pak
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Published
20 hours ago •
r-lib
r-lib
Feature request: Detect and let the user know when a package is no longer on CRAN (or any repo in the list) with a clearer error
When I just tried to install a long list of packages with pkg_install(), I got an error:
Error: ! error in pak subprocess
Caused by error:
! invalid version specification 'NA'
Reprex below:
install.packages("pak")
#> Installing package into 'C:/Users/wdenn/AppData/Local/R/win-library/4.2'
#> (as 'lib' is unspecified)
#> package 'pak' successfully unpacked and MD5 sums checked
#> Warning: cannot remove prior installation of package 'pak'
#> Warning in file.copy(savedcopy, lib, recursive = TRUE):
#> problem copying C:\Users\wdenn\AppData\Local\R\win-
#> library\4.2\00LOCK\pak\library\cli\libs\x64\cli.dll to C:
#> \Users\wdenn\AppData\Local\R\win-library\4.2\pak\library\cli\libs\x64\cli.dll:
#> Permission denied
#> Warning in file.copy(savedcopy, lib, recursive = TRUE):
#> problem copying C:\Users\wdenn\AppData\Local\R\win-
#> library\4.2\00LOCK\pak\library\curl\libs\x64\curl.dll to C:
#> \Users\wdenn\AppData\Local\R\win-library\4.2\pak\library\curl\libs\x64\curl.dll:
#> Permission denied
#> Warning in file.copy(savedcopy, lib, recursive = TRUE):
#> problem copying C:\Users\wdenn\AppData\Local\R\win-
#> library\4.2\00LOCK\pak\library\filelock\libs\x64\filelock.dll
#> to C:\Users\wdenn\AppData\Local\R\win-
#> library\4.2\pak\library\filelock\libs\x64\filelock.dll: Permission denied
#> Warning in file.copy(savedcopy, lib, recursive = TRUE):
#> problem copying C:\Users\wdenn\AppData\Local\R\win-
#> library\4.2\00LOCK\pak\library\glue\libs\x64\glue.dll to C:
#> \Users\wdenn\AppData\Local\R\win-library\4.2\pak\library\glue\libs\x64\glue.dll:
#> Permission denied
#> Warning in file.copy(savedcopy, lib, recursive = TRUE):
#> problem copying C:\Users\wdenn\AppData\Local\R\win-
#> library\4.2\00LOCK\pak\library\jsonlite\libs\x64\jsonlite.dll
#> to C:\Users\wdenn\AppData\Local\R\win-
#> library\4.2\pak\library\jsonlite\libs\x64\jsonlite.dll: Permission denied
#> Warning in file.copy(savedcopy, lib, recursive = TRUE):
#> problem copying C:\Users\wdenn\AppData\Local\R\win-
#> library\4.2\00LOCK\pak\library\lpSolve\libs\x64\lpSolve.dll
#> to C:\Users\wdenn\AppData\Local\R\win-
#> library\4.2\pak\library\lpSolve\libs\x64\lpSolve.dll: Permission denied
#> Warning in file.copy(savedcopy, lib, recursive = TRUE):
#> problem copying C:\Users\wdenn\AppData\Local\R\win-
#> library\4.2\00LOCK\pak\library\pkgcache\libs\x64\pkgcache.dll
#> to C:\Users\wdenn\AppData\Local\R\win-
#> library\4.2\pak\library\pkgcache\libs\x64\pkgcache.dll: Permission denied
#> Warning in file.copy(savedcopy, lib, recursive = TRUE):
#> problem copying C:\Users\wdenn\AppData\Local\R\win-
#> library\4.2\00LOCK\pak\library\processx\libs\x64\processx.dll
#> to C:\Users\wdenn\AppData\Local\R\win-
#> library\4.2\pak\library\processx\libs\x64\processx.dll: Permission denied
#> Warning in file.copy(savedcopy, lib, recursive = TRUE):
#> problem copying C:\Users\wdenn\AppData\Local\R\win-
#> library\4.2\00LOCK\pak\library\ps\libs\x64\ps.dll to C:
