Failure to retrieve annotations for some PDBs using pdb.annotate
Issue #830
resolved
I am trying to retrieve information on a list of PDBs and while most work several fail all with the same cryptic error - for example:
pdb_list = c("5FWI")
anno <- pdb.annotate(pdb_list)
Results in
Error in split.default(X, group) : first argument must be a vector
Output of sessionInfo()
:
R version 3.6.3 (2020-02-29)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3
locale:
[1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C LC_TIME=en_GB.UTF-8
[4] LC_COLLATE=en_GB.UTF-8 LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] LC_TELEPHONE=C LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] dplyr_1.0.7 bio3d_2.4-2
loaded via a namespace (and not attached):
[1] Rcpp_1.0.2 rstudioapi_0.11 magrittr_1.5 tidyselect_1.1.0 R6_2.4.0
[6] rlang_0.4.11 fansi_0.4.1 httr_1.4.2 blob_1.2.1 tools_3.6.3
[11] parallel_3.6.3 grid_3.6.3 xfun_0.12 tinytex_0.20 utf8_1.1.4
[16] DBI_1.1.0 ellipsis_0.3.2 assertthat_0.2.1 tibble_3.0.3 lifecycle_1.0.0
[21] crayon_1.3.4 purrr_0.3.4 vctrs_0.3.8 curl_4.3 glue_1.4.1
[26] compiler_3.6.3 pillar_1.6.1 generics_0.0.2 jsonlite_1.6 pkgconfig_2.0.2
Comments (2)
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Please install the development version and try again. This is a known bug and has been fixed but not yet released.
See here for how to install: https://bitbucket.org/Grantlab/bio3d/wiki/How to download and install the development version