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joseph
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@joseph-5658
Last seen 7.1 years ago
Hi, I get some errors when I run the demo data:
> data(gse16873.d) > data(demo.paths) > i <- 1 > pv.out <- pathview(gene.data = gse16873.d[, 1], pathway.id = + demo.paths$sel.paths[i], species = "hsa", out.suffix = "gse16873", + kegg.native = TRUE) Info: Downloading xml files for hsa04110, 1/1 pathways.. Info: Downloading png files for hsa04110, 1/1 pathways.. Error in select(db.obj, keys = in.ids, keytype = in.type, columns = c(in.type, : unused arguments (keys = in.ids, keytype = in.type, columns = c(in.type, out.type)) Error in `$<-.data.frame`(`*tmp*`, "labels", value = c("", "", "", "", : replacement has 78 rows, data has 92
> sessionInfo() R version 3.4.0 (2017-04-21) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1 Matrix products: default locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252 [4] LC_NUMERIC=C LC_TIME=English_United States.1252 attached base packages: [1] parallel stats4 stats graphics grDevices utils datasets methods base other attached packages: [1] statmod_1.4.30 calibrate_1.7.2 MASS_7.3-47 pathview_1.16.1 clusterProfiler_3.4.4 [6] DOSE_3.2.0 vsn_3.44.0 biomaRt_2.32.1 XML_3.98-1.9 org.Hs.eg.db_3.4.1 [11] DESeq2_1.16.1 SummarizedExperiment_1.6.3 DelayedArray_0.2.7 matrixStats_0.52.2 GenomicRanges_1.28.3 [16] GenomeInfoDb_1.12.2 edgeR_3.18.1 limma_3.32.2 AnnotationDbi_1.38.1 IRanges_2.10.2 [21] S4Vectors_0.14.3 Biobase_2.36.2 BiocGenerics_0.22.0 RSQLite_2.0 loaded via a namespace (and not attached): [1] bitops_1.0-6 bit64_0.9-7 httr_1.2.1 RColorBrewer_1.1-2 Rgraphviz_2.20.0 [6] tools_3.4.0 backports_1.1.0 R6_2.2.2 affyio_1.46.0 rpart_4.1-11 [11] Hmisc_4.0-3 DBI_0.7 lazyeval_0.2.0 colorspace_1.3-2 nnet_7.3-12 [16] gridExtra_2.2.1 bit_1.1-12 compiler_3.4.0 preprocessCore_1.38.1 graph_1.54.0 [21] htmlTable_1.9 KEGGgraph_1.34.0 scales_0.4.1 checkmate_1.8.2 genefilter_1.58.1 [26] affy_1.54.0 stringr_1.2.0 digest_0.6.12 foreign_0.8-69 XVector_0.16.0 [31] base64enc_0.1-3 pkgconfig_2.0.1 htmltools_0.3.6 htmlwidgets_0.8 rlang_0.1.1 [36] BiocInstaller_1.26.0 BiocParallel_1.10.1 acepack_1.4.1 GOSemSim_2.2.0 RCurl_1.95-4.8 [41] magrittr_1.5 GO.db_3.4.1 GenomeInfoDbData_0.99.0 Formula_1.2-1 Matrix_1.2-9 [46] Rcpp_0.12.11 munsell_0.4.3 stringi_1.1.5 zlibbioc_1.22.0 plyr_1.8.4 [51] qvalue_2.8.0 grid_3.4.0 blob_1.1.0 DO.db_2.9 lattice_0.20-35 [56] Biostrings_2.44.1 splines_3.4.0 annotate_1.54.0 KEGGREST_1.16.0 locfit_1.5-9.1 [61] knitr_1.16 fgsea_1.2.1 igraph_1.0.1 geneplotter_1.54.0 reshape2_1.4.2 [66] fastmatch_1.1-0 latticeExtra_0.6-28 data.table_1.10.4 png_0.1-7 gtable_0.2.0 [71] tidyr_0.6.3 ggplot2_2.2.1 xtable_1.8-2 survival_2.41-3 tibble_1.3.3 [76] rvcheck_0.0.8 memoise_1.1.0 cluster_2.0.6