Problem when constructing a TxDb with makeTxDbFromGFF:Error in dbGetQuery(conn,SQL) :

Question

[Wet&DryImmunology]

I was learning RNA-seq analysis following the RNA-seq workflow: gene-level exploratory analysis and differential expression.

I came to the step of constructing a TxDb:

gtffile <- file.path(dir,"Homo_sapiens.GRCh37.75_subset.gtf")
(txdb <- makeTxDbFromGFF(gtffile, format="gtf",circ_seqs=character()))

Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... Warning messages:
1: 'BiocGenerics:::updateS4' is deprecated.
Use 'replaceSlots' instead.
See help("Deprecated")
2: 'BiocGenerics:::updateS4' is deprecated.
Use 'replaceSlots' instead.
See help("Deprecated")
3: 'BiocGenerics:::updateS4' is deprecated.
Use 'replaceSlots' instead.
See help("Deprecated")
4: 'BiocGenerics:::updateS4' is deprecated.
Use 'replaceSlots' instead.
See help("Deprecated")
Error in dbGetQuery(conn, SQL) :
  error in evaluating the argument 'conn' in selecting a method for function 'dbGetQuery': Error in get(name, envir = asNamespace(pkg), inherits = FALSE) :
  object 'dbconn' not found

and:

(ebg <- exonsBy(txdb,by="gene"))
Error in exonsBy(txdb, by = "gene") : 
  error in evaluating the argument 'x' in selecting a method for function 'exonsBy': Error: object 'txdb' not found

I guess that I could not ignore the error (and warning?)

Some people also had similar problem with makeTxDbFromGFF

https://support.bioconductor.org/p/70695/

he solved his problem through installing a new version of R and GenomicFeatures, but I don't think that could apply to my problem, for both my R and GenomicFeatures are new:

sessionInfo()
R version 3.2.2 (2015-08-14)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.9.5 (Mavericks)

locale:
[1] C/UTF-8/C/C/C/C

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] GenomicFeatures_1.20.6 AnnotationDbi_1.30.1   Biobase_2.28.0
 [4] Rsamtools_1.20.5       Biostrings_2.36.4      XVector_0.8.0
 [7] airway_0.102.0         GenomicRanges_1.20.8   GenomeInfoDb_1.4.3
[10] IRanges_2.4.0          S4Vectors_0.8.0        BiocGenerics_0.14.0
[13] BiocInstaller_1.18.5

loaded via a namespace (and not attached):
 [1] zlibbioc_1.14.0         GenomicAlignments_1.4.2 BiocParallel_1.2.22
 [4] tools_3.2.2             DBI_0.3.1               lambda.r_1.1.7
 [7] futile.logger_1.4.1     rtracklayer_1.28.10     futile.options_1.0.0
[10] bitops_1.0-6            RCurl_1.95-4.7          biomaRt_2.24.1
[13] RSQLite_1.0.0           XML_3.98-1.3

Could anyone have any idea how to solve this problem?

Thanks very much!

Sorry I forgot to paste the traceback()

traceback()
13: dbGetQuery(conn, SQL)
12: AnnotationDbi:::dbEasyQuery(AnnotationDbi:::dbconn(annotationdb),
        paste(sql, collapse = "\n"))
11: queryAnnotationDb(txdb, sql)
10: load_chrominfo(.self, set.col.class = TRUE)
9: .Object$initialize(...)
8: initialize(value, ...)
7: initialize(value, ...)
6: methods::new(def, ...)
5: .TxDb$new(conn = conn)
4: TxDb(conn)
3: makeTxDb(transcripts, splicings, genes = genes, chrominfo = chrominfo, 
       metadata = metadata, reassign.ids = TRUE)
2: makeTxDbFromGRanges(gr, metadata = metadata)
1: makeTxDbFromGFF(gtffile, format = "gtf", circ_seqs = character())

(txdb <- makeTxDbFromGFF(gtffile, format="gtf",circ_seqs=character()))

Sorry that if some necessary information is left out, please kindly let me know if any further information is needed to evaluate the problem.

[Devon Ryan]

It looks like GenomicFeatures has some problems, at least on Linux. You have a mix of bioconductor 3.1 (e.g., GenomicFeatures) and 3.2 (e.g., IRanges) packages, which is probably causing the problem.

[Wet&DryImmunology]

Yes, actually,that is the problem.

Thank you very much. Ryan.

* Packages too new for Bioconductor version '3.1'

          Version
IRanges   "2.4.0"
S4Vectors "0.8.0"

Answer 1

[Wet&DryImmunology]

Problem solved. In case people have the same problem, please see the attached link.

https://support.bioconductor.org/p/73482/