#> \Users\wdenn\AppData\Local\R\win-library\4.2\pak\library\ps\libs\x64\ps.dll:
#> Permission denied
#> Warning in file.copy(savedcopy, lib, recursive = TRUE):
#> problem copying C:\Users\wdenn\AppData\Local\R\win-
#> library\4.2\00LOCK\pak\library\rappdirs\libs\x64\rappdirs.dll
#> to C:\Users\wdenn\AppData\Local\R\win-
#> library\4.2\pak\library\rappdirs\libs\x64\rappdirs.dll: Permission denied
#> Warning in file.copy(savedcopy, lib, recursive = TRUE):
#> problem copying C:\Users\wdenn\AppData\Local\R\win-
#> library\4.2\00LOCK\pak\library\zip\libs\x64\zip.dll to C:
#> \Users\wdenn\AppData\Local\R\win-library\4.2\pak\library\zip\libs\x64\zip.dll:
#> Permission denied
#> Warning: restored 'pak'
#>
#> The downloaded binary packages are in
#> C:\Users\wdenn\AppData\Local\Temp\RtmpGoSeR2\downloaded_packages
pak::repo_add("MRAN@2022-12-05")
pak::pkg_install(c(
"arsenal",
"assertr",
"bayesplot",
"binom",
"bit64",
"bookdown",
"brms",
"broom",
"broom.mixed",
"caTools",
"censReg",
"ciTools",
"clustermq",
"countrycode",
"covr",
"cowplot",
"crch",
"daff",
"devtools",
"DiagrammeR",
"DiagrammeRsvg",
"directlabels",
"digest",
"docxtractr",
"DoseFinding",
"dplyr",
"drake",
"emmeans",
"errors",
"extrafont",
"forcats",
"formulops",
"future",
"GGally",
"ggdendro",
"ggplot2",
"ggraph",
"ggsignif",
"glmmTMB",
"gsDesign",
"gt",
"gtools",
"hexbin",
"Hmisc",
"igraph",
"installr",
"janitor",
"kableExtra",
"knitcitations",
"knitr",
"lintr",
"lme4",
#"LogrankPower",
"longpower",
"loo",
"lubridate",
"microbenchmark",
"mrgsolve",
"mvtnorm",
"naturalsort",
"nlmixr",
"nlmixr2",
"NMdata",
"pander",
"parsnip",
"pdftools", # sudo apt-get install libpoppler-cpp-dev
"PKNCA",
#"PKPDmisc",
"physiology",
"pmxTools",
"PowerTOST",
"printr",
"purrr",
"pwr",
"Rcpp",
"readr",
"rentrez",
"reprex",
"reshape",
"reticulate",
"rio",
"riverplot",
# "rJava",
"rlang",
"rmarkdown",
"rmutil",
"roxygen2",
"rstan",
"rstanarm",
"rstantools",
"rsvg", # sudo apt-get install -y librsvg2-dev
"shiny",
"shinydashboard",
"simstudy",
"spelling",
"ssh", # sudo apt-get install -y libssh-dev
"stringi",
"stringr",
"styler",
"survminer",
"svglite",
"swCRTdesign",
"table1",
#"tabulizer",
"tarchetypes",
"targets",
"testthat",
"tibble",
"tidygraph",
"tidyr",
"tidyverse",
"tinytest",
"tidyxl",
"truncdist",
"truncnorm",
"units",
"unpivotr",
"vpc",
"vroom",
"XML",
"xpose",
# For nlmixr development version:
"symengine",
"inline",
"PreciseSums",
"RcppArmadillo"
))
#> ℹ Loading metadata database
#> ℹ Loading metadata database✔ Loading metadata database ... done✔ Loading metadata database ... done
#> Error: ! error in pak subprocess
#> Caused by error:
#> ! invalid version specification 'NA'
Created on 2022-12-05 with reprex v2.0.2
I traced it back to a much simpler reprex, the daff package is no longer on CRAN, so this reprex gives the same error.
pak::pkg_install("daff")
I think that changes the request to be:
- Please detect and let the user know when a package is no longer on CRAN (or any repo in the list) with a clearer error
In this case, I had to determine the package that wasn't working by bifurcation. A note for what package is giving the subprocess error would be very helpful.
