Error in unlist(metadata(TXDB))

[genomicspw]

I have all the latest packages and I am not new to R!
There is a problem with ChIPSeeker talking to TxDb objects. The TxDb object can be manually queried but cannot be queried through ChIPSeeker:

    >promoter <- getPromoters(TxDb=txdb, upstream=3000, downstream=3000)
    Error in unlist(metadata(TXDB)) :
    error in evaluating the argument 'x' in selecting a method for function 'unlist': Error in (function (classes, fdef, mtable) :
    unable to find an inherited method for function ‘metadata’ for signature ‘"character"’
    >txdb
    TxDb object:
    Db type: TxDb
    Supporting package: GenomicFeatures
    Data source: UCSC
    Genome: hg19
    Organism: Homo sapiens
    UCSC Table: knownGene
    Resource URL: http://genome.ucsc.edu/
    Type of Gene ID: Entrez Gene ID
    Full dataset: yes
    miRBase build ID: GRCh37
    transcript_nrow: 82960
    exon_nrow: 289969
    cds_nrow: 237533
    Db created by: GenomicFeatures package from Bioconductor
    Creation time: 2015-03-19 13:55:51 -0700 (Thu, 19 Mar 2015)
    GenomicFeatures version at creation time: 1.19.32
    RSQLite version at creation time: 1.0.0
    DBSCHEMAVERSION: 1.1

    >sessionInfo(package="ChIPseeker")
    R version 3.2.2 (2015-08-14)
    Platform: x86_64-pc-linux-gnu (64-bit)
    Running under: Ubuntu 14.04.1 LTS

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:
character(0)

other attached packages:
[1] ChIPseeker_1.4.7

loaded via a namespace (and not attached):
[1] Rcpp_0.12.1

[2] GO.db_3.1.2

[3] png_0.1-7

[4] Rsamtools_1.20.5

[5] Biostrings_2.36.4

[6] gtools_3.5.0

[7] assertthat_0.1

[8] digest_0.6.8

[9] BSgenome.Mmusculus.UCSC.mm10_1.4.0

[10] R6_2.1.1

[11] org.Mm.eg.db_3.1.2

[12] GenomeInfoDb_1.4.3

[13] plyr_1.8.3

[14] futile.options_1.0.0

[15] stats4_3.2.2

[16] RSQLite_1.0.0

[17] httr_1.0.0

[18] ggplot2_1.0.1

[19] BiocInstaller_1.18.4

[20] utils_3.2.2

[21] gplots_2.17.0

[22] zlibbioc_1.14.0

[23] GenomicFeatures_1.20.6

[24] gdata_2.17.0

[25] S4Vectors_0.6.6

[26] qvalue_2.0.0

[27] proto_0.3-10

[28] splines_3.2.2

[29] BiocParallel_1.2.22

[30] stringr_1.0.0

[31] igraph_1.0.1

[32] RCurl_1.95-4.7

[33] biomaRt_2.24.1

[34] munsell_0.4.2

[35] TxDb.Mmusculus.UCSC.mm10.knownGene_3.1.2
[36] rtracklayer_1.28.10

[37] stats_3.2.2

[38] BiocGenerics_0.14.0

[39] TxDb.Hsapiens.UCSC.hg19.knownGene_3.1.2
[40] KEGGREST_1.8.1

[41] IRanges_2.2.9

[42] grDevices_3.2.2

[43] XML_3.98-1.3

[44] dplyr_0.4.3

[45] GenomicAlignments_1.4.2

[46] MASS_7.3-44

[47] bitops_1.0-6

[48] grid_3.2.2

[49] gtable_0.1.2

[50] DBI_0.3.1

[51] magrittr_1.5

[52] datasets_3.2.2

[53] scales_0.3.0

[54] KernSmooth_2.23-15

[55] stringi_0.5-5

[56] GOSemSim_1.26.0

[57] XVector_0.8.0

[58] reshape2_1.4.1

[59] DO.db_2.9

[60] futile.logger_1.4.1

[61] clusterProfiler_2.2.7

[62] graphics_3.2.2

[63] boot_1.3-17

[64] base_3.2.2

[65] lambda.r_1.1.7

[66] RColorBrewer_1.1-2

[67] tools_3.2.2

[68] BSgenome_1.36.3

[69] Biobase_2.28.0

[70] plotrix_3.5-12

[71] parallel_3.2.2

[72] AnnotationDbi_1.30.1

[73] colorspace_1.2-6

[74] GenomicRanges_1.20.8

[75] caTools_1.17.1

[76] DOSE_2.6.6

[77] methods_3.2.2

[GuangchuangYu]

This is exactly the same issue of #7.

This issue is due to reloading old saved session, for file connection cannot be restored, see my answer in https://support.bioconductor.org/p/66576/#70476.

The TxDb is internally a file connection link to a sqlite file and it can't be restored in another R session.

Although this is not an issue of ChIPseeker, I try to fix it by detecting whether the file connection is broken, if yes, reload TxDb.

This error msg will be disappeared in next release (Oct. 14).