Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, : storing paths of more than 100 bytes is not portable:

[bschilder]

When installing echolocatoR, you'll probably see a long list of warnings like this:

...
...
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
   storing paths of more than 100 bytes is not portable:
   ‘echolocatoR/inst/tools/PAINTOR_V3.0/eigen/unsupported/Eigen/src/SparseExtra/BlockOfDynamicSparseMatrix.h’
 Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L,  :
   storing paths of more than 100 bytes is not portable:
   ‘echolocatoR/inst/tools/goshifter/test_data/bc.H3K4me1_vHMEC_strat_Myoepithelial_Cells.nperm1000.enrich’

This is coming from the fact that R doesn't like the folder naming scheme of some of the submodules echolocatoR depends on, specifically:

• PAINTOR_V3.0.
• goshifter

The only way I've come across to address this would be to fork my own version of these repos and rewrite the code so it uses a different directory structure. But this runs a very high risk of messing up these software entirely. So until I can figure out a smarter solution, we'll have to bear with loads of warning messages 😞

Sources

• Description of a similar problem with packrat here.
• Medium post on the general challenges of using git submodules.

[bschilder]

I found a way around this by adding these repos as git submodules.

The software is then installed the first time a function that uses it is run. This strategy is currently implemented for:

• [x] PAINTOR: via echofinemap
• [x] PolyFun: via echofinemap
• [ ] GOSHIFTER: via echoannot