GenomicFeatures: could not find symbol "recursive" in environment of the generic function
0
0
Entering edit mode
@lucasmacielbiotec-15278
Last seen 4.2 years ago
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  
genomicfeatures rnaseq txdb • 685 views
ADD COMMENT
0
Entering edit mode

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 REPLY

Login before adding your answer.

Traffic: 274 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6