Pretty much as the title says. Installing via
biocLite is fine, but calling:
... gives me the following error:
Error: package or namespace load failed for ‘Rhtslib’ in dyn.load(file, DLLpath = DLLpath, ...): unable to load shared object '/Users/lun01/Library/R/3.5/library/Rhtslib/libs/Rhtslib.so': dlopen(/Users/lun01/Library/R/3.5/library/Rhtslib/libs/Rhtslib.so, 6): Library not loaded: /usr/local/opt/xz/lib/liblzma.5.dylib Referenced from: /Users/lun01/Library/R/3.5/library/Rhtslib/libs/Rhtslib.so Reason: image not found
It seems my
liblzma.dylib is located at
/usr/lib instead. I'm not familiar enough with the Mac install process to know why the library location would differ between my machine and that used to build the binary for BioC, but it's not the first time something like this has happened, see https://stat.ethz.ch/pipermail/bioc-devel/2016-May/009317.html for a previous instance.
R version 3.5.0 RC (2018-04-16 r74624) Platform: x86_64-apple-darwin15.6.0 (64-bit) Running under: OS X El Capitan 10.11.6 Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRblas.0.dylib LAPACK: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib locale:  en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8 attached base packages:  stats graphics grDevices utils datasets methods base loaded via a namespace (and not attached):  zlibbioc_1.26.0 compiler_3.5.0
That seems to have addressed the issue. I consequently bumped the version of all packages that have Rhtslib in their
LinkingTofield (e.g. csaw, bamsignals, deepSNV, etc...), but only in release (RELEASE_3_7 branch) for now. See for example commit 6ea86c79cfbc2b9d765ed31b35364b5eb39c7671 in the RELEASE_3_7 branch of csaw:
Thanks Herve, looks good on my end as well.