I confirmed the "Post Title" with R 3.2.1(and 3.2.0), ath1121501.db 3.1.3, AnnotationDbi 1.30.1
This should return "Large character (20335 elements, 1.2 Mb)"
You can reproduce the "Large character (20335 elements, 1.2 Mb)" with R 3.1.3, ath1121501.db 3.0.0, AnnotationDbi 1.28.2
Thanks,
Kozo
Wow. Thanks for this bug report. I have code that checks for these things but apparently the probes for arabidopsis have slipped past my current dragnet for missing fields.
I will find out what went wrong and fix the package. And then I will update the dragnet so this kind of problem doesn't happen again. Once I have repaired the package I will let you know. But until I report back to this thread you won't be able to get much used out of the following two packages:
ag.db_3.1.2.tar.gz
ath1121501.db_3.1.2.tar.gz
The complementary arabidopsis OrgDb package (org.At.tair.db_3.1.2.tar.gz), is unaffected as the only problem seems to be the affy based probe data.
Marc
OK. I have just pushed repaired packages online for these two chip packages. Look for version 3.1.4 to appear within the next day or so on the website.
Marc
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version 2.3.6
I can confirm that this package is completely busted:
> dbGetQuery(ath1121501_dbconn(), "select * from map_counts;") map_name count 1 ACCNUM 0 2 GENENAME 0 3 SYMBOL 0 4 CHR 0 5 PMID 0 6 PMID2PROBE 0 7 CHRLENGTHS 7 8 GO 0 9 GO2PROBE 0 10 GO2ALLPROBES 0 11 PATH 0 12 PATH2PROBE 0 13 ENZYME 0 14 ENZYME2PROBE 0 15 CHRLOC 0 16 CHRLOCEND 0 17 ARACYC 0 18 ARACYCENZYME 0 19 TOTAL 22810 > sessionInfo() R version 3.2.0 (2015-04-16) Platform: x86_64-unknown-linux-gnu (64-bit) Running under: Debian GNU/Linux 8 (jessie) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets [8] methods base other attached packages: [1] hgu133plus2.db_3.1.3 org.Hs.eg.db_3.1.2 ath1121501.db_3.1.3 [4] org.At.tair.db_3.1.2 RSQLite_1.0.0 DBI_0.3.1 [7] AnnotationDbi_1.30.1 GenomeInfoDb_1.4.1 IRanges_2.2.4 [10] S4Vectors_0.6.0 Biobase_2.28.0 BiocGenerics_0.14.0 loaded via a namespace (and not attached): [1] tools_3.2.0Thanks James.
I review ath1121501.db schema and AnnotationDbi spec.