Comments (1)
Explaining the error
This is common to all R packages dependent on rJava, which is often a PITA to install. If you try to install another such package, e.g. rcdk, a similar problem will occur.
This type of error usually happens because the user's R installation cannot properly see all Java paths. It is an Operating System problem, which CRAN has no control over and thus doesn't prevent a package from being published on CRAN.
How to solve the issue
It is up to the user to solve the issue for their Operating System, and sites like stackoverflow are full of posts relating the problem and proposing solutions. Also, taking a closer look at the full output will often lead to some proposals from R itself. For instance, on Linux (and maybe macOS) you should:
- Install openjdk (including sources, which may be in a separate package from the JRE)
- Run
R CMD javareconf -e
(or, alternatively,sudo R CMD javareconf
) for R to search for the proper Java paths. - Reload your R session
Once install.packages("rJava")
runs successfully, you'll be able to install DIscBIO. If it doesn't, try closing and reopening R (so it picks up the proper Java paths). If you still run into problems, please post below.
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Related Issues (20)
- ClustDiffGenes is generating opposite tables HOT 3
- Failing TravisCI builds HOT 2
- Networking outputs different network from hyperlink HOT 2
- PPI error HOT 1
- Remove calls to KmeanOrder from notebook
- Replace call to boot() from Jaccard() HOT 2
- Standardize function names HOT 1
- Adapt package to different types of organisms HOT 3
- Retry URLs on Networking and PPI functions HOT 1
- Unable to view code of Binder notebook HOT 1
- Reorganize internal functions
- Aggregate K/MB selection into one function HOT 1
- The PPI function is writing to the user's disk HOT 4
- Recreate unit tests
- Unit tests failing
- Fix linting
- Binder links on README point to dev
- Binder failing to start
- Loading count matrix from 10x dataset in DIscBIO HOT 6
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from discbio.