renv 0.17.0 issues with provisioning non-CRAN packages #1156
Comments
This was referenced Mar 6, 2023
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This appears to be fixed for me: |
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Unfortunately I'm still getting the error with 9fd57df: tmp <- tempfile()
dir.create(tmp)
writeLines("library(SummarizedExperiment)", file.path(tmp, "test.R"))
setwd(tmp)
renv::init()
#> * Discovering package dependencies ... Done!
#> * Resolving missing dependencies ...
#> Warning in value[[3L]](cond): restarting interrupted promise evaluation
#> The version of R recorded in the lockfile will be updated:
#> - R [* -> 4.2.2]
#>
#> * Lockfile written to '/tmp/RtmpMHVYvp/file444e4877ccda/renv.lock'.
renv::install("bioc::SummarizedExperiment")
#> Warning in value[[3L]](cond): restarting interrupted promise evaluation
#> Error in object[[i]]: object of type 'promise' is not subsettableCreated on 2023-03-07 with reprex v2.0.2 Standard output and standard errorThe following package(s) were not installed successfully:
[SummarizedExperiment]: object of type 'promise' is not subsettable
You may need to manually download and install these packages.
The following package(s) will be updated in the lockfile:
# GitHub =============================
- renv [* -> rstudio/renv@HEAD]
Warning message:
In in_dir(input_dir(), expr) :
You changed the working directory to /tmp/RtmpMHVYvp/file444e4877ccda (probably via setwd()). It will be restored to /tmp/RtmpjnVuOY/reprex-3e0863d0d575-awful-dog. See the Note section in ?knitr::knitSession infosessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.2.2 Patched (2022-11-10 r83330)
#> os Ubuntu 20.04.5 LTS
#> system x86_64, linux-gnu
#> ui X11
#> language en_US:en
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz America/Los_Angeles
#> date 2023-03-07
#> pandoc 2.12 @ /home/zhian/anaconda3/bin/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> ! package * version date (UTC) lib source
#> R cli 3.6.0 <NA> [?] <NA>
#> R digest 0.6.31 <NA> [?] <NA>
#> R evaluate 0.20 <NA> [?] <NA>
#> R fastmap 1.1.1 <NA> [?] <NA>
#> R fs 1.6.1 <NA> [?] <NA>
#> R glue 1.6.2 <NA> [?] <NA>
#> R htmltools 0.5.4 <NA> [?] <NA>
#> R knitr 1.42 <NA> [?] <NA>
#> R lifecycle 1.0.3 <NA> [?] <NA>
#> R magrittr 2.0.3 <NA> [?] <NA>
#> R purrr 1.0.1 <NA> [?] <NA>
#> R R.cache 0.16.0 <NA> [?] <NA>
#> R R.methodsS3 1.8.2 <NA> [?] <NA>
#> R R.oo 1.25.0 <NA> [?] <NA>
#> R R.utils 2.12.2 <NA> [?] <NA>
#> P renv 0.17.0-22 2023-03-07 [?] Github (rstudio/renv@9fd57df)
#> R reprex 2.0.2 <NA> [?] <NA>
#> R rlang 1.0.6 <NA> [?] <NA>
#> R rmarkdown 2.20 <NA> [?] <NA>
#> R sessioninfo 1.2.2 <NA> [?] <NA>
#> R styler 1.9.1 <NA> [?] <NA>
#> R vctrs 0.5.2 <NA> [?] <NA>
#> R withr 2.5.0 <NA> [?] <NA>
#> R xfun 0.37 <NA> [?] <NA>
#> R yaml 2.3.7 <NA> [?] <NA>
#>
#> [1] /tmp/RtmpMHVYvp/file444e4877ccda/renv/library/R-4.2/x86_64-pc-linux-gnu
#> [2] /tmp/RtmpMHVYvp/file444e4877ccda/renv/sandbox/R-4.2/x86_64-pc-linux-gnu/9a444a72
#>
#> P ── Loaded and on-disk path mismatch.
#> R ── Package was removed from disk.
