Pathview error Warning: Parsing ./mmu04928.xml file failed, please check the file!
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@b0bebdcc
Last seen 18 days ago
United Kingdom

I am using pathview to produce a native KEGG plot in PNG from results of gseKEGG analysis.

I have succesfully produced and downloaded PNGs of other pathways using the same command and dataset but get this error when running the specific pathway mmu04938

# i use the code below, where kegg_gene_list is my list of genes with entrez IDs and corresponding fold changes, and kegg_organism is org.Mm.eg.db 

parathryoid <- pathview(gene.data = kegg_gene_list, pathway.id="mmu04928", species = kegg_organism)

# i get this error

Specification mandates value for attribute valu
attributes construct error
Couldn't find end of Start Tag subtype line 673
Premature end of data in tag relation line 672
Premature end of data in tag pathway line 4
Warning: Parsing ./mmu04928.xml file failed, please check the file!

sessionInfo( )
R version 4.2.0 (2022-04-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib

locale:
[1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] pathview_1.36.0

loaded via a namespace (and not attached):
  [1] fgsea_1.22.0           ggnewscale_0.4.7       colorspace_2.0-3       ggtree_3.4.0          
  [5] ellipsis_0.3.2         ggridges_0.5.3         qvalue_2.28.0          XVector_0.36.0        
  [9] aplot_0.1.6            rstudioapi_0.13        farver_2.1.0           graphlayouts_0.8.0    
 [13] ggrepel_0.9.1          bit64_4.0.5            AnnotationDbi_1.58.0   fansi_1.0.3           
 [17] scatterpie_0.1.7       codetools_0.2-18       splines_4.2.0          cachem_1.0.6          
 [21] GOSemSim_2.22.0        knitr_1.39             polyclip_1.10-0        jsonlite_1.8.0        
 [25] GO.db_3.15.0           png_0.1-7              graph_1.74.0           ggforce_0.3.3         
 [29] compiler_4.2.0         httr_1.4.3             assertthat_0.2.1       Matrix_1.4-1          
 [33] fastmap_1.1.0          lazyeval_0.2.2         cli_3.3.0              org.Mm.eg.db_3.15.0   
 [37] tweenr_1.0.2           tools_4.2.0            igraph_1.3.1           gtable_0.3.0          
 [41] glue_1.6.2             GenomeInfoDbData_1.2.8 reshape2_1.4.4         DO.db_2.9             
 [45] dplyr_1.0.9            fastmatch_1.1-3        Rcpp_1.0.8.3           enrichplot_1.16.1     
 [49] Biobase_2.56.0         vctrs_0.4.1            Biostrings_2.64.0      ape_5.6-2             
 [53] nlme_3.1-157           ggraph_2.0.5           xfun_0.31              stringr_1.4.0         
 [57] lifecycle_1.0.1        clusterProfiler_4.4.2  XML_3.99-0.9           DOSE_3.22.0           
 [61] org.Hs.eg.db_3.15.0    zlibbioc_1.42.0        MASS_7.3-57            scales_1.2.0          
 [65] tidygraph_1.2.1        parallel_4.2.0         KEGGgraph_1.56.0       RColorBrewer_1.1-3    
 [69] memoise_2.0.1          gridExtra_2.3          ggplot2_3.3.6          ggfun_0.0.6           
 [73] downloader_0.4         yulab.utils_0.0.4      stringi_1.7.6          RSQLite_2.2.14        
 [77] S4Vectors_0.34.0       tidytree_0.3.9         BiocGenerics_0.42.0    BiocParallel_1.30.3   
 [81] GenomeInfoDb_1.32.2    rlang_1.0.2            pkgconfig_2.0.3        bitops_1.0-7          
 [85] lattice_0.20-45        purrr_0.3.4            treeio_1.20.0          patchwork_1.1.1       
 [89] cowplot_1.1.1          shadowtext_0.1.2       bit_4.0.4              tidyselect_1.1.2      
 [93] plyr_1.8.7             magrittr_2.0.3         R6_2.5.1               IRanges_2.30.0        
 [97] generics_0.1.2         DBI_1.1.2              pillar_1.7.0           KEGGREST_1.36.0       
[101] RCurl_1.98-1.6         tibble_3.1.7           crayon_1.5.1           utf8_1.2.2            
[105] viridis_0.6.2          grid_4.2.0             data.table_1.14.2      Rgraphviz_2.40.0      
[109] blob_1.2.3             digest_0.6.29          tidyr_1.2.0            gridGraphics_0.5-1    
[113] stats4_4.2.0           munsell_0.5.0          viridisLite_0.4.0      ggplotify_0.1.0

Can anyone help me out with this? I have made over 10 other native KEGG plots and am stuck on the last one.

All my packages are up to date and I am using the latest version of R.

Thanks

KEGGgraph pathview • 70 views
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Entering edit mode
Guido Hooiveld ★ 3.3k
@guido-hooiveld-2020
Last seen 14 minutes ago
Wageningen University, Wageningen, the …

Did you see this (newer) thread? The suggestion/fix provided may solve your issue as well. Pathview unable to download pathways

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