installation error

[LiNk-NY]

Hi Hervé, @hpages I'm trying to install the package using the latest checkout (for testing and checking) and I am getting the error:

$ Rdev CMD INSTALL .
* installing to library '/home/user/R/bioc-devel'
* installing *source* package 'pwalign' ...
** using staged installation
** libs
using C compiler: 'gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0'
make: Nothing to be done for 'all'.
installing to /home/user/R/bioc-devel/00LOCK-pwalign/00new/pwalign/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for ‘pwalign’ in dyn.load(file, DLLpath = DLLpath, ...):
 unable to load shared object '/home/user/R/bioc-devel/00LOCK-pwalign/00new/pwalign/libs/pwalign.so':
  /home/user/R/bioc-devel/00LOCK-pwalign/00new/pwalign/libs/pwalign.so: undefined symbol: get_XStringSet_width
Error: loading failed
Execution halted
ERROR: loading failed
* removing '/home/user/R/bioc-devel/pwalign'

Any recommendations on how to fix it?

[hpages]

Maybe you don't have the latest Biostrings? See https://github.com/Bioconductor/pwalign/issues/1#issuecomment-2015415908

[hpages]

Also in your case, since you're running R CMD INSTALL on the package source tree (as opposed to running it on the source tarball), you'll need to remove all the object files (.o and .so files) with git clean -i before trying again.

[LiNk-NY]

Thanks!