I am encountering an issue running totalCounts with multiple files. I get the following error:

Error in h(simpleError(msg, call)) : 
  error in evaluating the argument 'x' in selecting a method for function 'nrow': attempt to apply non-function
Calls: totalCounts -> .addToTotal

The rest of the test code works fine, so it doesn't seem like an issue with the input files. Here is the test code:

library(rhdf5)
library(csaw)
library(diffHic)
library(edgeR)

hs.frag <- cutGenome("hg38.fa", "GATC", 4)
hs.param <- pairParam(hs.frag)

preparePairs("aligned_test1_REP1.bam", hs.param, file = "aligned_test1_REP1.h5", dedup = TRUE, minq=10)
preparePairs("aligned_test1_REP2.bam", hs.param, file = "aligned_test1_REP2.h5", dedup = TRUE, minq=10)
preparePairs("aligned_test2_REP2.bam", hs.param, file = "aligned_test2_REP2.h5", dedup = TRUE, minq=10)
preparePairs("aligned_test2_REP1.bam", hs.param, file = "aligned_test2_REP1.h5", dedup = TRUE, minq=10)

input <- c("aligned_test1_REP1.h5", "aligned_test1_REP2.h5","aligned_test2_REP2.h5","aligned_test2_REP1.h5")

bin.size <- 1e6
data <- squareCounts(input, hs.param, width = bin.size, filter=1)

finder <- domainDirections(input, hs.param, width=1e5, span=10)

all.counts <- cbind(assay(finder, "up"), assay(finder, "down"))
totals <- totalCounts(input, hs.param)

sessionInfo():

R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /spack/apps/linux-centos7-x86_64/gcc-8.3.0/openblas-0.3.8-2no6mfziiclwxb7lstxoos335gnhjpes/lib/libopenblasp-r0.3.8.so

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 utils     datasets 
[8] methods   base     

other attached packages:
 [1] edgeR_3.32.0                limma_3.46.0               
 [3] diffHic_1.24.0              InteractionSet_1.18.1      
 [5] csaw_1.24.3                 SummarizedExperiment_1.20.0
 [7] Biobase_2.50.0              MatrixGenerics_1.2.0       
 [9] matrixStats_0.57.0          GenomicRanges_1.42.0       
[11] GenomeInfoDb_1.26.2         IRanges_2.24.1             
[13] S4Vectors_0.28.1            BiocGenerics_0.36.0        
[15] rhdf5_2.34.0               

loaded via a namespace (and not attached):
 [1] locfit_1.5-9.4           Rcpp_1.0.5               lattice_0.20-41         
 [4] prettyunits_1.1.1        Rsamtools_2.6.0          Biostrings_2.58.0       
 [7] assertthat_0.2.1         digest_0.6.27            BiocFileCache_1.14.0    
[10] R6_2.5.0                 RSQLite_2.2.2            httr_1.4.2              
[13] pillar_1.4.7             zlibbioc_1.36.0          rlang_0.4.10            
[16] GenomicFeatures_1.42.1   progress_1.2.2           curl_4.3                
[19] blob_1.2.1               Matrix_1.3-2             BiocParallel_1.24.1     
[22] Rhtslib_1.20.0           stringr_1.4.0            RCurl_1.98-1.2          
[25] bit_4.0.4                biomaRt_2.46.0           DelayedArray_0.16.0     
[28] compiler_4.0.3           rtracklayer_1.50.0       pkgconfig_2.0.3         
[31] askpass_1.1              openssl_1.4.3            tidyselect_1.1.0        
[34] tibble_3.0.4             GenomeInfoDbData_1.2.4   XML_3.99-0.5            
[37] crayon_1.3.4             dplyr_1.0.2              dbplyr_2.0.0            
[40] GenomicAlignments_1.26.0 bitops_1.0-6             rhdf5filters_1.2.1      
[43] rappdirs_0.3.1           grid_4.0.3               lifecycle_1.0.0         
[46] DBI_1.1.0                magrittr_2.0.1           stringi_1.5.3           
[49] XVector_0.30.0           xml2_1.3.2               ellipsis_0.3.1          
[52] generics_0.1.0           vctrs_0.3.6              Rhdf5lib_1.12.1         
[55] tools_4.0.3              bit64_4.0.5              BSgenome_1.58.0         
[58] glue_1.4.2               purrr_0.3.4              hms_0.5.3               
[61] AnnotationDbi_1.52.0     memoise_1.1.0

I think I've identified the problem - try installing from the master branch of https://github.com/LTLA/diffHic and see whether that solves it.