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grimbough / Rhdf5lib

Distribution of the HDF5 library in an R package
https://bioconductor.org/packages/Rhdf5lib/
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Fails to install in lib path with space #18

Closed stanstrup closed 5 years ago

stanstrup commented 5 years ago

Installing from source fails where there are space in the lib path. Note the last line where it thinks the path starts with App/.

mkdir -p "/srv/shiny-server/QC4Metabolomics/Shiny App/packrat/lib/x86_64-pc-linux-gnu/3.6.0/00LOCK-Rhdf5lib/00new/Rhdf5lib/include"
cp hdf5/src/*.h /srv/shiny-server/QC4Metabolomics/Shiny App/packrat/lib/x86_64-pc-linux-gnu/3.6.0/00LOCK-Rhdf5lib/00new/Rhdf5lib/include
cp: target 'App/packrat/lib/x86_64-pc-linux-gnu/3.6.0/00LOCK-Rhdf5lib/00new/Rhdf5lib/include' is not a directory

It looks like there are missing brackets somewhere causing this. If I remove the space in the lib path the it works.

grimbough commented 5 years ago

Does this works for you?

BiocManager::install('grimbough/Rhdf5lib', ref='spaces')
stanstrup commented 5 years ago

Yep that solved it. Thanks!

grimbough commented 5 years ago

Thanks for the bug report and confirmation that it is working now. I'll merge the change into the versions on Bioconductor shortly.

scottgigante commented 5 years ago

This is still an issue as of October 3 on Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.1 (2019-07-05). Installing from master solves the problem.