hi all

i am working genomic feature but i am get this error:

> library(GenomicFeatures)

> nrow(supportedUCSCtables())
[1] 20
> supportedUCSCtables()
        tablename          track           subtrack
1   knownGene     UCSC Genes                        <NA>
2   knownGeneOld8 Old UCSC Genes               <NA>
3   knownGeneOld7 Old UCSC Genes               <NA>
4   knownGeneOld6 Old UCSC Genes               <NA>
5   knownGeneOld4 Old UCSC Genes               <NA>
6   knownGeneOld3 Old UCSC Genes               <NA>
7        ccdsGene           CCDS               <NA>
8         refGene   RefSeq Genes               <NA>
9     xenoRefGene   Other RefSeq               <NA>
10       vegaGene     Vega Genes Vega Protein Genes
11 vegaPseudoGene     Vega Genes   Vega Pseudogenes
12        ensGene  Ensembl Genes               <NA>
13        acembly  AceView Genes               <NA>
14        sibGene      SIB Genes               <NA>
15  nscanPasaGene         N-SCAN    N-SCAN PASA-EST
16      nscanGene         N-SCAN             N-SCAN
17        sgpGene      SGP Genes               <NA>
18         geneid   Geneid Genes               <NA>
19        genscan  Genscan Genes               <NA>
20       exoniphy       Exoniphy               <NA>
> hg38 <- makeTxDbFromUCSC(genome = "hg38",
+ tablename = "knownGene")
Download the knownGene table ... OK
Download the knownToLocusLink table ... OK
Extract the 'transcripts' data frame ... OK
Extract the 'splicings' data frame ... OK
Download and preprocess the 'chrominfo' data frame ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... OK
Warning messages:
1: In .extractCdsLocsFromUCSCTxTable(ucsc_txtable, exon_locs) :
  UCSC data anomaly in 20500 transcript(s): the cds cumulative length is
  not a multiple of 3 for transcripts ‘uc057axw.1’ ‘uc031pko.2’
  ‘uc057ayh.1’ ‘uc057ayr.1’ ‘uc057azl.1’ ‘uc057azn.1’ ‘uc057azp.1’
  ‘uc057azt.1’ ‘uc057azy.1’ ‘uc057bad.1’ ‘uc057bap.1’ ‘uc057bav.1’
  ‘uc057bay.1’ ‘uc057bbh.1’ ‘uc057bbv.1’ ‘uc057bcm.1’ ‘uc057bcp.1’
  ‘uc057bcw.1’ ‘uc057bcx.1’ ‘uc057bdf.1’ ‘uc057bdj.1’ ‘uc057bdk.1’
  ‘uc057bdl.1’ ‘uc057bdp.1’ ‘uc057beb.1’ ‘uc057beq.1’ ‘uc057bfn.1’
  ‘uc057bfs.1’ ‘uc057bgm.1’ ‘uc057bgo.1’ ‘uc057bgt.1’ ‘uc057bhd.1’
  ‘uc057bhi.1’ ‘uc057bio.1’ ‘uc057biu.1’ ‘uc057bji.1’ ‘uc057bjj.1’
  ‘uc057bjk.1’ ‘uc057bkd.1’ ‘uc057bkf.1’ ‘uc057bkj.1’ ‘uc057bkl.1’
  ‘uc057bkt.1’ ‘uc057bld.1’ ‘uc057bli.1’ ‘uc057blj.1’ ‘uc057blz.1’
  ‘uc057bmf.1’ ‘uc057bmr.1’ ‘uc057bmv.1’ ‘uc057bni.1’ ‘uc057bnj.1’
  ‘uc057bnk.1’ ‘uc057bnl.1’ ‘uc057bnv.1’ ‘uc057bob.1’ ‘uc057bod.1’
  ‘uc057boe.1’ ‘uc057bpl.1’ ‘uc057bpm.1’ ‘uc057bpr.1’ ‘uc057bpw.1’
  ‘uc057bqa.1’ ‘uc057bqb.1’ ‘uc057bqt.1’ ‘uc057bqx.1’ ‘uc057b [... truncated]
2: RSQLite::dbGetPreparedQuery() is deprecated, please switch to DBI::dbGetQuery(params = bind.data). 
3: Named parameters not used in query: internal_chrom_id, chrom, length, is_circular 
4: Named parameters not used in query: internal_id, name, type, chrom, strand, start, end 
5: Named parameters not used in query: internal_id, name, chrom, strand, start, end 
6: Named parameters not used in query: internal_id, name, chrom, strand, start, end 
7: Named parameters not used in query: internal_tx_id, exon_rank, internal_exon_id, internal_cds_id 
8: Named parameters not used in query: gene_id, internal_tx_id 
> saveFeatures(hg38KG, file="hg38_knownGene.sqlite")
Error: could not find function "saveFeatures"
> txdb <-
+ loadFeatures(system.file("extdata", "hg38_knownGene.sqlite",
+ package = "SeattleIntro2010"))
Error: could not find function "loadFeatures"
What am I missing??

please help me

thanks

> sessionInfo()
R version 3.3.2 (2016-10-31)
Platform: i386-w64-mingw32/i386 (32-bit)
Running under: Windows 7 (build 7601) Service Pack 1

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
[1] GenomicFeatures_1.26.2 AnnotationDbi_1.36.0   Biobase_2.34.0        
[4] GenomicRanges_1.26.2   GenomeInfoDb_1.10.2    IRanges_2.8.1         
[7] S4Vectors_0.12.1       BiocGenerics_0.20.0   

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.8                XVector_0.14.0            
 [3] zlibbioc_1.20.0            GenomicAlignments_1.10.0  
 [5] BiocParallel_1.8.1         lattice_0.20-34           
 [7] tools_3.3.2                grid_3.3.2                
 [9] SummarizedExperiment_1.4.0 DBI_0.5-1                 
[11] digest_0.6.11              Matrix_1.2-7.1            
[13] rtracklayer_1.34.1         bitops_1.0-6              
[15] RCurl_1.95-4.8             biomaRt_2.30.0            
[17] memoise_1.0.0              RSQLite_1.1-2             
[19] Biostrings_2.42.1          Rsamtools_1.26.1          
[21] XML_3.98-1.5              
 

It's not clear what you are trying to do. Why not just use the existing package for those data? Re-creating an already extant package is a waste of time, I would think.

library(BiocInstaller)
biocLite("TxDb.Hsapiens.UCSC.hg38.knownGene")
library(TxDb.Hsapiens.UCSC.hg38.knownGene)