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Question: GenomicFeatures: could not find symbol "recursive" in environment of the generic function
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gravatar for lucasmacielbiotec
5 months ago by
lucasmacielbiotec0 wrote:
Hello, 

I have been trying to make a TxDb from na gtf but always occur this error. I already saw posts about reinstallation of packages but I tried almost everything and I couldn't fix it. Could anyone helpe me, please?

txdb = GenomicFeatures::makeTxDbFromGFF("schisto-transcriptome/schisto.gtf",format="gtf")
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

Session info:

R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS

Matrix products: default
BLAS: /usr/lib/openblas-base/libblas.so.3
LAPACK: /usr/lib/libopenblasp-r0.2.18.so

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

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

other attached packages:
 [1] BiocInstaller_1.24.0       edgeR_3.16.5               limma_3.30.13             
 [4] GenomicAlignments_1.10.0   Rsamtools_1.26.1           Biostrings_2.42.0         
 [7] XVector_0.14.0             GenomicFeatures_1.26.0     AnnotationDbi_1.36.0      
[10] tximportData_1.2.0         DESeq2_1.14.1              SummarizedExperiment_1.4.0
[13] Biobase_2.34.0             GenomicRanges_1.26.1       GenomeInfoDb_1.10.0       
[16] IRanges_2.8.0              S4Vectors_0.12.0           BiocGenerics_0.20.0       

loaded via a namespace (and not attached):
 [1] genefilter_1.56.0   locfit_1.5-9.1      splines_3.4.3       lattice_0.20-35     colorspace_1.2-7   
 [6] rtracklayer_1.34.0  yaml_2.1.13         survival_2.41-3     XML_3.98-1.3        rlang_0.2.0        
[11] pillar_1.2.1        foreign_0.8-69      glue_1.2.0          DBI_0.8             BiocParallel_1.8.1 
[16] RColorBrewer_1.1-2  bindrcpp_0.2        plyr_1.8.4          bindr_0.1.1         zlibbioc_1.20.0    
[21] munsell_0.4.3       gtable_0.2.0        latticeExtra_0.6-28 biomaRt_2.30.0      geneplotter_1.52.0 
[26] Rcpp_0.12.16        acepack_1.4.1       xtable_1.8-2        scales_0.5.0        Hmisc_3.17-4       
[31] annotate_1.52.1     gridExtra_2.2.1     ggplot2_2.2.1       dplyr_0.7.4         grid_3.4.3         
[36] tools_3.4.3         bitops_1.0-6        magrittr_1.5        lazyeval_0.2.1      RCurl_1.95-4.8     
[41] tibble_1.4.2        RSQLite_1.0.0       Formula_1.2-1       cluster_2.0.6       pkgconfig_2.0.1    
[46] Matrix_1.2-11       data.table_1.10.4-3 assertthat_0.2.0    R6_2.2.2            rpart_4.1-13       
[51] nnet_7.3-12         compiler_3.4.3  
ADD COMMENTlink written 5 months ago by lucasmacielbiotec0

Sounds like you may have out of date packages. Please run BiocInstaller::biocValid(), update old packages and let us know if the error persists.

Valerie

ADD REPLYlink written 4 months ago by Valerie Obenchain ♦♦ 6.5k
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