source("https://bioconductor.org/biocLite.R")
biocLite()   

> install.packages("qAlign")
Installing package into ‘/Users/babumalik/Library/R/3.5/library’
(as ‘lib’ is unspecified)
Warning in install.packages :
  package ‘qAlign’ is not available (for R version 3.5.0)
> biocLite("qAlign")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.7 (BiocInstaller 1.30.0), R 3.5.0 (2018-04-23).
Installing package(s) ‘qAlign’
installation path not writeable, unable to update packages:
  DelayedArray, highr, MLSeq, munsell, progress, RcppRoll, recipes,
  rmarkdown, S4Vectors, stringi, xfun
Warning message:
package ‘qAlign’ is not available (for R version 3.5.0) 

Hi Fatima

qAlign is part of the QuasR package (https://bioconductor.org/packages/3.8/bioc/html/QuasR.html)

Hence, you should do:

source("https://bioconductor.org/biocLite.R")
biocLite("QuasR")

Regards, Hans-Rudolf