Hi,

I have the following command which always worked well, until now.

     txdb <- makeTxDbFromGFF("/path/to/gencode.v19.annotation.gtf", dataSource="Gencode", organism="Homo sapiens", format="gtf")

Now I get the following output:

     Import genomic features from the file as a GRanges object ... OK
     Prepare the 'metadata' data frame ... OK
     Make the TxDb object ... Error in c(x, value) :
       could not find symbol "recursive" in environment of the generic function

After some research I came to the conclusion it might be due to incompatibility(?). I use R version 3.3.3,  Bioconductor 3.4 (BiocInstaller 1.24.0) and the GenomicFeatures from 1.26.3.

* I tried it on my Mac and there it works as expected. But there I use 1.26.2.

Here the output of sessionInfo:

R version 3.3.3 (2017-03-06)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.1 LTS

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

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

other attached packages:
 [1] BiocInstaller_1.24.0       GenomicAlignments_1.10.0   SummarizedExperiment_1.4.0 Rsamtools_1.26.1           Biostrings_2.42.1         
 [6] XVector_0.14.0             GenomicFeatures_1.26.3     AnnotationDbi_1.36.2       Biobase_2.34.0             GenomicRanges_1.26.3      
[11] GenomeInfoDb_1.10.3        IRanges_2.8.1              S4Vectors_0.12.1           BiocGenerics_0.20.0       

loaded via a namespace (and not attached):
 [1] httr_1.2.1                    AnnotationHub_2.6.4           splines_3.3.3                 Formula_1.2-1                
 [5] shiny_1.0.0                   assertthat_0.1                interactiveDisplayBase_1.12.0 latticeExtra_0.6-28          
 [9] RBGL_1.50.0                   BSgenome_1.42.0               yaml_2.1.14                   RSQLite_1.1-2                
[13] backports_1.0.5               lattice_0.20-34               biovizBase_1.22.0             digest_0.6.12                
[17] RColorBrewer_1.1-2            checkmate_1.8.2               colorspace_1.3-2              ggbio_1.22.3                 
[21] htmltools_0.3.5               httpuv_1.3.3                  Matrix_1.2-8                  plyr_1.8.4                   
[25] OrganismDbi_1.16.0            XML_3.98-1.5                  biomaRt_2.30.0                zlibbioc_1.20.0              
[29] xtable_1.8-2                  scales_0.4.1                  BiocParallel_1.8.1            htmlTable_1.9                
[33] tibble_1.2                    ggplot2_2.2.1                 nnet_7.3-12                   lazyeval_0.2.0               
[37] survival_2.40-1               magrittr_1.5                  mime_0.5                      memoise_1.0.0                
[41] GGally_1.3.0                  foreign_0.8-67                graph_1.52.0                  tools_3.3.3                  
[45] data.table_1.10.4             stringr_1.2.0                 munsell_0.4.3                 cluster_2.0.5                
[49] ensembldb_1.6.2               grid_3.3.3                    RCurl_1.95-4.8                dichromat_2.0-0              
[53] VariantAnnotation_1.20.2      htmlwidgets_0.8               bitops_1.0-6                  base64enc_0.1-3              
[57] gtable_0.2.0                  DBI_0.6                       reshape_0.8.6                 reshape2_1.4.2               
[61] R6_2.2.0                      gridExtra_2.2.1               knitr_1.15.1                  rtracklayer_1.34.2           
[65] Hmisc_4.0-2                   stringi_1.1.2                 Rcpp_0.12.9                   rpart_4.1-10                 
[69] acepack_1.4.1  

I think it's related to a stale methods table as described here Combining RangedData objects is broken (IRanges 2.8.1 with R version 3.3.3 RC). You could try re-installing GenomicFeatures and it's dependencies. FYI, when you post a question you should include the output from sessionInfo().

Valerie