Hello,

rtracklayer can export a GRange as GFF3 even when there is no CDS defined, however when trying to do the same from a TxDb it fails with this error message:

Error in `[[<-`(`*tmp*`, name, value = NA) : 
  1 elements in value to replace 0 elements

I think it happens while applying asGFF().

I believe this is not the expected behavior for GFF3, even though there is a simple workaround using transcriptsBy().

Minimal example:

library(GenomicRanges)
library(GenomicFeatures)
library(rtracklayer)

gr <- GRanges("chrI", IRanges(c(1,5,8), c(3,7,12)), strand = "+")
mcols(gr)$type <- "exon"
mcols(gr)$exon_id <- 1:3
mcols(gr)$transcript_id <- 1
mcols(gr)$transcript_name <- "1"
mcols(gr)$gene_id <- 1
mcols(gr)$gene_name <- "1"
txdb <- makeTxDbFromGRanges(gr)

# fails in asGFF:
rtracklayer::export(txdb, "example.gff3")

# works:
rtracklayer::export(transcriptsBy(txdb), "example.gff3")

And here is the sessionInfo.

> sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 10 x64 (build 17763)

Matrix products: default

locale:
[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] rtracklayer_1.46.0     GenomicFeatures_1.38.1 AnnotationDbi_1.48.0   Biobase_2.46.0         GenomicRanges_1.38.0   GenomeInfoDb_1.22.0   
[7] IRanges_2.20.2         S4Vectors_0.24.3       BiocGenerics_0.32.0   

loaded via a namespace (and not attached):
 [1] SummarizedExperiment_1.16.1 progress_1.2.2              tidyselect_1.0.0            purrr_0.3.3                
 [5] lattice_0.20-38             vctrs_0.2.2                 BiocFileCache_1.10.2        blob_1.2.1                 
 [9] XML_3.99-0.3                rlang_0.4.4                 pillar_1.4.3                glue_1.3.1                 
[13] DBI_1.1.0                   BiocParallel_1.20.1         rappdirs_0.3.1              bit64_0.9-7                
[17] dbplyr_1.4.2                matrixStats_0.55.0          GenomeInfoDbData_1.2.2      stringr_1.4.0              
[21] zlibbioc_1.32.0             Biostrings_2.54.0           memoise_1.1.0               biomaRt_2.42.0             
[25] curl_4.3                    Rcpp_1.0.3                  openssl_1.4.1               DelayedArray_0.12.2        
[29] XVector_0.26.0              bit_1.1-15.1                Rsamtools_2.2.1             hms_0.5.3                  
[33] askpass_1.1                 digest_0.6.23               stringi_1.4.4               dplyr_0.8.4                
[37] grid_3.6.2                  tools_3.6.2                 bitops_1.0-6                magrittr_1.5               
[41] RCurl_1.98-1.1              RSQLite_2.2.0               tibble_2.1.3                crayon_1.3.4               
[45] pkgconfig_2.0.3             Matrix_1.2-18               prettyunits_1.1.1           assertthat_0.2.1           
[49] httr_1.4.1                  rstudioapi_0.11             R6_2.4.1                    GenomicAlignments_1.22.1   
[53] compiler_3.6.2

Thanks, fixed in rtracklayer 1.38.2.