I see this for daff:
❯ pak::pkg_install("daff")
✔ Updated metadata database: 5.02 MB in 6 files.
✔ Updating metadata database ... done
→ Will install 1 package.
→ Will download 1 CRAN package (1.74 MB).
+ daff 0.3.5 ⬇ (1.74 MB)
ℹ Getting 1 pkg (1.74 MB)
✖ Failed to download daff 0.3.5 (aarch64-apple-darwin20)
✖ Failed to download 1 package.
Error:
! error in pak subprocess
Caused by error:
! Failed to download daff from `https://cloud.r-project.org/bin/macosx/big-sur-arm64/contrib/4.2/daff_0.3.5.tgz` and `https://mac.r-project.org/bin/macosx/big-sur-arm64/contrib/4.2/daff_0.3.5.tgz`.
Type .Last.error to see the more details.
I guess it was just archived, and the CRAN metadata is inconsistent.
For an archived/non-existent package I get this:
❯ pak::pkg_install("qwertyqwerty")
Error:
! error in pak subprocess
Caused by error:
! Could not solve package dependencies:
* qwertyqwerty: Can't find package called qwertyqwerty.
Type .Last.error to see the more details.
How would you improve this?
Hi @gaborcsardi, apologies, I thought that my reprex was self-contained but it was not. I had set the MRAN repo as well, and that makes the error different. I agree that the errors you're seeing above are good. Here is the reprex I'm getting now with the current CRAN version of pak (version 0.3.1):
pak::repo_add("MRAN@2022-12-05")
pak::pkg_install("daff")
#> ℹ Loading metadata databaseℹ Loading metadata database✔ Loading metadata database ... done✔ Loading metadata database ... done
#> Error: ! error in pak subprocess
#> Caused by error:
#> ! invalid version specification 'NA'
Created on 2022-12-06 with reprex v2.0.2
Session info
sessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.2.1 (2022-06-23 ucrt)
#> os Windows 10 x64 (build 22621)
#> system x86_64, mingw32
#> ui RTerm
#> language (EN)
#> collate English_United States.utf8
#> ctype English_United States.utf8
#> tz America/New_York
#> date 2022-12-06
#> pandoc 2.19.2 @ C:/Program Files/RStudio/resources/app/bin/quarto/bin/tools/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> package * version date (UTC) lib source
#> cli 3.4.1 2022-09-23 [1] CRAN (R 4.2.1)
#> digest 0.6.30 2022-10-18 [1] CRAN (R 4.2.2)
#> evaluate 0.18 2022-11-07 [1] CRAN (R 4.2.2)
#> fastmap 1.1.0 2021-01-25 [1] CRAN (R 4.2.1)
#> fs 1.5.2 2021-12-08 [1] CRAN (R 4.2.1)
#> glue 1.6.2 2022-02-24 [1] CRAN (R 4.2.1)
#> highr 0.9 2021-04-16 [1] CRAN (R 4.2.1)
#> htmltools 0.5.3 2022-07-18 [1] CRAN (R 4.2.1)
#> knitr 1.41 2022-11-18 [1] CRAN (R 4.2.2)
#> lifecycle 1.0.3 2022-10-07 [1] CRAN (R 4.2.1)
#> magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.1)
#> pak 0.3.1 2022-09-08 [1] CRAN (R 4.2.2)
#> purrr 0.3.5 2022-10-06 [1] CRAN (R 4.2.1)
#> R.cache 0.16.0 2022-07-21 [1] CRAN (R 4.2.1)
#> R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.2.0)
#> R.oo 1.25.0 2022-06-12 [1] CRAN (R 4.2.0)
#> R.utils 2.12.0 2022-06-28 [1] CRAN (R 4.2.1)
#> reprex 2.0.2 2022-08-17 [1] CRAN (R 4.2.1)
#> rlang 1.0.6 2022-09-24 [1] CRAN (R 4.2.1)
#> rmarkdown 2.18 2022-11-09 [1] CRAN (R 4.2.2)
#> rstudioapi 0.14 2022-08-22 [1] CRAN (R 4.2.1)
#> sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.1)
#> stringi 1.7.8 2022-07-11 [1] CRAN (R 4.2.1)
#> stringr 1.5.0 2022-12-02 [1] CRAN (R 4.2.2)
#> styler 1.8.1 2022-11-07 [1] CRAN (R 4.2.2)
#> vctrs 0.5.0 2022-10-22 [1] CRAN (R 4.2.2)
#> withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.1)
#> xfun 0.34 2022-10-18 [1] CRAN (R 4.2.2)
#> yaml 2.3.6 2022-10-18 [1] CRAN (R 4.2.1)
#>
#> [1] C:/Users/wdenn/AppData/Local/R/win-library/4.2
#> [2] C:/Program Files/R/R-4.2.1/library
#>
#> ──────────────────────────────────────────────────────────────────────────────
I see that you're using a mac while I'm on Windows. Could that make a difference?
