[Bioc-devel] makeTxDbFromGFF fails in Bioc 3.4 when run through Rscript

[Marcin Cieślik]

Dear All,

I ran into the following problem when porting my package from Bioc 3.3 to
3.4. When I attach my package interactively (library(package), or via
load_all from devtools) everything works fine on both 3.3 and 3.4. However,
when I install my package (p.arc) and call it using:

Rscript -e 'p.arc::config()'

I get this error:

Error in as.data.frame.default(x[[i]], optional = TRUE) :
  cannot coerce class "structure("Rle", package = "S4Vectors")" to a
data.frame
Calls: <Anonymous> ... data.frame -> as.data.frame -> as.data.frame.default
Execution halted

Through painful debugging I found that it fails during a call to:

makeTxDbFromGFF (GenomicFeatures)

I dug further and found that the difference was that the methods package is
attached for Bioc 3.3 and is not attached for Bioc 3.4. I tried:

1. adding methods to Imports: and/or Depends: in DESCRIPTION
2. adding import(methods) to NAMESPACE

But this did not help. The only work-around is to require(methods) before
calling makeTxDbFromGFF.

I wonder if you could help me out

- Is this a problem with my code?
- How does "methods" get attached in Bioc 3.3 (I use R 3.3.2 for all the
tests)?

I will be happy to provide more info if needed.

I addition (but not related to the above) makeTxDbFromGFF does not like the
new RSQlite (1.1) version:

Warning messages:
1: RSQLite::dbGetPreparedQuery() is deprecated, please switch to
DBI::dbGetQuery(params = bind.data).
2: Named parameters not used in query: internal_chrom_id, chrom, length,
is_circular
3: Named parameters not used in query: internal_id, name, type, chrom,
strand, start, end
4: Named parameters not used in query: internal_id, name, chrom, strand,
start, end
5: Named parameters not used in query: internal_id, name, chrom, strand,
start, end
6: Named parameters not used in query: internal_tx_id, exon_rank,
internal_exon_id, internal_cds_id
7: Named parameters not used in query: gene_id, internal_tx_id

Thanks,
Marcin

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