I am receiving a warning message for nearestKNeighbors that I don't receive for nearest that also seems to alter the output of the function.

using the data p_ran and e_ran below

p_ran <- GRanges(c("chr1:248836765-248839421",
"chr1:248857227-248860010",
"chr1:248905669-248907808",
"chr2:263751-265942",
"chr2:283627-286204",
"chr2:287549-288546",
"chr2:317349-318734",
"chr2:674901-679175",
"chr2:692014-694241",
"chr2:739716-741208",
"chr2:1579709-1580907"))
e_ran <- GRanges(c("chr1:248842064-248842915",
"chr1:248862738-248863858",
"chr1:248924237-248927727",
"chr2:246452-247319",
"chr2:280784-281089",
"chr2:673304-674615",
"chr2:690001-690466",
"chr2:694530-694842",
"chr2:1572461-1573381",
"chr2:349126-349492",
"chr2:1586877-1589526"))

when running nearestKNeighbors I receive the warning:

Warning message:
In ans[] <- x :
  number of items to replace is not a multiple of replacement length

This, or something else causes the result of nearest and nearestKNeighbors to differ at 4 positions which you can see in the code below:

p_ran
e_ran
which(nearest(p_ran, e_ran) != unlist(nearestKNeighbors(p_ran, e_ran, k = 1)))
e_ran[nearest(p_ran, e_ran)]
e_ran[unlist(nearestKNeighbors(p_ran, e_ran, k = 1))]

here are the results:

> p_ran
GRanges object with 11 ranges and 0 metadata columns:
       seqnames              ranges strand
          <Rle>           <IRanges>  <Rle>
   [1]     chr1 248836765-248839421      *
   [2]     chr1 248857227-248860010      *
   [3]     chr1 248905669-248907808      *
   [4]     chr2       263751-265942      *
   [5]     chr2       283627-286204      *
   [6]     chr2       287549-288546      *
   [7]     chr2       317349-318734      *
   [8]     chr2       674901-679175      *
   [9]     chr2       692014-694241      *
  [10]     chr2       739716-741208      *
  [11]     chr2     1579709-1580907      *
  -------
  seqinfo: 2 sequences from an unspecified genome; no seqlengths
> e_ran
GRanges object with 11 ranges and 0 metadata columns:
       seqnames              ranges strand
          <Rle>           <IRanges>  <Rle>
   [1]     chr1 248842064-248842915      *
   [2]     chr1 248862738-248863858      *
   [3]     chr1 248924237-248927727      *
   [4]     chr2       246452-247319      *
   [5]     chr2       280784-281089      *
   [6]     chr2       673304-674615      *
   [7]     chr2       690001-690466      *
   [8]     chr2       694530-694842      *
   [9]     chr2     1572461-1573381      *
  [10]     chr2       349126-349492      *
  [11]     chr2     1586877-1589526      *
  -------
  seqinfo: 2 sequences from an unspecified genome; no seqlengths
> which(nearest(p_ran, e_ran) != unlist(nearestKNeighbors(p_ran, e_ran, k = 1)))
[1]  4  7  9 11
Warning message:
In ans[] <- x :
  number of items to replace is not a multiple of replacement length
> e_ran[nearest(p_ran, e_ran)]
GRanges object with 11 ranges and 0 metadata columns:
       seqnames              ranges strand
          <Rle>           <IRanges>  <Rle>
   [1]     chr1 248842064-248842915      *
   [2]     chr1 248862738-248863858      *
   [3]     chr1 248924237-248927727      *
   [4]     chr2       280784-281089      *
   [5]     chr2       280784-281089      *
   [6]     chr2       280784-281089      *
   [7]     chr2       349126-349492      *
   [8]     chr2       673304-674615      *
   [9]     chr2       694530-694842      *
  [10]     chr2       694530-694842      *
  [11]     chr2     1586877-1589526      *
  -------
  seqinfo: 2 sequences from an unspecified genome; no seqlengths
> e_ran[unlist(nearestKNeighbors(p_ran, e_ran, k = 1))]
GRanges object with 11 ranges and 0 metadata columns:
       seqnames              ranges strand
          <Rle>           <IRanges>  <Rle>
   [1]     chr1 248842064-248842915      *
   [2]     chr1 248862738-248863858      *
   [3]     chr1 248924237-248927727      *
   [4]     chr2       246452-247319      *
   [5]     chr2       280784-281089      *
   [6]     chr2       280784-281089      *
   [7]     chr2       280784-281089      *
   [8]     chr2       673304-674615      *
   [9]     chr2       690001-690466      *
  [10]     chr2       694530-694842      *
  [11]     chr2     1572461-1573381      *
  -------
  seqinfo: 2 sequences from an unspecified genome; no seqlengths
Warning message:
In ans[] <- x :
  number of items to replace is not a multiple of replacement length

This is a small reproducible version of a larger data-set where this happens many more times. I don't understand why this is.

sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 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_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] stats4    stats     graphics  grDevices utils     datasets  methods
[8] base

other attached packages:
[1] GenomicRanges_1.48.0   GenomeInfoDb_1.32.2    IRanges_2.30.0
[4] S4Vectors_0.34.0       BiocGenerics_0.42.0    RhpcBLASctl_0.21-247.1

loaded via a namespace (and not attached):
[1] zlibbioc_1.42.0        compiler_4.2.1         tools_4.2.1
[4] XVector_0.36.0         GenomeInfoDbData_1.2.8 RCurl_1.98-1.7
[7] bitops_1.0-7