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Question: Get bugs from pathview package
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gravatar for joseph
4 months ago by
joseph40
joseph40 wrote:

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  
ADD COMMENTlink written 4 months ago by joseph40
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