#>
#> ──────────────────────────────────────────────────────────────────────────────Here is the traceback: 15: renv::install("bioc::SummarizedExperiment")
14: retrieve(names(remotes))
13: handler(package, renv_retrieve_impl(package))
12: renv_retrieve_impl(package)
11: renv_scope_bioconductor(project = project)
10: renv_bioconductor_repos(project = project, version = version)
9: renv_bioconductor_init()
8: renv_bioconductor_init_biocmanager(library)
7: install("BiocManager", library = library)
6: retrieve(names(remotes))
5: handler(package, renv_retrieve_impl(package))
4: renv_retrieve_impl(package)
3: renv_available_packages_latest(package)
2: stopf("package '%s' is not available", package)
1: stop(sprintf(fmt, ...), call. = call.) |
zkamvar
added a commit
to carpentries/sandpaper
that referenced
this issue
Mar 7, 2023
this will help prevent failures until rstudio/renv#1156 is fixed.
This was referenced Mar 7, 2023
|
Note: this is not just a problem with Bioc: tmp <- tempfile()
dir.create(tmp)
writeLines("1 + 1", file.path(tmp, "test.R"))
setwd(tmp)
renv::init()
#> * Discovering package dependencies ... Done!
#> Warning in value[[3L]](cond): restarting interrupted promise evaluation
#> The version of R recorded in the lockfile will be updated:
#> - R [* -> 4.2.2]
#>
#> * Lockfile written to '/tmp/RtmpR0tPjC/file145a2135215a9/renv.lock'.
renv::install("cowsay")
#> Warning in value[[3L]](cond): restarting interrupted promise evaluation
#> Warning in value[[3L]](cond): restarting interrupted promise evaluation
#> Error in object[[i]]: object of type 'promise' is not subsettableCreated on 2023-03-07 with reprex v2.0.2 Standard output and standard errorThe following package(s) will be updated in the lockfile:
# GitHub =============================
- renv [* -> rstudio/[email protected]]
Warning message:
In in_dir(input_dir(), expr) :
You changed the working directory to /tmp/RtmpR0tPjC/file145a2135215a9 (probably via setwd()). It will be restored to /tmp/RtmpHqgOuS/reprex-139322b756a18-hexed-tuna. See the Note section in ?knitr::knitSession infosessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.2.2 Patched (2022-11-10 r83330)
#> os Ubuntu 20.04.5 LTS
#> system x86_64, linux-gnu
#> ui X11
#> language en_US:en
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz America/Los_Angeles
#> date 2023-03-07
#> pandoc 2.12 @ /home/zhian/anaconda3/bin/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> ! package * version date (UTC) lib source
#> R cli 3.6.0 <NA> [?] <NA>
#> R digest 0.6.31 <NA> [?] <NA>
#> R evaluate 0.20 <NA> [?] <NA>
#> R fastmap 1.1.1 <NA> [?] <NA>
#> R fs 1.6.1 <NA> [?] <NA>
#> R glue 1.6.2 <NA> [?] <NA>
#> R htmltools 0.5.4 <NA> [?] <NA>
#> R knitr 1.42 <NA> [?] <NA>
#> R lifecycle 1.0.3 <NA> [?] <NA>
#> R magrittr 2.0.3 <NA> [?] <NA>
#> R purrr 1.0.1 <NA> [?] <NA>
#> R R.cache 0.16.0 <NA> [?] <NA>
#> R R.methodsS3 1.8.2 <NA> [?] <NA>
#> R R.oo 1.25.0 <NA> [?] <NA>
#> R R.utils 2.12.2 <NA> [?] <NA>
#> P renv 0.17.0-22 2023-03-07 [?] local
#> R reprex 2.0.2 <NA> [?] <NA>
#> R rlang 1.0.6 <NA> [?] <NA>
#> R rmarkdown 2.20 <NA> [?] <NA>
#> R sessioninfo 1.2.2 <NA> [?] <NA>
#> R styler 1.9.1 <NA> [?] <NA>
#> R vctrs 0.5.2 <NA> [?] <NA>
#> R withr 2.5.0 <NA> [?] <NA>
#> R xfun 0.37 <NA> [?] <NA>
#> R yaml 2.3.7 <NA> [?] <NA>
#>
#> [1] /tmp/RtmpR0tPjC/file145a2135215a9/renv/library/R-4.2/x86_64-pc-linux-gnu
#> [2] /tmp/RtmpR0tPjC/file145a2135215a9/renv/sandbox/R-4.2/x86_64-pc-linux-gnu/9a444a72
#>
#> P ── Loaded and on-disk path mismatch.
