Sorry for my super abbreviated post.

I agree that package updating is likely the culprit, but I also can't figure out if the build error on the most recent version of R for GenomicRanges could be causing the problem instead?

I'm currently using R-3.3.1.

Looking for overlaps between two GRanges objects:

> gtex_regions
GRanges object with 7149 ranges and 6 metadata columns:
            
> sra_regions
GRanges object with 7149 ranges and 0 metadata columns:

> ov <- GenomicRanges::findOverlaps(gtex_regions,sra_regions)
Error in validObject(.Object) :
  invalid class “PartitioningByEnd” object: undefined class for slot "elementMetadata" ("DataTable_OR_NULL")

Thanks for the first suggestion. Definitely a good check and something I hadn't done.:

> BiocInstaller::biocValid()
[1] TRUE​

Lastly, I was having the issue in R-devel also ....but I'll try working there. For now, here is sessionInfo() in case something is glaringly obvious...: 

> sessionInfo()
R version 3.3.1 Patched (2016-09-30 r71426)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.6 (Santiago)

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

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

other attached packages:
[1] BiocInstaller_1.24.0       genefilter_1.56.0
[3] minfi_1.20.2               bumphunter_1.14.0
[5] locfit_1.5-9.1             iterators_1.0.8
[7] foreach_1.4.3              Biostrings_2.42.1
[9] XVector_0.14.0             SummarizedExperiment_1.4.0
[11] Biobase_2.34.0             dplyr_0.5.0
[13] purrr_0.2.2                readr_1.0.0
[15] tidyr_0.6.1                tibble_1.2
[17] ggplot2_2.2.1              tidyverse_1.1.1
[19] GenomicRanges_1.26.2       GenomeInfoDb_1.10.3
[21] IRanges_2.8.1              S4Vectors_0.12.1
[23] BiocGenerics_0.20.0

loaded via a namespace (and not attached):
[1] nlme_3.1-131             bitops_1.0-6             matrixStats_0.51.0
[4] lubridate_1.6.0          RColorBrewer_1.1-2       httr_1.2.1
[7] tools_3.3.1              doRNG_1.6                nor1mix_1.2-2
[10] R6_2.2.0                 DBI_0.5-1                lazyeval_0.2.0
[13] colorspace_1.3-2         mnormt_1.5-5             base64_2.0
[16] curl_2.3                 preprocessCore_1.36.0    rvest_0.3.2
[19] xml2_1.1.1               pkgmaker_0.22            rtracklayer_1.34.1
[22] scales_0.4.1             psych_1.6.12             quadprog_1.5-5
[25] stringr_1.1.0            digest_0.6.12            Rsamtools_1.26.1
[28] foreign_0.8-67           illuminaio_0.16.0        siggenes_1.48.0
[31] GEOquery_2.40.0          limma_3.30.10            readxl_0.1.1
[34] RSQLite_1.1-2            jsonlite_1.2             mclust_5.2.2
[37] BiocParallel_1.8.1       RCurl_1.95-4.8           magrittr_1.5
[40] Matrix_1.2-8             Rcpp_0.12.9              munsell_0.4.3
[43] stringi_1.1.2            MASS_7.3-45              zlibbioc_1.20.0
[46] plyr_1.8.4               grid_3.3.1               forcats_0.2.0
[49] lattice_0.20-34          haven_1.0.0              splines_3.3.1
[52] annotate_1.52.1          multtest_2.30.0          GenomicFeatures_1.26.2
[55] hms_0.3                  beanplot_1.2             rngtools_1.2.4
[58] reshape2_1.4.2           codetools_0.2-15         biomaRt_2.30.0
[61] XML_3.98-1.5             data.table_1.10.4        modelr_0.1.0
[64] openssl_0.9.6            gtable_0.2.0             reshape_0.8.6
[67] assertthat_0.1           xtable_1.8-2             broom_0.4.1
[70] survival_2.40-1          GenomicAlignments_1.10.0 AnnotationDbi_1.36.2
[73] registry_0.3             memoise_1.0.0