I tried to install ChIPseqR and ran into an error with one of its dependencies, HilbertVis. It appears that there may be an error in the source code for HilbertVis.

> BiocManager::install("HilbertVis")

'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories",
package = "BiocManager")' for details.
Replacement repositories:
CRAN: https://cloud.r-project.org
Bioconductor version 3.19 (BiocManager 1.30.25), R 4.4.2 (2024-10-31)
Installing package(s) 'HilbertVis'
trying URL 'https://bioconductor.org/packages/3.19/bioc/src/contrib/HilbertVis_1.62.0.tar.gz'
Content type 'application/gzip' length 1037414 bytes (1013 KB)
==================================================
downloaded 1013 KB

* installing *source* package 'HilbertVis' ...
** using staged installation
** libs
using C compiler: 'gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0'
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-6tgf7J/r-base-4.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c hilbert.c -o hilbert.o
gcc -I"/usr/share/R/include" -DNDEBUG -fpic -g -O2 -ffile-prefix-map=/build/r-base-6tgf7J/r-base-4.4.2=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -c make_wiggle_vector.c -o make_wiggle_vector.o
make_wiggle_vector.c: In function 'make_wiggle_vector':
make_wiggle_vector.c:16:17: error: format not a string literal and no format arguments [-Werror=format-security]
16 | error( buf );
| ^~~
cc1: some warnings being treated as errors
make: *** [/usr/lib/R/etc/Makeconf:195: make_wiggle_vector.o] Error 1
ERROR: compilation failed for package 'HilbertVis'
* removing '/home/chase/R/x86_64-pc-linux-gnu-library/4.4/HilbertVis'

The downloaded source packages are in
'/tmp/Rtmp8uprGA/downloaded_packages'
Installation paths not writeable, unable to update packages
path: /usr/lib/R/library
packages:
boot, codetools, foreign, lattice, nlme, spatial
Warning message:
In install.packages(...) :
installation of package 'HilbertVis' had non-zero exit status

> sessionInfo():

R version 4.4.2 (2024-10-31)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 22.04.5 LTS

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.10.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0

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

time zone: America/Chicago
tzcode source: system (glibc)

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

other attached packages:
[1] AnnotationHub_3.12.0 BiocFileCache_2.12.0 dbplyr_2.5.0 BiocGenerics_0.50.0

loaded via a namespace (and not attached):
[1] SummarizedExperiment_1.34.0 KEGGREST_1.44.1 rjson_0.2.23
[4] lattice_0.22-5 Biobase_2.64.0 vctrs_0.6.5
[7] tools_4.4.2 bitops_1.0-9 generics_0.1.3
[10] stats4_4.4.2 curl_6.0.1 parallel_4.4.2
[13] tibble_3.2.1 fansi_1.0.6 AnnotationDbi_1.66.0
[16] RSQLite_2.3.8 blob_1.2.4 pkgconfig_2.0.3
[19] Matrix_1.7-1 S4Vectors_0.42.1 lifecycle_1.0.4
[22] GenomeInfoDbData_1.2.12 compiler_4.4.2 Rsamtools_2.20.0
[25] Biostrings_2.72.1 codetools_0.2-19 GenomeInfoDb_1.40.1
[28] RCurl_1.98-1.16 yaml_2.3.10 pillar_1.9.0
[31] crayon_1.5.3 BiocParallel_1.38.0 DelayedArray_0.30.1
[34] cachem_1.1.0 abind_1.4-8 mime_0.12
[37] tidyselect_1.2.1 dplyr_1.1.4 purrr_1.0.2
[40] restfulr_0.0.15 BiocVersion_3.19.1 grid_4.4.2
[43] fastmap_1.2.0 SparseArray_1.4.8 cli_3.6.3
[46] magrittr_2.0.3 S4Arrays_1.4.1 XML_3.99-0.17
[49] utf8_1.2.4 withr_3.0.2 filelock_1.0.3
[52] UCSC.utils_1.0.0 rappdirs_0.3.3 bit64_4.5.2
[55] XVector_0.44.0 httr_1.4.7 matrixStats_1.4.1
[58] bit_4.5.0 png_0.1-8 memoise_2.0.1
[61] GenomicRanges_1.56.2 IRanges_2.38.1 BiocIO_1.14.0
[64] rtracklayer_1.64.0 rlang_1.1.4 glue_1.8.0
[67] DBI_1.2.3 BiocManager_1.30.25 rstudioapi_0.17.1
[70] jsonlite_1.8.9 R6_2.5.1 MatrixGenerics_1.16.0
[73] GenomicAlignments_1.40.0 zlibbioc_1.50.0

It appears you have compiler flags set that preclude you from compiling (-Werror=format-security). If I install HilbertVis on my work box (CentOS 7) with R-4.4.0/Bioc 3.19 it compiles without complaint, and no -W compiler flags. If I compile on the release version of R/Bioc in a Singularity container (Ubuntu 24), it compiles with a complaint, but it installs

gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2 -fstack-protector-strong -Wformat -Wformat-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c make_wiggle_vector.c -o make_wiggle_vector.o
make_wiggle_vector.c: In function 'make_wiggle_vector':
make_wiggle_vector.c:16:17: warning: format not a string literal and no format arguments [-Wformat-security]
   16 |          error( buf );
      |                 ^~~
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include    -fpic  -g -O2 -fstack-protector-strong -Wformat -Wformat-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c shrink_vector.c -o shrink_vector.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o HilbertVis.so hilbert.o make_wiggle_vector.o shrink_vector.o -L/usr/local/lib/R/lib -lR
installing to /usr/local/lib/R/host-site-library/00LOCK-HilbertVis/00new/HilbertVis/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (HilbertVis)

But I have -Wformat-security set rather than -Werror-format-security.

I don't see a makefile for HilbertVis, so I imagine it's picking up the GCC flags from some environmental variable. I know very little abou setting compiler flags, so you will need to get your Google-fu on, or maybe ask over on r-help@r-project.org.