#> R ── Package was removed from disk.
#>
#> ────────────────────────────────────────────────────────────────────────────── |
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I think I understand what's happening now: I have the r-universe set as one of my repositories. If I set my repositories to the default CRAN, then I get no error: tmp <- tempfile()
dir.create(tmp)
writeLines("1 + 1", file.path(tmp, "test.R"))
setwd(tmp)
renv::init(repos = c("https://cran.r-project.org"))
#> * Discovering package dependencies ... Done!
#> The version of R recorded in the lockfile will be updated:
#> - R [* -> 4.2.2]
#>
#> * Lockfile written to '/tmp/RtmpShym2N/file1c59a3b01be0e/renv.lock'.
renv::install("cowsay")
#> Installing crayon [1.5.2] ...
#> OK [linked cache in 0.11 milliseconds]
#> Installing fortunes [1.5-4] ...
#> OK [linked cache in 0.097 milliseconds]
#> Installing rmsfact [0.0.3] ...
#> OK [linked cache in 0.094 milliseconds]
#> Installing cowsay [0.8.0] ...
#> OK [linked cache in 0.11 milliseconds]
#> * Installed 4 packages in 43 milliseconds.Created on 2023-03-07 with reprex v2.0.2 Standard output and standard errorThe following package(s) will be updated in the lockfile:
# CRAN ===============================
- renv [* -> 0.17.0-22]
Warning message:
In in_dir(input_dir(), expr) :
You changed the working directory to /tmp/RtmpShym2N/file1c59a3b01be0e (probably via setwd()). It will be restored to /tmp/RtmpNtvTbJ/reprex-1b9c552a5b445-drear-kitty. See the Note section in ?knitr::knitSession infosessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.2.2 Patched (2022-11-10 r83330)
#> os Ubuntu 20.04.5 LTS
#> system x86_64, linux-gnu
#> ui X11
#> language en_US:en
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz America/Los_Angeles
#> date 2023-03-07
#> pandoc 2.12 @ /home/zhian/anaconda3/bin/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> ! package * version date (UTC) lib source
#> R cli 3.6.0 <NA> [?] <NA>
#> R digest 0.6.31 <NA> [?] <NA>
#> R evaluate 0.20 <NA> [?] <NA>
#> R fastmap 1.1.1 <NA> [?] <NA>
#> R fs 1.6.1 <NA> [?] <NA>
#> R glue 1.6.2 <NA> [?] <NA>
#> R htmltools 0.5.4 <NA> [?] <NA>
#> R knitr 1.42 <NA> [?] <NA>
#> R lifecycle 1.0.3 <NA> [?] <NA>
#> R magrittr 2.0.3 <NA> [?] <NA>
#> R purrr 1.0.1 <NA> [?] <NA>
#> R R.cache 0.16.0 <NA> [?] <NA>
#> R R.methodsS3 1.8.2 <NA> [?] <NA>
#> R R.oo 1.25.0 <NA> [?] <NA>
#> R R.utils 2.12.2 <NA> [?] <NA>
#> P renv 0.17.0-22 2023-03-07 [?] local
#> R reprex 2.0.2 <NA> [?] <NA>
#> R rlang 1.0.6 <NA> [?] <NA>
#> R rmarkdown 2.20 <NA> [?] <NA>
#> R sessioninfo 1.2.2 <NA> [?] <NA>
#> R styler 1.9.1 <NA> [?] <NA>
#> R vctrs 0.5.2 <NA> [?] <NA>
#> R withr 2.5.0 <NA> [?] <NA>
#> R xfun 0.37 <NA> [?] <NA>
#> R yaml 2.3.7 <NA> [?] <NA>
#>
#> [1] /tmp/RtmpShym2N/file1c59a3b01be0e/renv/library/R-4.2/x86_64-pc-linux-gnu
#> [2] /tmp/RtmpShym2N/file1c59a3b01be0e/renv/sandbox/R-4.2/x86_64-pc-linux-gnu/9a444a72
#>
#> P ── Loaded and on-disk path mismatch.
