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

[Eszter Ari]

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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