Package cannot be loaded/attached if offline

[PeteHaitch]

I appreciate depmap is mostly about downloading data from a portal, but shouldn't it be possible to load/attach the package if offline? Here's what happens when I try (by simply disabling wifi on my laptop)

library(depmap)
#> Loading required package: dplyr
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
#> Cannot connect to ExperimentHub server, using 'localHub=TRUE' instead
#> Using 'localHub=TRUE'
#>   If offline, please also see BiocManager vignette section on offline use
#> Error: package or namespace load failed for 'depmap':
#>  .onLoad failed in loadNamespace() for 'depmap', details:
#>   call: FUN(X[[i]], ...)
#>   error: 'crispr_22Q1' not found in ExperimentHub

^{Created on 2024-03-16 with reprex v2.1.0}

Session info

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[lgatto]

Thank you for the report.

I don't think this is of depmap specifically, it's a feature of ExperimentHub packages. I tried in another of my ExperimentHub packages, but maybe you have a different experience with other packages, and there's a feature I'm missing.

Anyway, this is from ?ExperimentHub::createHubAccessors:

For developers:

     ‘createHubAccessors(pkgname, titles): ’ This helper is intended to
     be used by ExperimentHub package developers in their .onLoad()
     function in zzz.R. It generates and exports functions by resource
     name which allows the resource to be loaded with resource123() in
     addition to the standard method via the ExperimentHub interface,
     e.g., ehub[["EH123"]]. When 'metadata=TRUE' just the metadata are
     displayed, when 'metadata=FALSE' the full resource is loaded, e.g,
     resource123(metadata=TRUE). See vignette for more information.

Here's the line in depmap.

I suppose that one should check if there's connectivity before calling createHubAccessors(). I'll look into this.

[lgatto]

I have asked about this on bioc-devel.

In the meantime, there's branch issue92, where when loading depmap with a disabled wifi, I get:

> suppressPackageStartupMessages(library(depmap))
Warning message:
Not internet connectivity. Unable to create Hub accessors. 

[PeteHaitch]

Thank you for looking into this, Laurent. I only came across this issue because I happened to be working offline when writing a Bioconductor package review (https://github.com/Bioconductor/Contributions/issues/3066) where we had requested the authors use depmap to retrieve data from data portal rather than their existing ad hoc solution.

[lgatto]

OK, thanks for letting me know. You are right, that it is better to be able to use ExeprimentHub packages when offline.

The author got in touch with me and I implemented the features she needed to make use of depmap.

[PeteHaitch]

That's really helpful of you, thank you!

[TrinhNguyenP]

Hi @PeteHaitch,

The features that @lgatto implemented recently will be added into Deeptarget and I will re-submit.

Thanks,

Trinh