That should not make a difference:
❯ pak::repo_add("MRAN@2022-12-05")
❯ pak::pkg_install("daff")
✔ Loading metadata database ... done
→ Will install 1 package.
→ Will download 1 CRAN package (1.74 MB).
+ daff 0.3.5 ⬇ (1.74 MB)
ℹ Getting 1 pkg (1.74 MB)
✖ Failed to download daff 0.3.5 (aarch64-apple-darwin20)
✖ Failed to download 1 package.
Error:
! error in pak subprocess
Caused by error:
! Failed to download daff from `https://cran.microsoft.com/snapshot/2022-12-05/bin/macosx/big-sur-arm64/contrib/4.2/daff_0.3.5.tgz` and `https://mac.r-project.org/bin/macosx/big-sur-arm64/contrib/4.2/daff_0.3.5.tgz`.
Type .Last.error to see the more details.
❯ Sys.setenv(PKG_PLATFORMS = "source")
❯ pak::repo_add("MRAN@2022-12-05")
❯ pak::pkg_install("daff")
✔ Updating metadata database ... done
Error:
! error in pak subprocess
Caused by error:
! Could not solve package dependencies:
* daff: Can't find package called daff.
Type .Last.error to see the more details.
I got the same error with the nightly devel build (installed with install.packages("pak", repos = sprintf("https://r-lib.github.io/p/pak/devel/%s/%s/%s", .Platform$pkgType, R.Version()$os, R.Version()$arch))).
Can you show the output of the installation, please? I.e. the output of
install.packages(
"pak",
repos = sprintf(
"https://r-lib.github.io/p/pak/devel/%s/%s/%s",
.Platform$pkgType, R.Version()$os, R.Version()$arch
)
)
> install.packages(
+ "pak",
+ repos = sprintf(
+ "https://r-lib.github.io/p/pak/devel/%s/%s/%s",
+ .Platform$pkgType, R.Version()$os, R.Version()$arch
+ )
+ )
Installing package into ‘C:/Users/wdenn/AppData/Local/R/win-library/4.2’
(as ‘lib’ is unspecified)
trying URL 'https://r-lib.github.io/p/pak/devel/win.binary/mingw32/x86_64/bin/windows/contrib/4.2/../../../../../../../mingw32/x86_64/pak_0.3.1.9000_R-4-2_x86_64-mingw32.zip'
Content type 'application/zip' length 8111747 bytes (7.7 MB)
downloaded 7.7 MB
The downloaded binary packages are in
C:\Users\wdenn\AppData\Local\Temp\Rtmp8UNEqn\downloaded_packages
>
I still get this:
❯ pak::repo_add("MRAN@2022-12-05")
❯ pak::pkg_install("daff")
✔ Updated metadata database: 3.71 MB in 4 files.
✔ Updating metadata database ... done
Error:
! error in pak subprocess
Caused by error:
! Could not solve package dependencies:
* daff: Can't find package called daff.
Type .Last.error to see the more details.
which is not bad. Do you still have this issue?