makeTxDbFromBiomart fails on Ensembl 85 human
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@ryan-c-thompson-5618
Last seen 14 months ago
Scripps Research, La Jolla, CA

I'm testing the makeTxDbFromBiomart function, and I'm noticing that it seems to encounter an error, but only on the current version of Ensembl (85). Running it on version 84 works just fine. Is there a problem with the current Ensembl version's Biomart server, or the biomaRt package, or something else?

> txdb <- makeTxDbFromBiomart()
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Download and preprocess the 'splicings' data frame ... Error in value[[3L]](cond) :
  Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.
> traceback()
9: stop("Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.")
8: value[[3L]](cond)
7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
6: tryCatchList(expr, classes, parentenv, handlers)
5: tryCatch(postForm(paste(martHost(mart), "?", sep = ""), query = xmlQuery),
       error = function(e) {
           stop("Request to BioMart web service failed. Verify if you are still connected to the internet.  Alternatively the BioMart web service is temporarily down.")
       })
4: getBM(attributes, filters = bm_filters, values = bm_values, ...)
3: .getBM2(attributes, filter, mart = mart, bmHeader = FALSE)
2: .makeBiomartSplicings(filter, mart, transcripts_tx_id, recognized_attribs,
       id_prefix = id_prefix)
1: makeTxDbFromBiomart()

> makeTxDbFromBiomart(host="e84.ensembl.org")
Download and preprocess the 'transcripts' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Download and preprocess the 'splicings' data frame ... OK
Download and preprocess the 'genes' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
> sessionInfo()
R version 3.3.1 (2016-06-21)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 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:
[1] grDevices datasets  parallel  graphics  stats4    stats     utils
[8] methods   base

other attached packages:
 [1] GenomicFeatures_1.24.5 AnnotationDbi_1.34.4   Biobase_2.32.0
 [4] GenomicRanges_1.24.2   GenomeInfoDb_1.8.3     openxlsx_3.0.0
 [7] magrittr_1.5           dplyr_0.5.0            foreach_1.4.3
[10] plyr_1.8.4             stringr_1.0.0          IRanges_2.6.1
[13] ggplot2_2.1.0          S4Vectors_0.10.2       BiocGenerics_0.18.0
[16] BiocInstaller_1.22.3

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.6                XVector_0.12.1
 [3] bitops_1.0-6               iterators_1.0.8
 [5] tools_3.3.1                zlibbioc_1.18.0
 [7] biomaRt_2.28.0             RSQLite_1.0.0
 [9] tibble_1.1                 gtable_0.2.0
[11] DBI_0.4-1                  rtracklayer_1.32.2
[13] Biostrings_2.40.2          grid_3.3.1
[15] R6_2.1.2                   BiocParallel_1.6.4
[17] XML_3.98-1.4               GenomicAlignments_1.8.4
[19] scales_0.4.0               Rsamtools_1.24.0
[21] codetools_0.2-14           SummarizedExperiment_1.2.3
[23] assertthat_0.1             colorspace_1.2-6
[25] stringi_1.1.1              RCurl_1.95-4.8
[27] munsell_0.4.3
biomart maketxdbfrombiomart genomicfeatures • 644 views
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Are you still experiencing this issue?  It works fine on my system with the same package versions.  The ensembl BioMart servers have been a little temperamental for me recently, so maybe the archive host was performing more reliably?

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I tried again today, and it worked this time. I thought for sure it was a bug and not a transient error, since I got the exact same error + traceback every time.

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@ryan-c-thompson-5618
Last seen 14 months ago
Scripps Research, La Jolla, CA

Apparently this was a transient server issue that seems to have resolved itself.

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