Hi Mike, Many thanks!
Does this: "Please take the time to address this by committing and pushing changes to your package at git.bioconductor.org" mean that I have to push it to the devel branch like this? Is this mean that I have to push the changes to the devel branch of the # to connect with the bioC repo - need to be done only once git remote add upstream g...@git.bioconductor.org:packages/muleaData.git # after every update in the main repo that we want to push to the upstream/devel branch of BioC git fetch --all # change to the main branch git checkout main git merge origin/main # change to the devel branch git checkout devel git merge main git push upstream devel # change back to the main branch git checkout main Best, Eszter On Wed, 20 Mar 2024 at 10:07, Mike Smith <grimbo...@gmail.com> wrote: > 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 >> > -- 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