error in running the Vignette example

[ngoccalico]

Hi, I am trying to run your vignette but ran into a problem early on. line #60

> lipidr::list_mw_studies(keyword = "lipid")
Error: 'list_mw_studies' is not an exported object from 'namespace:lipidr'

Could you let me know what the problem was?

[ahmohamed]

Not quite sure why it's saying that, but you should be able to run it if you load the package first with library(lipidr)

[ngoccalico]

Yes I did that, and it is strange that it showed this error:

[ahmohamed]

I suspect lipidr is not installed correctly. What does library('lipidr') show?

[ngoccalico]

this is what the message was

> library(lipidr)
Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap,
    parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
    Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit,
    which, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite
    Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: ‘matrixStats’

The following objects are masked from ‘package:Biobase’:

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: ‘DelayedArray’

The following objects are masked from ‘package:matrixStats’:

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from ‘package:base’:

    aperm, apply, rowsum

> 

[ngoccalico]

When I tried to look for the function "list_mw_studies" it didn't show up as anything

[ahmohamed]

Thanks for these. Try with triple colons lipidr:::list. Really strange.

[ngoccalico]

I noticed the version of lipidr I have was 1.0.0, could you let me know how I can update the package?

[ahmohamed]

Aah, this is too old. I didn't even ask about the version because this function was added way back. Which R version are you using? You might need to update R (4 or later) and Bioconductor versions, and simply reinstall using BiocManager::install('lipidr')

[ahmohamed]

Closing as version was clearly the cause. Feel free to reopen if not.