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 <ariesz...@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-nore...@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 > ariesz...@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* > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel