rstudio / rstudio/packrat

Snaphot error

Open
#463 9 comments 1 reaction 0 assignees View on GitHub

Nobody has claimed this yet.

Dominant language
R
Stars
409
Forks
89
PR merge metrics
No merged PRs in 30d

Description

Is there a possibility to snapshot a package that has a lower build number then the one on bioconductor and is installed locally?

packrat::set_opts(local.repos = c("~/R/x86_64-pc-linux-gnu-library/3.4"))
packrat::install_local("AUCell_0.99.5.tar.gz")
packrat::snapshot()
Adding these packages to packrat:
                         _       
    AUCell                 0.99.5
    GENIE3                 1.0.0 
    RcisTarget             0.99.0
    SCENIC                 0.1.7 
    SingleCellExperiment   1.0.0 
    devtools               1.13.5
    git2r                  0.21.0
    rstudioapi             0.7   
    whisker                0.3-2 
    withr                  2.1.2 

Fetching sources for AUCell (0.99.5) ... curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
FAILED
Fetching sources for RcisTarget (0.99.0) ... curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
curl: (22) The requested URL returned error: 404 Not Found
FAILED
Error in snapshotSources(project, activeRepos(project), allRecordsFlat) : 
  Errors occurred when fetching source files:
Error in getSourceForPkgRecord(pkgRecord, sourceDir, availablePkgs, repos) : 
  Failed to retrieve package sources for AUCell 0.99.5 from CRAN (internet connectivity issue?) [1.0.0 is current]
Error in getSourceForPkgRecord(pkgRecord, sourceDir, availablePkgs, repos) : 
  Failed to retrieve package sources for RcisTarget 0.99.0 from CRAN (internet connectivity issue?)

Ignoring packages also didn't work to avoid snapshot

packrat::get_opts()
$auto.snapshot
[1] FALSE

$use.cache
[1] FALSE

$print.banner.on.startup
[1] "auto"

$vcs.ignore.lib
[1] TRUE

$vcs.ignore.src
[1] FALSE

$external.packages
character(0)

$local.repos
[1] "~/R/x86_64-pc-linux-gnu-library/3.4"

$load.external.packages.on.startup
[1] TRUE

$ignored.packages
[1] "RcisTarget.mm9.motifDatabases.20k"  "RcisTarget"                         "AUCell"                             "RcisTarget.hg19.motifDatabases.20k"

$ignored.directories
[1] "data" "inst"

$quiet.package.installation
[1] TRUE

$snapshot.recommended.packages
[1] FALSE

$snapshot.fields
[1] "Imports"   "Depends"   "LinkingTo"

As you can see they should be ignored but in the snapshot call they are still considered.

Contributor guide

No contributing guide indexed for this repository

First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Reproduce the behavior with packrat::set_opts(), packrat::install_local(), packrat::snapshot(), and the ignored.packages configuration shown in the report. Check why AUCell 0.99.5 and RcisTarget 0.99.0 are fetched from CRAN despite being local or ignored; done means snapshot no longer attempts those unavailable sources.

Written by the indexing model from the issue text.

Assessment

Tech stack
r
Domain
tooling
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

Get new issues in your inbox

A short digest of beginner-friendly GitHub issues.