Entering edit mode
Using devel:
> src <- src_organism("TxDb.Hsapiens.UCSC.hg38.knownGene")
Using temporary cache /data3/tmp/RtmpL4Yacm/BiocFileCache
adding rname 'dplyr.TxDb.Hsapiens.UCSC.hg38.knownGene.sqlite'
Error in bfcrpath(bfc, rnames = txdb_name) :
not all 'rnames' found or unique.
> traceback()
6: stop(e)
5: value[[3L]](cond)
4: tryCatchOne(expr, names, parentenv, handlers[[1L]])
3: tryCatchList(expr, classes, parentenv, handlers)
2: tryCatch({
suppressWarnings({
bfcrpath(bfc, rnames = txdb_name)
})
}, error = function(e) {
test <- identical(conditionMessage(e), "all 'rnames' not found or valid.")
if (!test)
stop(e)
bfcnew(bfc, txdb_name)
})
1: src_organism("TxDb.Hsapiens.UCSC.hg38.knownGene")
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)
Matrix products: default
BLAS: /data/oldR/R-devel/lib64/R/lib/libRblas.so
LAPACK: /data/oldR/R-devel/lib64/R/lib/libRlapack.so
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] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0
[2] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
[3] GenomicFeatures_1.33.0
[4] AnnotationDbi_1.43.1
[5] Biobase_2.41.2
[6] GenomicRanges_1.33.13
[7] GenomeInfoDb_1.17.1
[8] IRanges_2.15.16
[9] S4Vectors_0.19.19
[10] BiocGenerics_0.27.1
[11] bindrcpp_0.2.2
[12] Organism.dplyr_1.9.0
[13] AnnotationFilter_1.5.2
[14] dplyr_0.7.6
loaded via a namespace (and not attached):
[1] SummarizedExperiment_1.11.6 progress_1.2.0
[3] tidyselect_0.2.4 purrr_0.2.5
[5] lattice_0.20-35 BiocFileCache_1.5.5
[7] rtracklayer_1.41.3 blob_1.1.1
[9] XML_3.98-1.13 rlang_0.2.1
[11] pillar_1.3.0 glue_1.3.0
[13] DBI_1.0.0 BiocParallel_1.15.8
[15] rappdirs_0.3.1 bit64_0.9-7
[17] dbplyr_1.2.2 matrixStats_0.54.0
[19] GenomeInfoDbData_1.1.0 bindr_0.1.1
[21] stringr_1.3.1 zlibbioc_1.27.0
[23] Biostrings_2.49.1 memoise_1.1.0
[25] biomaRt_2.37.4 Rcpp_0.12.18
[27] DelayedArray_0.7.24 org.Hs.eg.db_3.6.0
[29] XVector_0.21.3 bit_1.1-14
[31] Rsamtools_1.33.3 hms_0.4.2
[33] digest_0.6.15 stringi_1.2.4
[35] grid_3.5.0 tools_3.5.0
[37] bitops_1.0-6 magrittr_1.5
[39] lazyeval_0.2.1 RCurl_1.95-4.11
[41] tibble_1.4.2 RSQLite_2.1.1
[43] crayon_1.3.4 pkgconfig_2.0.1
[45] Matrix_1.2-14 prettyunits_1.0.2
[47] assertthat_0.2.0 httr_1.3.1
[49] R6_2.2.2 GenomicAlignments_1.17.3
[51] compiler_3.5.0
And using release:
> src <- src_organism("TxDb.Hsapiens.UCSC.hg38.knownGene")
> genes(src)
Error: Can't convert a NULL to a quosure
> sessionInfo()
R version 3.5.0 (2018-04-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 8 (jessie)
Matrix products: default
BLAS: /data/oldR/R-3.5.0/lib64/R/lib/libRblas.so
LAPACK: /data/oldR/R-3.5.0/lib64/R/lib/libRlapack.so
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] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] bindrcpp_0.2.2
[2] TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0
[3] GenomicFeatures_1.32.0
[4] AnnotationDbi_1.42.1
[5] Biobase_2.40.0
[6] GenomicRanges_1.32.3
[7] GenomeInfoDb_1.16.0
[8] IRanges_2.14.10
[9] S4Vectors_0.18.3
[10] BiocGenerics_0.26.0
[11] Organism.dplyr_1.8.0
[12] AnnotationFilter_1.4.0
[13] dplyr_0.7.6
[14] BiocInstaller_1.30.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.17 lattice_0.20-35
[3] circlize_0.4.4 prettyunits_1.0.2
[5] Rsamtools_1.32.2 Biostrings_2.48.0
[7] assertthat_0.2.0 digest_0.6.15
[9] BiocFileCache_1.4.0 R6_2.2.2
[11] RSQLite_2.1.1 httr_1.3.1
[13] pillar_1.2.3 GlobalOptions_0.1.0
[15] zlibbioc_1.26.0 rlang_0.2.1
[17] progress_1.2.0 lazyeval_0.2.1
[19] blob_1.1.1 GetoptLong_0.1.7
[21] Matrix_1.2-14 BiocParallel_1.14.2
[23] stringr_1.3.1 RCurl_1.95-4.10
[25] bit_1.1-14 biomaRt_2.36.1
[27] DelayedArray_0.6.1 compiler_3.5.0
[29] rtracklayer_1.40.3 pkgconfig_2.0.1
[31] shape_1.4.4 tidyselect_0.2.4
[33] SummarizedExperiment_1.10.1 tibble_1.4.2
[35] GenomeInfoDbData_1.1.0 matrixStats_0.53.1
[37] XML_3.98-1.11 crayon_1.3.4
[39] dbplyr_1.2.1 GenomicAlignments_1.16.0
[41] bitops_1.0-6 rappdirs_0.3.1
[43] grid_3.5.0 DBI_1.0.0
[45] magrittr_1.5 stringi_1.2.3
[47] XVector_0.20.0 org.Hs.eg.db_3.6.0
[49] rjson_0.2.20 RColorBrewer_1.1-2
[51] tools_3.5.0 bit64_0.9-7
[53] glue_1.2.0 purrr_0.2.5
[55] hms_0.4.2 colorspace_1.3-2
[57] ComplexHeatmap_1.18.1 memoise_1.1.0
[59] bindr_0.1.1
>
Huh. It seems a restart was all I needed for the devel issue. Sorry for the noise.
> library(BiocFileCache) Loading required package: dbplyr > bfc <- BiocFileCache() ## got no tidyverse, let's wrap in as.data.frame() ;P > as.data.frame(bfcquery(bfc, "dplyr"))[,c("rid","rname","fpath")] rid rname fpath 1 BFC1 dplyr.TxDb.Hsapiens.UCSC.hg38.knownGene.sqlite 796150c6fd7c > library(Organism.dplyr) > src <- src_organism("TxDb.Hsapiens.UCSC.hg38.knownGene")Thank you for posting about this issue. Any criticism about the package is helpful. It allowed Martin and I to discuss and make a few small changes that needed to be made.