Works for me now

> suppressPackageStartupMessages(library(UniProt.ws))
> up <- UniProt.ws(taxId=9606)
> keys <- c("1", "2")
> columns <- c("PDB", "UNIGENE", "SEQUENCE")
> kt <- "ENTREZ_GENE"
> res <- select(up, keys, columns, kt)
Getting mapping data for 1 ... and ACC
Getting mapping data for P04217 ... and UNIGENE_ID
Getting mapping data for P04217 ... and PDB_ID
Getting extra data for P04217,V9HWD8,P01023
'select()' returned 1:many mapping between keys and columns
> str(res)
'data.frame':    8 obs. of  4 variables:
 $ ENTREZ_GENE: chr  "1" "1" "2" "2" ...
 $ PDB        : chr  NA NA "1BV8" "2P9R" ...
 $ UNIGENE    : chr  "Hs.709582" "Hs.529161" "Hs.212838" "Hs.212838" ...
 $ SEQUENCE   : chr  "MSMLVVFLLLWGVTWGPVTEAAIFYETQPSLWAESESLLKPLANVTLTCQAHLETPDFQLFKNGVAQEPVHLDSPAIKHQFLLTGDTQGRYRCRSGLSTGWTQLSKLLELTGPKSLPAPWLSMAPVS"| __truncated__ "MSMLVVFLLLWGVTWGPVTEAAIFYETQPSLWAESESLLKPLANVTLTCQAHLETPDFQLFKNGVAQEPVHLDSPAIKHQFLLTGDTQGRYRCRSGLSTGWTQLSKLLELTGPKSLPAPWLSMAPVS"| __truncated__ "MGKNKLLHPSLVLLLLVLLPTDASVSGKPQYMVLVPSLLHTETTEKGCVLLSYLNETVTVSASLESVRGNRSLFTDLEAENDVLHCVAFAVPKSSSNEEVMFLTVQVKGPTQEFKKRTTVMVKNEDS"| __truncated__ "MGKNKLLHPSLVLLLLVLLPTDASVSGKPQYMVLVPSLLHTETTEKGCVLLSYLNETVTVSASLESVRGNRSLFTDLEAENDVLHCVAFAVPKSSSNEEVMFLTVQVKGPTQEFKKRTTVMVKNEDS"| __truncated__ ...

using

> sessionInfo()
R version 3.3.1 Patched (2016-08-02 r71022)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.4 LTS

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

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

other attached packages:
[1] UniProt.ws_2.13.0   BiocGenerics_0.19.2 RCurl_1.95-4.8     
[4] bitops_1.0-6        RSQLite_1.0.0       DBI_0.4-1          

loaded via a namespace (and not attached):
[1] compiler_3.3.1       IRanges_2.7.12       tools_3.3.1         
[4] msdata_0.12.1        Biobase_2.33.0       AnnotationDbi_1.35.4
[7] S4Vectors_0.11.10    stats4_3.3.1       

Are your packages in sync? Test this with

BiocInstaller::biocValid()

If so, EDIT your question to include the output of the command

traceback()

immediately after the error. And also include the output of the command

sessionInfo()