**0**wrote:

Hi,

I've been following the vignette, but I keep getting the following error with supportedOrganisms() from goseq:

**Error in matrix(unlist(pairs), nrow = 2) :
'data' must be of a vector type, was 'NULL'**

Is there something I am doing wrong?

Many thanks in advance!!

Victoria

R version 3.3.2 (2016-10-31) -- "Sincere Pumpkin Patch"

Copyright (C) 2016 The R Foundation for Statistical Computing

Platform: x86_64-apple-darwin13.4.0 (64-bit)

> library(goseq)

Loading required package: BiasedUrn

Loading required package: geneLenDataBase

> supportedOrganisms()

Loading required package: rtracklayer

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, xtabs

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

anyDuplicated, append, as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq, Filter, Find, get, grep, grepl,

intersect, is.unsorted, lapply, lengths, 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 objects are masked from ‘package:base’:

colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges

Loading required package: GenomeInfoDb

Error in matrix(unlist(pairs), nrow = 2) :

'data' must be of a vector type, was 'NULL'

> traceback()

14: matrix(unlist(pairs), nrow = 2)

13: .local(object, ...)

12: ucscCart(x)

11: ucscCart(x)

10: genome(ucscCart(x))

9: genome(x)

8: genome(x)

7: `genome<-`(`*tmp*`, value = "hg19")

6: `genome<-`(`*tmp*`, value = "hg19")

5: GenomicFeatures:::supportedUCSCtables()

4: is.factor(var)

3: unfactor(GenomicFeatures:::supportedUCSCtables())

2: supportedGeneIDs()

1: supportedOrganisms()

**35k**• written 21 months ago by starbug16 •

**0**

Hi Victoria,

Thanks for reporting this. The parsing in the underlying function

is broken because the web page it queried has been overhauled. It may take a little while to fix this. We'll report back when it's done.

Valerie

6.6kOops, not related. Sorry for the misdiagnosis.

Valerie

6.6k