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

Hi, I get some errors when I run the demo data:

> data(gse16873.d)
> data(demo.paths)
> i <- 1
> pv.out <- pathview( = gse16873.d[, 1], =
+                      demo.paths$sel.paths[i], species = "hsa", out.suffix = "gse16873",
+                    kegg.native = TRUE)
Info: Downloading xml files for hsa04110, 1/1 pathways..
Info: Downloading png files for hsa04110, 1/1 pathways..
Error in select(db.obj, keys = in.ids, keytype = in.type, columns = c(in.type,  : 
  unused arguments (keys = in.ids, keytype = in.type, columns = c(in.type, out.type))
Error in `$<`(`*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

[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             
[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  
pathview • 325 views
ADD COMMENTlink written 22 months ago by joseph40
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 115 users visited in the last hour