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