#> R ── Package was removed from disk.
#>
#> ──────────────────────────────────────────────────────────────────────────────However, once I add the Carpentries universe, things go haywire: tmp <- tempfile()
dir.create(tmp)
writeLines("1 + 1", file.path(tmp, "test.R"))
setwd(tmp)
renv::init(repos = c("https://carpentries.r-universe.dev", "https://cran.r-project.org"))
#> * Discovering package dependencies ... Done!
#> Warning in value[[3L]](cond): restarting interrupted promise evaluation
#> The version of R recorded in the lockfile will be updated:
#> - R [* -> 4.2.2]
#>
#> * Lockfile written to '/tmp/RtmpBRKoYF/file1c2995b709133/renv.lock'.
renv::install("cowsay")
#> Warning in value[[3L]](cond): restarting interrupted promise evaluation
#> Warning in value[[3L]](cond): restarting interrupted promise evaluation
#> Error in object[[i]]: object of type 'promise' is not subsettableCreated on 2023-03-07 with reprex v2.0.2 Standard output and standard errorThe following package(s) will be updated in the lockfile:
# GitHub =============================
- renv [* -> rstudio/[email protected]]
Warning message:
In in_dir(input_dir(), expr) :
You changed the working directory to /tmp/RtmpBRKoYF/file1c2995b709133 (probably via setwd()). It will be restored to /tmp/RtmpNtvTbJ/reprex-1b9c56a6d2a44-woody-kiwi. See the Note section in ?knitr::knitSession infosessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.2.2 Patched (2022-11-10 r83330)
#> os Ubuntu 20.04.5 LTS
#> system x86_64, linux-gnu
#> ui X11
#> language en_US:en
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz America/Los_Angeles
#> date 2023-03-07
#> pandoc 2.12 @ /home/zhian/anaconda3/bin/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> ! package * version date (UTC) lib source
#> R cli 3.6.0 <NA> [?] <NA>
#> R digest 0.6.31 <NA> [?] <NA>
#> R evaluate 0.20 <NA> [?] <NA>
#> R fastmap 1.1.1 <NA> [?] <NA>
#> R fs 1.6.1 <NA> [?] <NA>
#> R glue 1.6.2 <NA> [?] <NA>
#> R htmltools 0.5.4 <NA> [?] <NA>
#> R knitr 1.42 <NA> [?] <NA>
#> R lifecycle 1.0.3 <NA> [?] <NA>
#> R magrittr 2.0.3 <NA> [?] <NA>
#> R purrr 1.0.1 <NA> [?] <NA>
#> R R.cache 0.16.0 <NA> [?] <NA>
#> R R.methodsS3 1.8.2 <NA> [?] <NA>
#> R R.oo 1.25.0 <NA> [?] <NA>
#> R R.utils 2.12.2 <NA> [?] <NA>
#> P renv 0.17.0-22 2023-03-07 [?] local
#> R reprex 2.0.2 <NA> [?] <NA>
#> R rlang 1.0.6 <NA> [?] <NA>
#> R rmarkdown 2.20 <NA> [?] <NA>
#> R sessioninfo 1.2.2 <NA> [?] <NA>
#> R styler 1.9.1 <NA> [?] <NA>
#> R vctrs 0.5.2 <NA> [?] <NA>
#> R withr 2.5.0 <NA> [?] <NA>
#> R xfun 0.37 <NA> [?] <NA>
#> R yaml 2.3.7 <NA> [?] <NA>
#>
#> [1] /tmp/RtmpBRKoYF/file1c2995b709133/renv/library/R-4.2/x86_64-pc-linux-gnu
#> [2] /tmp/RtmpBRKoYF/file1c2995b709133/renv/sandbox/R-4.2/x86_64-pc-linux-gnu/9a444a72
#>
#> P ── Loaded and on-disk path mismatch.
#> R ── Package was removed from disk.
#>
#> ──────────────────────────────────────────────────────────────────────────────Note: I have tested this with the bioc packages and it also succeeds when I take away the universe. Digging into the errorsThe R-universe registry does not have Lines 98 to 130 in 9fd57df While the error propogation is catching this, there is something happening in the mechanism where the error object stored is not parsed correctly. I ran > renv::install("cowsay")
Error: package 'cowsay' is not available
In addition: Warning messages:
1: In value[[3L]](cond) : restarting interrupted promise evaluation
2: In value[[3L]](cond) : restarting interrupted promise evaluation
3: In object[[i]] : object of type 'promise' is not subsettable
Enter a frame number, or 0 to exit
1: renv::install("cowsay")
2: retrieve(names(remotes))
3: handler(package, renv_retrieve_impl(package))
4: renv_retrieve_impl(package)
5: renv_available_packages_latest(package)
6: stopf("package '%s' is not available", package)
Selection: 5I then looked at the objects in Line 316 in 9fd57df and selected the Traceback of errors objecterrors$data()[[1]]$message
[1] "object of type 'promise' is not subsettable"
errors$data()[[1]]$traceback
36: renv::install("cowsay")
35: retrieve(names(remotes))
34: handler(package, renv_retrieve_impl(package))
33: renv_retrieve_impl(package)
32: renv_available_packages_latest(package)
31: lapply(methods, function(method) {
if (is.null(method))
return(NULL)
entry <- catch(method(package, type, repos))
if (inherits(entry, "error")) {
errors$push(entry)
return(NULL)
}
entry
})
30: FUN(X[[i]], ...)
29: catch(method(package, type, repos))
28: tryCatch(withCallingHandlers(expr, error = renv_error_capture),
error = renv_error_tag)
27: tryCatchList(expr, classes, parentenv, handlers)
26: tryCatchOne(expr, names, parentenv, handlers[[1L]])
25: doTryCatch(return(expr), name, parentenv, handler)
24: withCallingHandlers(expr, error = renv_error_capture)
23: method(package, type, repos)
22: renv_available_packages_latest_repos_impl(package, "source",
repos)
21: available_packages(type = type, repos = repos, quiet = TRUE)
20: index(scope = "available-packages", key = key, value = renv_available_packages
_impl(type,
repos, quiet), limit = as.integer(limit))
19: tryCatch(renv_index_impl(root, scope, key, value, now, limit),
error = function(e) value)
18: tryCatchList(expr, classes, parentenv, handlers)
17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
16: value[[3L]](cond)
15: renv_available_packages_impl(type, repos, quiet)
14: lapply(urls, renv_available_packages_query, errors = errors)
13: FUN(X[[i]], ...)
