I was trying to map a list of genes to Oryza sativa (rice) KEGG pathways using [pathview][1] R package. But failed to map genes. I followed  [this][2] tutorial. 

For example, the code below 

    library("pathview")
    geneList<-read.table("genes.txt",header=T,sep="\t") 
    pathway <- pathview(gene.data  = geneList,
                     pathway.id = "00195",
                     gene.idtype = "RAPDB",
                     species    = "Oryza sativa japonica"                     
                     )

with the input "genes.txt"

    Os03t0659266-00
    Os04t0473150-00

Should map input genes to a specific pathway. But showing error

    Error in pathview(gene.data = geneList, pathway.id = "00195", gene.idtype = "RAPDB",  : 
     No proper gene annotation package available!

However, the online version shows mapping with the same input. So how can I solve this problem?





  [1]: https://bioconductor.org/packages/release/bioc/html/pathview.html
  [2]: https://bioconductor.org/packages/devel/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html
Your gene IDs (eg Os03t0659266-00) are not Entrez or KEGG gene ID, hence can’t be mapped to KEGG osa pathways. That’s why you saw the warning and plain graph with no data. you can generate simulated osa data with entrez/kegg ID as below, and it will work. So you need to convert your gene IDs to entrez/kegg gene IDs manually.

>gdata.osa=sim.mol.data(mol.type="gene", species ="osa", id.type="kegg", nmol=10000)
>pv.out=pathview(gene.data  = gdata.osa, pathway.id = "00195", gene.idtype = "KEGG", species    = "Oryza sativa japonica")

FYI, you can check the ID type supported by pathview for your target species (i.e. osa) using korg data in pathview like:
>data(korg)  
> ri=korg[,"kegg.code"]=="osa"  
> korg[ri,]  

                ktax.id                  tax.id               kegg.code
               "T01015"                 "39947"                   "osa"
        scientific.name             common.name           entrez.gnodes
        "Oryza sativa japonica"         "Japanese rice"            "1"
             kegg.geneid             ncbi.geneid          ncbi.proteinid
              "4349630"               "4349630"          "XP_015615283"
                uniprot
           "A0A0P0XY71"

So supported gene ID for osa include: kegg.geneid, ncbi.geneid (entrez), ncbi.proteinid, uniprot.  
The simulated data with Entrez/KEGG IDs look like:
> head(gdata.osa)

     4328398    4326389    4338593  107277186    4334918    4335759
    -1.4462875  0.3158558 -0.3427475 -1.9313531  0.2428210 -0.3627679
