop username base on command prompt
C:\Users\User>whoami
laptop-kv3ishkr\user

@david616007
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What I have on my RStudio is INLAspacetime. It runs well, but of course it won't work for the inla(). I just confuse what is wrong with my device. My main reference is Blangiardo, M. and Cameletti, M. (2015) Spatial and Spatio-temporal Bayesian Models with R-INLA and of course your paper.

Thank you in advance, Sir.

@david616007
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Sir, I want to inform you that the INLA has worked. I truly apologize to disturb your day. I have one last question, is there any chance if I email you one day when I need something to ask about the INLA based on your work?

@hrue
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hrue commented May 11, 2024 via email

@hrue
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hrue commented May 11, 2024 via email

@hrue
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hrue commented May 11, 2024 via email

@david616007
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Proffesor, it worked, thanks a lot for your help. I appreciate. Thank you sir.

@will17cr
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Good evening,

I got the same error and I am unable to fix it.

I am using macOS 15.1, RStudio 2024.09.0 Build 375, R version 4.4.1 (2024-06-14) and R-INLA version 24.10.13

I ran these commands:

> install.packages("INLA", repos = c(getOption("repos"), INLA = "https://inla.r-inla-download.org/R/testing"), dep = TRUE, force = TRUE)
Installing package into ‘/Users/wilmerramirez/Library/R/arm64/4.4/library’
(as ‘lib’ is unspecified)
trying URL 'https://inla.r-inla-download.org/R/testing/src/contrib/INLA_24.10.13.tar.gz'
Content type 'application/x-gzip' length 63007167 bytes (60.1 MB)
==================================================
downloaded 60.1 MB

* installing *binary* package ‘INLA’ ...
* DONE (INLA)

The downloaded source packages are in
	‘/private/var/folders/km/hm_26xjx6y10c_l11frw_xg40000gn/T/RtmpiezAST/downloaded_packages’

But when trying any model I got inla.call.builtin error

> library("INLA")
Loading required package: Matrix
Loading required package: sp
This is INLA_24.10.13 built 2024-10-13
                           07:33:29 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 137Mb of storage running 'inla.prune()'
> hgt.inla <- inla(hgt ~ age + sex, data = fdgs.sub,control.predictor = list(compute = TRUE))
Error in inla.call.builtin() : INLA installation error; no such file 

Any help is highly appreciate it

@hrue
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hrue commented Oct 20, 2024 via email

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