12: withCallingHandlers(catch(method(url)), warning = seize(restart = "muffleWarni
ng"),
message = seize(restart = "muffleMessage"))
11: catch(method(url))
10: tryCatch(withCallingHandlers(expr, error = renv_error_capture),
error = renv_error_tag)
9: tryCatchList(expr, classes, parentenv, handlers)
8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
7: doTryCatch(return(expr), name, parentenv, handler)
6: withCallingHandlers(expr, error = renv_error_capture)
5: method(url)
4: download(url = path, destfile = destfile, quiet = TRUE)
3: renv_download_error(url, "%s", conditionMessage(status))
2: stopf("error downloading '%s' [%s]", url, msg, call. = FALSE)
1: stop(sprintf(fmt, ...), call. = call.)Looking further into this, it the specific error is coming from Lines 50 to 67 in 9fd57df where the Browse[3]> object
<promise: 0x560ef1e98ff0>
Browse[3]> str(object)
promise to symbol url
Browse[3]> eval(object)
[1] "https://carpentries.r-universe.dev/src/contrib"The only thing is I'm having a really difficult time figuring out where that promise slipped in. |
zkamvar
changed the title
bioc:: prefix
|
Thank you! I'll see if I can reproduce with those instructions. |
|
Ok, I can reproduce. I think I know what's going on -- the available packages database returned by r-universe doesn't include some fields; e.g. "OS_type", and we're failing to account for that. I'll try to fix this up. |
|
Should be fixed with 7aa92a0. Let me know if that does the trick for you. |
zkamvar
added a commit
to carpentries/carpentries.r-universe.dev
that referenced
this issue
Mar 7, 2023
This will address carpentries/sandpaper#406 and rstudio/renv#1156 until the next version of {renv} is sent to CRAN
|
It woorrrkssss! Thank you for being so quick in fixing this! tmp <- tempfile()
dir.create(tmp)
writeLines("library(SummarizedExperiment)", file.path(tmp, "test.R"))
setwd(tmp)
renv::init(repos = c("https://carpentries.r-universe.dev/", "https://cran.r-project.org/"))
#> * Discovering package dependencies ... Done!
#> * Resolving missing dependencies ...
#> The version of R recorded in the lockfile will be updated:
#> - R [* -> 4.2.2]
#>
#> * Lockfile written to '/tmp/RtmpXKN45H/file26079355a7a4a/renv.lock'.
renv::install("bioc::SummarizedExperiment")
#> Installing BiocManager [1.30.20] ...
#> OK [linked cache in 0.13 milliseconds]
#> * Installed 1 package in 3 seconds.
#> Installing BiocGenerics [0.44.0] ...
#> OK [linked cache in 0.11 milliseconds]
#> Installing S4Vectors [0.36.2] ...
#> OK [linked cache in 0.11 milliseconds]
#> Installing IRanges [2.32.0] ...
#> OK [linked cache in 0.092 milliseconds]
#> Installing bitops [1.0-7] ...
#> OK [linked cache in 0.096 milliseconds]
#> Installing RCurl [1.98-1.10] ...
#> OK [linked cache in 0.14 milliseconds]
#> Installing GenomeInfoDbData [1.2.9] ...
#> OK [linked cache in 0.14 milliseconds]
#> Installing GenomeInfoDb [1.34.9] ...
#> OK [linked cache in 0.11 milliseconds]
#> Installing matrixStats [0.63.0] ...
#> OK [linked cache in 0.098 milliseconds]
#> Installing MatrixGenerics [1.10.0] ...
#> OK [linked cache in 0.095 milliseconds]
#> Installing DelayedArray [0.24.0] ...
#> OK [linked cache in 0.12 milliseconds]
#> Installing zlibbioc [1.44.0] ...
#> OK [linked cache in 0.12 milliseconds]
#> Installing XVector [0.38.0] ...
#> OK [linked cache in 0.1 milliseconds]
#> Installing GenomicRanges [1.50.2] ...
#> OK [linked cache in 0.17 milliseconds]
#> Installing Biobase [2.58.0] ...
#> OK [linked cache in 0.097 milliseconds]
#> Installing SummarizedExperiment [1.28.0] ...
#> OK [linked cache in 0.11 milliseconds]
#> * Installed 15 packages in 8.9 seconds.Created on 2023-03-07 with reprex v2.0.2 Standard output and standard errorThe following package(s) were not installed successfully:
[SummarizedExperiment]: package 'SummarizedExperiment' is not available
You may need to manually download and install these packages.
