consider adding biocViews: to DESCRIPTION

Solution

You might consider following this answer from StackOverflow and modifying your DESCRIPTION file to something like the following:

Depends:
    R (>= 3.3.0)
biocViews:
Imports:
    methods,
    snpStats,
    dplyr

Notice the string biocViews:, which should help R to find the pathview dependency from Bioconductor.

Problem

I tried:

install.packages("pathfindR")

I got:

Installing package into ‘/PHShome/ks38/.local/lib/R/x86_64-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
Warning: dependency ‘pathview’ is not available
trying URL 'https://cran.rstudio.com/src/contrib/pathfindR_1.3.0.tar.gz'
Content type 'application/x-gzip' length 6072721 bytes (5.8 MB)
==================================================
downloaded 5.8 MB

ERROR: dependency ‘pathview’ is not available for package ‘pathfindR’
* removing ‘/PHShome/ks38/.local/lib/R/x86_64-linux-gnu-library/3.4/pathfindR’

The downloaded source packages are in
        ‘/tmp/RtmpRLpeNb/downloaded_packages’
Warning message:
In install.packages("pathfindR") :
  installation of package ‘pathfindR’ had non-zero exit status

I had to install pathview first.

> source("http://bioconductor.org/biocLite.R")
> biocLite("pathview")

Now it works:

> install.packages("pathfindR")
Installing package into ‘/PHShome/ks38/.local/lib/R/x86_64-linux-gnu-library/3.4’
(as ‘lib’ is unspecified)
trying URL 'https://cran.rstudio.com/src/contrib/pathfindR_1.3.0.tar.gz'
Content type 'application/x-gzip' length 6072721 bytes (5.8 MB)
==================================================
downloaded 5.8 MB

* installing *source* package ‘pathfindR’ ...
** package ‘pathfindR’ successfully unpacked and MD5 sums checked
** R
** data
*** moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (pathfindR)

egeulgen / pathfindR

consider adding biocViews: to DESCRIPTION #14

Solution

Problem