[R-pkg-devel] Package dependency graphs of packages in development (local)
Rainer M Krug
R@|ner @end|ng |rom krug@@de
Thu May 9 13:34:16 CEST 2019
Nope:
```
> meta_cache_update()
ℹ Checking for package metadata updates
✔ Downloaded metadata files, 1.37 MB in 5 files.
✔ Updating metadata database
> itdepends::dep_plot_size(".")
ℹ Checking for package metadata updates
✖ Metadata download failed
Error in stop(http_error(resp)) :
Not Found (HTTP 404).
Could not load or update metadata cache. If you think your local cache is broken, try deleting it with `meta_cache_cleanup()`, or the
`$cleanup()` method.
>
I can download the cache manually (see above).
Rainer
```
> On 9 May 2019, at 13:16, Gábor Csárdi <csardi.gabor using gmail.com> wrote:
>
> It fails to download package metadata. Maybe your internet access is
> restricted?
>
> Gabor
>
> On Thu, May 9, 2019 at 12:12 PM Rainer M Krug <Rainer using krugs.de> wrote:
>>
>> But I don’t get it to run.
>>
>> When I do
>>
>>> itdepends::dep_plot_size(".")
>> ℹ Checking for package metadata updates
>> ✖ Metadata download failed
>> Error in stop(http_error(resp)) :
>> Not Found (HTTP 404).
>>
>> Could not load or update metadata cache. If you think your local cache is broken, try deleting it with `meta_cache_cleanup()`, or the
>> `$cleanup()` method.
>> d>
>>
>> I get an error. Suggestions?
>>
>> Rainer
>>
>>
>>
>> On 9 May 2019, at 12:20, Rainer M Krug <Rainer using krugs.de> wrote:
>>
>> Thanks.
>>
>> This sounds like a really useful package - I’ll check it out.
>>
>>
>> On 9 May 2019, at 12:15, Maëlle SALMON <maelle.salmon using yahoo.se> wrote:
>>
>> Could https://github.com/jimhester/itdepends help?
>>
>> Maëlle.
>> Den torsdag 9 maj 2019 12:10:14 CEST, Rainer M Krug <Rainer using krugs.de> skrev:
>>
>>
>> Thanks Gabor.
>>
>> This gives me an impressive long list. Is there a way to see this graphically? Parsing seems to be a long, tedious process.
>>
>> I want to identify packages which I should leave out to reduce the number of (indirect) dependencies.
>>
>> Rainer
>>
>>
>>> On 9 May 2019, at 11:24, Gábor Csárdi <csardi.gabor using gmail.com> wrote:
>>>
>>> You can do something like this with https://github.com/r-lib/pkgdepends:
>>>
>>> pr <- pkgdepends::remotes()$new("local::.", library = tempfile())
>>> #> ℹ Creating library directory:
>>> `/var/folders/59/0gkmw1yj2w7bf2dfc3jznv5w0000gn/T//Rtmpo5NL9R/filee95427c73f55`
>>>
>>> pr$solve()
>>> #> ℹ Checking for package metadata updates
>>> #> ✔ All 10 metadata files are current.
>>> #> ✔ Using session cached package metadata
>>> #> ✔ Using cached package metadata
>>> #> PKG SOLUTION, 1 refs, resolved in 1.2s, solved in 193ms
>>> ───────────────────────
>>> #> local::.
>>> #> Dependencies:
>>> #> github:
>>> #> r-lib/crancache, r-lib/rcmdcheck
>>> #> standard:
>>> #> askpass, assertthat, backports, base64enc, bit, bit64, blob, callr,
>>> #> cli, clisymbols, cranlike, crayon, curl, DBI, debugme, desc,
>>> #> digest, evaluate, fansi, glue, gmailr, highr, hms, httr, jsonlite,
>>> #> knitr, magrittr, markdown, memoise, mime, openssl, parsedate,
>>> #> pillar, pkgbuild, pkgconfig, prettyunits, processx, progress, ps,
>>> #> R6, rappdirs, Rcpp, rematch2, remotes, rlang, rprojroot, RSQLite,
>>> #> sessioninfo, stringi, stringr, sys, tibble, utf8, whoami, withr,
>>> #> xfun, xopen, yaml
>>>
>>> tibble::as_tibble(pr$get_solution()$data)
>>> #> # A tibble: 61 x 27
>>> #> ref type direct status package version license
>>> needscompilation priority
>>> #> <chr> <chr> <lgl> <chr> <chr> <chr> <chr> <lgl> <chr>
>>> #> 1 loca… local TRUE OK revdep… 1.0.0.… MIT + … NA NA
>>> #> 2 askp… stan… FALSE OK askpass 1.1 NA FALSE NA
>>> #> 3 asse… stan… FALSE OK assert… 0.2.1 NA FALSE NA
>>> #> 4 back… stan… FALSE OK backpo… 1.1.4 NA FALSE NA
>>> #> 5 base… stan… FALSE OK base64… 0.1-3 NA FALSE NA
>>> #> 6 bit64 stan… FALSE OK bit64 0.9-7 NA FALSE NA
>>> #> 7 bit stan… FALSE OK bit 1.1-14 NA FALSE NA
>>> #> 8 blob stan… FALSE OK blob 1.1.1 NA FALSE NA
>>> #> 9 callr stan… FALSE OK callr 3.2.0 NA FALSE NA
>>> #> 10 cli stan… FALSE OK cli 1.1.0 NA FALSE NA
>>> #> # … with 51 more rows, and 18 more variables: md5sum <chr>, sha256 <chr>,
>>> #> # filesize <int>, built <chr>, platform <chr>, rversion <chr>,
>>> repodir <chr>,
