I am getting an error when I try and create an ensDb object using a GENCODE .gtf annotation file for GRCh38 downloaded directly from the GENCODE website.

> gtffile <- "/user/Downloads/gencode.v26.annotation.gtf"

> DB <- ensDbFromGtf(gtffile)
Error in `colnames<-`(`*tmp*`, value = c("name", "value")) : 
  length of 'dimnames' [2] not equal to array extent

I tried downloading the .gtf from Ensembl in case the issue was the file but I get a different set of errors:

> gtffile <- "/Users/Bongani/Downloads/Homo_sapiens.GRCh38.88.gtf.gz"
> DB <- ensDbFromGtf(gtffile)
Error in checkValidEnsDb(EnsDb(dbname), verbose = verbose) :
  Provided exon index in transcript does not match with ordering of the exons by chromosomal coordinates for1of the101167transcripts encoded on the + strand!
In addition: Warning messages:
1: In rsqlite_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
2: In rsqlite_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
3: In rsqlite_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
4: In rsqlite_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
5: In rsqlite_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries
6: In rsqlite_fetch(res@ptr, n = n) :
  Don't need to call dbFetch() for statements, only for queries

Is there a package I am missing? The errors seem to suggest an error in formatting but I have not modified the .gtf files in any way before passing them to ensDb.

> sessionInfo()
R version 3.2.3 (2015-12-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.6 (El Capitan)

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

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

other attached packages:
 [1] ensembldb_1.2.2         GenomicFeatures_1.22.13 AnnotationDbi_1.32.3   
 [4] Biobase_2.30.0          GenomicRanges_1.22.4    GenomeInfoDb_1.6.3     
 [7] IRanges_2.4.8           S4Vectors_0.8.11        AnnotationHub_2.2.5    
[10] BiocGenerics_0.16.1    

Regarding the GENCODE gtf file - for that you might want to use the makeTxDbFromGFF function from the GenomicFeatures package since the ensembldb::ensDbFromGtf works only for gtf files from Ensembl as it requires certain fields/columns to be present in the file.

Regarding the error you get with the release 88 GTF - I have to check that. The database is created, but there seems to be a discrepancy between the index of the exon within the transcript and its chromosomal coordinates for one transcript. It seems to be specific for GTF files for Homo sapiens Ensembl releases 88 and 89. I didn't get any error with the Ensembl 90 GTF.

Note that for newer releases of R/Bioconductor you can also fetch EnsDb databases from AnnotationHub. I am adding EnsDbs for every new Ensembl release. Note that the result below is for Bioconductor 3.6 devel. Bioconductor 3.5 has also EnsDbs in AnnotationHub, but not the most recent releases.

> library(AnnotationHub)
> ah <- AnnotationHub()
snapshotDate(): 2017-09-07
> query(ah, "EnsDb")
AnnotationHub with 282 records
# snapshotDate(): 2017-09-07
# $dataprovider: Ensembl
# $species: Ailuropoda Melanoleuca, Anas Platyrhynchos, Anolis Carolinensis,...
# $rdataclass: EnsDb
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype
# retrieve records with, e.g., 'object[["AH53185"]]'

            title                                      
  AH53185 | Ensembl 87 EnsDb for Anolis Carolinensis   
  AH53186 | Ensembl 87 EnsDb for Ailuropoda Melanoleuca
  AH53187 | Ensembl 87 EnsDb for Astyanax Mexicanus    
  AH53188 | Ensembl 87 EnsDb for Anas Platyrhynchos    
  AH53189 | Ensembl 87 EnsDb for Bos Taurus            
  ...       ...                                        
  AH57800 | Ensembl 90 EnsDb for Takifugu Rubripes     
  AH57801 | Ensembl 90 EnsDb for Tursiops Truncatus    
  AH57802 | Ensembl 90 EnsDb for Vicugna Pacos         
  AH57803 | Ensembl 90 EnsDb for Xiphophorus Maculatus
  AH57804 | Ensembl 90 EnsDb for Xenopus Tropicalis    

> sessionInfo()
R version 3.4.1 (2017-06-30)
Platform: x86_64-pc-linux-gnu/x86_64 (64-bit)
Running under: Linux Mint 18.1

Matrix products: default
BLAS: /home/jo/R/2017-07/R-3.4.1-BioC3.6-devel/lib/R/lib/x86_64/libRblas.so
LAPACK: /home/jo/R/2017-07/R-3.4.1-BioC3.6-devel/lib/R/lib/x86_64/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=it_IT.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=it_IT.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=it_IT.UTF-8 LC_IDENTIFICATION=C       

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

other attached packages:
[1] AnnotationHub_2.9.12 BiocGenerics_0.23.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.12                  AnnotationDbi_1.39.3         
 [3] IRanges_2.11.15               bit_1.1-12                   
 [5] xtable_1.8-2                  R6_2.2.2                     
 [7] rlang_0.1.2                   blob_1.1.0                   
 [9] httr_1.3.1                    tools_3.4.1                  
[11] Biobase_2.37.2                DBI_0.7                      
[13] htmltools_0.3.6               yaml_2.1.14                  
[15] bit64_0.9-7                   digest_0.6.12                
[17] tibble_1.3.4                  interactiveDisplayBase_1.15.0
[19] shiny_1.0.5                   S4Vectors_0.15.7             
[21] curl_2.8.1                    memoise_1.1.0                
[23] RSQLite_2.0                   mime_0.5                     
[25] compiler_3.4.1                BiocInstaller_1.27.4         
[27] stats4_3.4.1                  httpuv_1.3.5                 
[29] pkgconfig_2.0.1              

cheers, jo