[Bioc-devel] Stackoverflow Bounty: pkgdown R package build_site function causes dependent packages unable to be loaded

[Marcin Kosiński]

Thanks Herve for comments.

I think I have found a solution for my problem, even though it wasn't
really reproducible, I admit.

It looks like I have found a nasty work-around.
`RTCGA` software package uses 8 data packages in its examples. Each data
package required RTCGA to be loaded. `pkgdown::build_site()` uses
`devtools::load_all()` which weirdly loads only objects from RTCGA but does
not allow to load this package during examples run.

I have removed `RTCGA` from `Depends` of the data packages by changing
those packages meta-informations like

    packages_to_remove_RTCGA_from_Depends <-
      c("RTCGA.clinical",
        "RTCGA.mutations",
        "RTCGA.rnaseq",
        "RTCGA.RPPA",
        "RTCGA.mRNA",
        "RTCGA.miRNASeq",
        "RTCGA.methylation",
        "RTCGA.CNV")

    sapply(packages_to_remove_RTCGA_from_Depends, function(data_package){
      Meta <- readRDS(file.path(.libPaths()[1], data_package, "Meta",
"package.rds"))
      Meta$Depends <- list()
      saveRDS(Meta, file.path(.libPaths()[1], data_package, "Meta",
"package.rds"))
    })

2016-12-16 6:43 GMT+01:00 Hervé Pagès <hpages at fredhutch.org>:

> Hi Marcin,
>
> You posted this 7 months ago, it has been viewed 100 times, and nobody
> commented or tried to answer. I don't know if a bounty is going to help
> though.
>
> To me, a much more effective way to get people help you is by providing
> enough information so that people can easily reproduce the problem.
> Honestly, right now, I don't see how people could easily reproduce
> this. I guess most people have never heard of pkgdown, or don't know
> where to find it, or don't know how to install it, or don't know which
> version you used. They don't know which version of R or RTCGA you used
> either, or what you did before calling pkgdown::build_site(), or what
> platform you are on.
>
> So if you manage to provide code that people can just copy/paste in
> a fresh session in order to see the problem, that will greatly help.
> Your code should show how to install pkgdown (don't assume people have
> it installed already). After your code has loaded all the required
> packages, show the output of your sessionInfo().
>
> This is general advice for any bug report. I don't know if you found
> a bug but it could be (hard to tell without being able to reproduce).
>
> Also did you try to contact the pkgdown folks? This is probably a more
> efficient way to report a bug than using stackoverflow.
>
> Cheers,
> H.
>
>
>
> On 12/15/2016 07:21 AM, Marcin Kosiński wrote:
>
>> I am trying to build a pkgdown documentation for Bioconductor package.
>> I have wrote about it on the stackoverflow
>> http://stackoverflow.com/questions/36874972/pkgdown-r-packag
>> e-build-site-function-causes-dependent-packages-unable-to-be-loa
>> but the question didn't receivew the expected attention.
>>
>> I have started a bounty, looking to give 50 points of my reputation for
>> the
>> best answer.
>>
>>         [[alternative HTML version deleted]]
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>
>>
> --
> Hervé Pagès
>
> Program in Computational Biology
> Division of Public Health Sciences
> Fred Hutchinson Cancer Research Center
> 1100 Fairview Ave. N, M1-B514
> P.O. Box 19024
> Seattle, WA 98109-1024
>
> E-mail: hpages at fredhutch.org
> Phone:  (206) 667-5791
> Fax:    (206) 667-1319
>

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