>>> #> # target <chr>, deps <list>, mirror <chr>, sources <list>, remote <list>,
>>> #> # error <list>, metadata <list>, extra <list>, dep_types <list>,
>>> #> # cache_status <chr>, lib_status <chr>
>>>
>>> And the `deps` column there shows the direct dependencies of the dependencies:
>>>
>>> ❯ pr$get_solution()$data$deps[1:2]
>>> #> [[1]]
>>> #> # A tibble: 25 x 5
>>> #> ref type package op version
>>> #> <chr> <chr> <chr> <chr> <chr>
>>> #> 1 assertthat Imports assertthat "" ""
>>> #> 2 callr Imports callr "" ""
>>> #> 3 cli Imports cli "" ""
>>> #> 4 clisymbols Imports clisymbols "" ""
>>> #> 5 r-lib/crancache Imports crancache >= 0.0.0.9001
>>> #> 6 crayon Imports crayon "" ""
>>> #> 7 DBI Imports DBI "" ""
>>> #> 8 desc Imports desc >= 1.1.1.9002
>>> #> 9 glue Imports glue "" ""
>>> #> 10 gmailr Imports gmailr "" ""
>>> #> # … with 15 more rows
>>> #>
>>> #> [[2]]
>>> #> # A tibble: 2 x 5
>>> #> ref type package op version
>>> #> <chr> <chr> <chr> <chr> <chr>
>>> #> 1 testthat suggests testthat "" ""
>>> #> 2 sys imports sys >= 2.1
>>>
>>> Gabor
>>>
>>> On Thu, May 9, 2019 at 8:53 AM Rainer M Krug <Rainer using krugs.de> wrote:
>>>>
>>>> Hi
>>>>
>>>> I am quite sure, there was a recent discussion about dependency graphs of packages. I saw the post from Dirk at http://dirk.eddelbuettel.com/blog/2018/02/28/#017_dependencies but `tools::package_dependencies()` does only work on packages on CRAN.
>>>>
>>>> But my package is not yet on CRAN (but on GitHub and a drat repo), and I would like to look at the package dependencies BEFORE submitting to CRAN.
>>>>
>>>> Is there a tool which allows me to plot a dependency graph for my local package?
>>>>
>>>> Thanks,
>>>>
>>>> Rainer
>>>>
>>>>
>>>> --
>>>> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)
>>>>
>>>> Orcid ID: 0000-0002-7490-0066
>>>>
>>>> Department of Evolutionary Biology and Environmental Studies
>>>> University of Zürich
>>>> Office Y34-J-74
>>>> Winterthurerstrasse 190
>>>> 8075 Zürich
>>>> Switzerland
>>>>
>>>> Office: +41 (0)44 635 47 64
>>>> Cell: +41 (0)78 630 66 57
>>>> email: Rainer.Krug using uzh.ch
>>>> Rainer using krugs.de
>>>> Skype: RMkrug
>>>>
>>>> PGP: 0x0F52F982
>>>>
>>>> ______________________________________________
>>>> R-package-devel using r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
>> --
>> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)
>>
>> Orcid ID: 0000-0002-7490-0066
>>
>> Department of Evolutionary Biology and Environmental Studies
>> University of Zürich
>> Office Y34-J-74
>> Winterthurerstrasse 190
>> 8075 Zürich
>> Switzerland
>>
>> Office: +41 (0)44 635 47 64
>> Cell: +41 (0)78 630 66 57
>> email: Rainer.Krug using uzh.ch
>> Rainer using krugs.de
>> Skype: RMkrug
>>
>> PGP: 0x0F52F982
>>
>>
>>
>>
>> [[alternative HTML version deleted]]
>>
>>
>> ______________________________________________
>> R-package-devel using r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/r-package-devel
>>
>>
>> --
>> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)
>>
>> Orcid ID: 0000-0002-7490-0066
>>
>> Department of Evolutionary Biology and Environmental Studies
>> University of Zürich
>> Office Y34-J-74
>> Winterthurerstrasse 190
>> 8075 Zürich
>> Switzerland
>>
>> Office: +41 (0)44 635 47 64
>> Cell: +41 (0)78 630 66 57
>> email: Rainer.Krug using uzh.ch
>> Rainer using krugs.de
>> Skype: RMkrug
>>
>> PGP: 0x0F52F982
>>
>>
>>
>>
>> --
>> Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)
>>
>> Orcid ID: 0000-0002-7490-0066
>>
>> Department of Evolutionary Biology and Environmental Studies
>> University of Zürich
>> Office Y34-J-74
>> Winterthurerstrasse 190
>> 8075 Zürich
>> Switzerland
>>
>> Office: +41 (0)44 635 47 64
>> Cell: +41 (0)78 630 66 57
>> email: Rainer.Krug using uzh.ch
>> Rainer using krugs.de
>> Skype: RMkrug
>>
>> PGP: 0x0F52F982
>>
>>
>>
--
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, UCT), Dipl. Phys. (Germany)
Orcid ID: 0000-0002-7490-0066
Department of Evolutionary Biology and Environmental Studies
University of Zürich
Office Y34-J-74
Winterthurerstrasse 190
8075 Zürich
Switzerland
Office: +41 (0)44 635 47 64
Cell: +41 (0)78 630 66 57
email: Rainer.Krug using uzh.ch
Rainer using krugs.de
Skype: RMkrug
PGP: 0x0F52F982
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