I have been trying to install ATACseqQC in R/3.5.1, but the install fails at shiny step. Usually, bioconductor packages can manage their dependencies and are straightforward to install. Please see below the error message.

R version 3.5.1 (2018-07-02) -- "Feather Spray"
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Platform: x86_64-pc-linux-gnu (64-bit)

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> library(BiocManager)
Bioconductor version 3.8 (BiocManager 1.30.4), ?BiocManager::install for help
Bioconductor version '3.8' is out-of-date; the current release version '3.9' is
  available with R version '3.6'; see https://bioconductor.org/install
> BiocManager::install("ATACseqQC")
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02)
Installing package(s) 'ATACseqQC'
also installing the dependencies ‘shiny’, ‘interactiveDisplayBase’, ‘AnnotationHub’, ‘GenomicScores’

trying URL 'https://cran.rstudio.com/src/contrib/shiny_1.3.2.tar.gz'
Content type 'application/x-gzip' length 2991469 bytes (2.9 MB)
==================================================
downloaded 2.9 MB

trying URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/interactiveDisplayBase_1.20.0.tar.gz'
Content type 'application/x-gzip' length 13893 bytes (13 KB)
==================================================
downloaded 13 KB

trying URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/AnnotationHub_2.14.5.tar.gz'
Content type 'application/x-gzip' length 1056330 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

trying URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/GenomicScores_1.6.0.tar.gz'
Content type 'application/x-gzip' length 2460395 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

trying URL 'https://bioconductor.org/packages/3.8/bioc/src/contrib/ATACseqQC_1.6.4.tar.gz'
Content type 'application/x-gzip' length 13563753 bytes (12.9 MB)
==================================================
downloaded 12.9 MB

* installing *source* package ‘shiny’ ...
** package ‘shiny’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: S3 methods ‘format.staticPath’, ‘format.staticPathOptions’, ‘print.staticPath’, ‘print.staticPathOptions’ were declared in NAMESPACE but not found
Error in library.dynam(lib, package, package.lib) : 
  shared object ‘httpuv.so’ not found
ERROR: lazy loading failed for package ‘shiny’
* removing ‘/home/kesara/R/x86_64-pc-linux-gnu-library/3.5/shiny’
ERROR: dependency ‘shiny’ is not available for package ‘interactiveDisplayBase’
* removing ‘/home/kesara/R/x86_64-pc-linux-gnu-library/3.5/interactiveDisplayBase’
ERROR: dependency ‘interactiveDisplayBase’ is not available for package ‘AnnotationHub’
* removing ‘/home/kesara/R/x86_64-pc-linux-gnu-library/3.5/AnnotationHub’
ERROR: dependency ‘AnnotationHub’ is not available for package ‘GenomicScores’
* removing ‘/home/kesara/R/x86_64-pc-linux-gnu-library/3.5/GenomicScores’
ERROR: dependency ‘GenomicScores’ is not available for package ‘ATACseqQC’
* removing ‘/home/kesara/R/x86_64-pc-linux-gnu-library/3.5/ATACseqQC’

The downloaded source packages are in
    ‘/scratch/RtmpKj7FWW/downloaded_packages’
installation path not writeable, unable to update packages: assertthat, BH,
  blob, boot, class, cluster, codetools, data.table, digest, foreign, jsonlite,
  lattice, MASS, Matrix, mgcv, nlme, pkgconfig, Rcpp, RcppEigen, rpart,
  RSQLite, survival, yaml
Warning messages:
1: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘shiny’ had non-zero exit status
2: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘interactiveDisplayBase’ had non-zero exit status
3: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘AnnotationHub’ had non-zero exit status
4: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘GenomicScores’ had non-zero exit status
5: In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘ATACseqQC’ had non-zero exit status
> BiocManager::install("Shiny")
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02)
Installing package(s) 'Shiny'
installation path not writeable, unable to update packages: assertthat, BH,
  blob, boot, class, cluster, codetools, data.table, digest, foreign, jsonlite,
  lattice, MASS, Matrix, mgcv, nlme, pkgconfig, Rcpp, RcppEigen, rpart,
  RSQLite, survival, yaml
Warning messages:
1: package ‘Shiny’ is not available (for R version 3.5.1) 
2: Perhaps you meant ‘shiny’ ? 
> shiny
Error: object 'shiny' not found
> BiocManager::install("shiny")
Bioconductor version 3.8 (BiocManager 1.30.4), R 3.5.1 (2018-07-02)
Installing package(s) 'shiny'
trying URL 'https://cran.rstudio.com/src/contrib/shiny_1.3.2.tar.gz'
Content type 'application/x-gzip' length 2991469 bytes (2.9 MB)
==================================================
downloaded 2.9 MB

* installing *source* package ‘shiny’ ...
** package ‘shiny’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: S3 methods ‘format.staticPath’, ‘format.staticPathOptions’, ‘print.staticPath’, ‘print.staticPathOptions’ were declared in NAMESPACE but not found
Error in library.dynam(lib, package, package.lib) : 
  shared object ‘httpuv.so’ not found
ERROR: lazy loading failed for package ‘shiny’
* removing ‘/home/kesara/R/x86_64-pc-linux-gnu-library/3.5/shiny’

The downloaded source packages are in
    ‘/scratch/RtmpKj7FWW/downloaded_packages’
installation path not writeable, unable to update packages: assertthat, BH,
  blob, boot, class, cluster, codetools, data.table, digest, foreign, jsonlite,
  lattice, MASS, Matrix, mgcv, nlme, pkgconfig, Rcpp, RcppEigen, rpart,
  RSQLite, survival, yaml
Warning message:
In install.packages(pkgs = doing, lib = lib, repos = repos, ...) :
  installation of package ‘shiny’ had non-zero exit status
> 

You NEVER need to use install.packages, and should try to break yourself of that habit. Instead use the BiocManager package and BiocManager::install, which uses install.packages under the hood, but after ensuring that you are installing the right versions for any Bioconductor packages.