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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