The following package(s) will be updated in the lockfile:
# GitHub =============================
- renv [* -> rstudio/renv@HEAD]
Warning message:
In in_dir(input_dir(), expr) :
You changed the working directory to /tmp/RtmpXKN45H/file26079355a7a4a (probably via setwd()). It will be restored to /tmp/Rtmplh5kah/reprex-25b5657a3ad1-next-esok. See the Note section in ?knitr::knitSession infosessioninfo::session_info()
#> ─ Session info ───────────────────────────────────────────────────────────────
#> setting value
#> version R version 4.2.2 Patched (2022-11-10 r83330)
#> os Ubuntu 20.04.5 LTS
#> system x86_64, linux-gnu
#> ui X11
#> language en_US:en
#> collate en_US.UTF-8
#> ctype en_US.UTF-8
#> tz America/Los_Angeles
#> date 2023-03-07
#> pandoc 2.12 @ /home/zhian/anaconda3/bin/ (via rmarkdown)
#>
#> ─ Packages ───────────────────────────────────────────────────────────────────
#> ! package * version date (UTC) lib source
#> P BiocManager 1.30.20 2023-02-24 [?] CRAN (R 4.2.2)
#> R cli 3.6.0 <NA> [?] <NA>
#> R digest 0.6.31 <NA> [?] <NA>
#> R evaluate 0.20 <NA> [?] <NA>
#> R fastmap 1.1.1 <NA> [?] <NA>
#> R fs 1.6.1 <NA> [?] <NA>
#> R glue 1.6.2 <NA> [?] <NA>
#> R htmltools 0.5.4 <NA> [?] <NA>
#> R knitr 1.42 <NA> [?] <NA>
#> R lifecycle 1.0.3 <NA> [?] <NA>
#> R magrittr 2.0.3 <NA> [?] <NA>
#> R purrr 1.0.1 <NA> [?] <NA>
#> R R.cache 0.16.0 <NA> [?] <NA>
#> R R.methodsS3 1.8.2 <NA> [?] <NA>
#> R R.oo 1.25.0 <NA> [?] <NA>
#> R R.utils 2.12.2 <NA> [?] <NA>
#> P renv 0.17.0-26 2023-03-07 [?] Github (rstudio/renv@9b48ce7)
#> R reprex 2.0.2 <NA> [?] <NA>
#> R rlang 1.0.6 <NA> [?] <NA>
#> R rmarkdown 2.20 <NA> [?] <NA>
#> R sessioninfo 1.2.2 <NA> [?] <NA>
#> R styler 1.9.1 <NA> [?] <NA>
#> R vctrs 0.5.2 <NA> [?] <NA>
#> R withr 2.5.0 <NA> [?] <NA>
#> R xfun 0.37 <NA> [?] <NA>
#> R yaml 2.3.7 <NA> [?] <NA>
#>
#> [1] /tmp/RtmpXKN45H/file26079355a7a4a/renv/library/R-4.2/x86_64-pc-linux-gnu
#> [2] /tmp/RtmpXKN45H/file26079355a7a4a/renv/sandbox/R-4.2/x86_64-pc-linux-gnu/9a444a72
#>
#> P ── Loaded and on-disk path mismatch.
#> R ── Package was removed from disk.
#>
#> ──────────────────────────────────────────────────────────────────────────────
I'm wondering, if it's possible for @jeroen to address this in the R-universe, will the R-universe repos work with {renv} 0.17.0? |
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This is a bug in |
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update: I have determined that the problem lies with how {renv} handles non-CRAN repositories mixed with CRAN repositories. Details in #1156 (comment)
Problem
If I try to use
renv::install()with a bioconductor package (e.g.renv::install("bioc::SummarizedExperiment")(related to #1110), the process fails:Note: I am using the most recent GitHub version of {renv}: https://github.com/rstudio/renv/tree/0.17.0-16
(to avoid having to copy/paste/delete, here is the reprex code to generate the output)
Created on 2023-03-06 with reprex v2.0.2
Standard output and standard error
The process now fails with a message that says "object of type 'promise' is not subsettable" and I now have a sandbox folder that I can no longer remove without sudo even though its permissions are set to my user.
This was originally reported in carpentries-incubator/bioc-intro#82 where they were seeing this behavior in a previously working lesson: Here is a backtrace of the error from the log:
version 0.16.0 behavior
I could previously rescue failed bootstraps of BioConductor packages by using
bioc::<PKG>withrenv::install():Created on 2023-03-06 with reprex v2.0.2
Standard output and standard error
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