I am a beginner in R and currently taking the course "Bioconductor for Genomic Data Science" on Coursera and faced a problem which I was unable to solve. When trying to download a dataset obtained with the AnnotationHub package I face the following error message:
> ahub = AnnotationHub() > ahub = subset(ahub, species == "Homo sapiens") > qhs = query(ahub, c("H3K4me3", "Gm12878")) > gr1 = qhs[] require(“rtracklayer”) downloading from ‘https://annotationhub.bioconductor.org/fetch/32503’ retrieving 1 resource |=======================================================| 100% Error: failed to load resource name: AH27075 title: wgEncodeUwHistoneGm12878H3k4me3StdHotspotsRep1.broadPeak.gz reason: scan() expected 'a real', got '%A' In addition: Warning message: In read.table(con, colClasses = bedClasses, as.is = TRUE, na.strings = ".", : line 2 appears to contain embedded nulls
If I download the dataset manually from a browser and then import it there are no problems. Anyone had this problem before or has any tips on how to solve it?
> sessionInfo() R version 3.4.1 (2017-06-30) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows >= 8 x64 (build 9200) Matrix products: default locale:  LC_COLLATE=English_United Kingdom.1252 LC_CTYPE=English_United Kingdom.1252 LC_MONETARY=English_United Kingdom.1252 LC_NUMERIC=C  LC_TIME=English_United Kingdom.1252 attached base packages:  stats4 parallel stats graphics grDevices utils datasets methods base other attached packages:  rtracklayer_1.36.4 GenomicRanges_1.28.5 GenomeInfoDb_1.12.2 IRanges_2.10.3 S4Vectors_0.14.4 AnnotationHub_2.8.2 BiocGenerics_0.22.0 loaded via a namespace (and not attached):  Rcpp_0.12.12 BiocInstaller_1.26.1 compiler_3.4.1 XVector_0.16.0 bitops_1.0-6  tools_3.4.1 zlibbioc_1.22.0 digest_0.6.12 bit_1.1-12 lattice_0.20-35  RSQLite_2.0 memoise_1.1.0 tibble_1.3.4 pkgconfig_2.0.1 rlang_0.1.2  Matrix_1.2-11 DelayedArray_0.2.7 shiny_1.0.5 DBI_0.7 curl_2.8.1  yaml_2.1.14 GenomeInfoDbData_0.99.0 httr_1.3.1 Biostrings_2.44.2 grid_3.4.1  bit64_0.9-7 Biobase_2.36.2 R6_2.2.2 AnnotationDbi_1.38.2 BiocParallel_1.10.1  XML_3.98-1.9 blob_1.1.0 matrixStats_0.52.2 GenomicAlignments_1.12.2 Rsamtools_1.28.0  htmltools_0.3.6 SummarizedExperiment_1.6.3 mime_0.5 interactiveDisplayBase_1.14.0 xtable_1.8-2  httpuv_1.3.5 RCurl_1.95-4.8