error in running the Vignette example
ngoccalico opened this issue · comments
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?
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)
Yes I did that, and it is strange that it showed this error:
I suspect lipidr is not installed correctly. What does library('lipidr') show?
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
>
When I tried to look for the function "list_mw_studies" it didn't show up as anything
Thanks for these. Try with triple colons lipidr:::list. Really strange.
I noticed the version of lipidr I have was 1.0.0, could you let me know how I can update the package?
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')
Closing as version was clearly the cause. Feel free to reopen if not.