Question: PANTHER.db- external pointer error
gravatar for krc3004
2.0 years ago by
krc300410 wrote:


I'm trying to use PANTHER.db to conduct pathway analysis on a set of differentially expressed genes, and I'm running into an error when loading PANTHER.  I install as usual:


But when I type PANTHER.db at the console, I obtain the following error:

Error in rsqlite_send_query(conn@ptr, statement) :
  external pointer is not valid

This error is quite frustrating, as there is little to no documentation for it and none for PANTHER, as far as I know.  Without properly loading PANTHER.db, there is no analysis that can be done with the PANTHER package.

Is this a version issue? Perhaps another package needs to be updated/installed?  I tried updating rsqlite with no luck.  Thanks very much for your help.

R version 3.2.3 (2015-12-10)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X 10.11.4 (El Capitan)

[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] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] PANTHER.db_1.0.3     RSQLite_2.0          AnnotationDbi_1.32.3 IRanges_2.4.8       
[5] S4Vectors_0.8.11     Biobase_2.30.0       BiocGenerics_0.16.1  BiocInstaller_1.20.3

loaded via a namespace (and not attached):
 [1] locfit_1.5-9.1             Rcpp_0.12.14               lattice_0.20-35           
 [4] tidyr_0.7.2                assertthat_0.2.0           digest_0.6.12             
 [7] R6_2.2.2                   GenomeInfoDb_1.6.3         plyr_1.8.4                
[10] futile.options_1.0.0       backports_1.1.1            acepack_1.4.1             
[13] ggplot2_2.2.1              zlibbioc_1.16.0            rlang_0.1.4               
[16] lazyeval_0.2.1             rstudioapi_0.7             data.table_1.10.4-3       
[19] annotate_1.48.0            blob_1.1.0                 rpart_4.1-11              
[22] checkmate_1.8.5            splines_3.2.3              BiocParallel_1.4.3        
[25] geneplotter_1.48.0         stringr_1.2.0              foreign_0.8-69            
[28] htmlwidgets_0.9            bit_1.1-12                 munsell_0.4.3             
[31] pkgconfig_2.0.1            base64enc_0.1-3            htmltools_0.3.6           
[34] nnet_7.3-12                SummarizedExperiment_1.0.2 tibble_1.3.4              
[37] gridExtra_2.3              htmlTable_1.11.0           Hmisc_4.0-3               
[40] XML_3.98-1.9               dplyr_0.7.4                grid_3.2.3                
[43] xtable_1.8-2               gtable_0.2.0               DBI_0.7                   
[46] magrittr_1.5               scales_0.5.0               stringi_1.1.6             
[49] XVector_0.10.0             genefilter_1.52.1          RcppArmadillo_0.
[52] bindrcpp_0.2               latticeExtra_0.6-28        futile.logger_1.4.3       
[55] Formula_1.2-2              lambda.r_1.2               RColorBrewer_1.1-2        
[58] tools_3.2.3                bit64_0.9-7                glue_1.2.0                
[61] DESeq2_1.10.1              purrr_0.2.4                survival_2.41-3           
[64] colorspace_1.3-2           cluster_2.0.6              GenomicRanges_1.22.4      
[67] memoise_1.1.0              knitr_1.17                 bindr_0.1
ADD COMMENTlink modified 2.0 years ago by James W. MacDonald52k • written 2.0 years ago by krc300410
Answer: PANTHER.db- external pointer error
gravatar for James W. MacDonald
2.0 years ago by
United States
James W. MacDonald52k wrote:

We cannot support any versions of Bioconductor other than the current release version. I would recommend upgrading to the current versions of R/Bioc, as you are two (!) years out of date.

ADD COMMENTlink written 2.0 years ago by James W. MacDonald52k
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