[Bioc-devel] muleaData problems reported in the Build/check report for BioC 3.19 experimental data

[Mike Smith]

Hi Eszter,

If you're using ExperimentHub in your vignette then you need to add that to
the Suggests field in your DESCRIPTION file.

The R CMD check output you linked to mentions a similar issue for the code
in your examples:

* checking for unstated dependencies in examples ... WARNING
'::' or ':::' imports not declared from:
  ‘ExperimentHub’ ‘dplyr’
'library' or 'require' calls not declared from:
  ‘ExperimentHub’ ‘dplyr’

That should also be fixed by putting those packages in Suggests.

Cheers,
Mike

On Wed, 20 Mar 2024 at 09:54, Eszter Ari <arieszter using gmail.com> wrote:

> Hi,
>
> I have a question a problem reported in the Build/check report for BioC
> 3.19 experimental data:
> I have created an experimental data package:
> https://github.com/ELTEbioinformatics/muleaData
> I have got this message from
> BBS-noreply using bioconductor.org:
> According to the Build/check report for BioC 3.19 experimental data,
> the muleaData package has the following problem(s):  o ERROR for 'R CMD
> check' on nebbiolo1. See the details here:
>
>
> https://master.bioconductor.org/checkResults/3.19/data-experiment-LATEST/muleaData/nebbiolo1-checksrc.htmlAs
> I see on the link there is a problem with the muleaData.Rmd file.
> Previously I have been asked by @lshepherd
> <https://community-bioc.slack.com/team/U42NFBN2C> to make the 'install' R
> code chunk to eval=FALSE:
>
> https://github.com/Bioconductor/Contributions/issues/3291#issuecomment-1978971419
>
> ```{r 'install', eval=FALSE}
> if (!require("BiocManager", quietly = TRUE))
>     install.packages("BiocManager")
>
> BiocManager::install("ExperimentHub")
> BiocManager::install("muleaData")
> ```
>
> Then the next 'example' chunk cannot be run:
>
> ```{r 'example'}
>
> # Calling the ExperimentHub library.
> library(ExperimentHub)
>
> # Downloading the metadata from ExperimentHub.
> eh <- ExperimentHub()
>
> # Creating the muleaData variable.
> muleaData <- query(eh, "muleaData")
>
> # Checking the muleaData variable.
> muleaData
>
> # Looking for the ExperimentalHub ID of i.e. target genes of transcription
> # factors from TFLink in Caenorhabditis elegans.
> mcols(muleaData) %>%
>     as.data.frame() %>%
>     dplyr::filter(species == "Caenorhabditis elegans" &
>         sourceurl == "https://tflink.net/")
>
> # Creating a variable for the GMT data.frame of EH8735.
> # EH8735 contains small-scale measurement results, where the target genes
> are
> # coded with Ensembl ID-s
> Transcription_factor_TFLink_Caenorhabditis_elegans_SS_EnsemblID <-
>     muleaData[["EH8735"]]
> ```
>
> *Should I change to eval=FALSE this chunk as well? *
>
> Ari, Eszter, habil, PhD
> arieszter using gmail.com +36 (70) 380 9833
> postdoctoral researcher at *Synthetic and Systems Biology Unit, Biological
> Research Centre, ELKH, Szeged, Hungary*
> assistant professor at *Dep. Genetics, Eötvös Loránd University, Budapest,
> Hungary*
>
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>
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