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.
sessionInfo() 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) locale:  en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 attached base packages:  parallel stats4 stats graphics grDevices utils datasets methods base other attached packages:  PANTHER.db_1.0.3 RSQLite_2.0 AnnotationDbi_1.32.3 IRanges_2.4.8  S4Vectors_0.8.11 Biobase_2.30.0 BiocGenerics_0.16.1 BiocInstaller_1.20.3 loaded via a namespace (and not attached):  locfit_1.5-9.1 Rcpp_0.12.14 lattice_0.20-35  tidyr_0.7.2 assertthat_0.2.0 digest_0.6.12  R6_2.2.2 GenomeInfoDb_1.6.3 plyr_1.8.4  futile.options_1.0.0 backports_1.1.1 acepack_1.4.1  ggplot2_2.2.1 zlibbioc_1.16.0 rlang_0.1.4  lazyeval_0.2.1 rstudioapi_0.7 data.table_1.10.4-3  annotate_1.48.0 blob_1.1.0 rpart_4.1-11  checkmate_1.8.5 splines_3.2.3 BiocParallel_1.4.3  geneplotter_1.48.0 stringr_1.2.0 foreign_0.8-69  htmlwidgets_0.9 bit_1.1-12 munsell_0.4.3  pkgconfig_2.0.1 base64enc_0.1-3 htmltools_0.3.6  nnet_7.3-12 SummarizedExperiment_1.0.2 tibble_1.3.4  gridExtra_2.3 htmlTable_1.11.0 Hmisc_4.0-3  XML_3.98-1.9 dplyr_0.7.4 grid_3.2.3  xtable_1.8-2 gtable_0.2.0 DBI_0.7  magrittr_1.5 scales_0.5.0 stringi_1.1.6  XVector_0.10.0 genefilter_1.52.1 RcppArmadillo_0.8.100.1.0  bindrcpp_0.2 latticeExtra_0.6-28 futile.logger_1.4.3  Formula_1.2-2 lambda.r_1.2 RColorBrewer_1.1-2  tools_3.2.3 bit64_0.9-7 glue_1.2.0  DESeq2_1.10.1 purrr_0.2.4 survival_2.41-3  colorspace_1.3-2 cluster_2.0.6 GenomicRanges_1.22.4  memoise_1.1.0 knitr_1.17 bindr_0.1