Snaphot error
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
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- 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