[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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