Re: Rhdf5 issue

[Dirk Eddelbuettel <edd@debian.org>]

On 26 April 2019 at 18:13, Andreas Tille wrote:
| I'd like to package r-other-wasabi[1] for the Debian Med team.  It
| depends r-bioc-rhdf5[2] which in turn depends r-bioc-rhdf5lib[3]
| which I just uploaded to new after linking against libhdf5.  However,
| I have the impression that I did something wrong since there is an
| issue with r-bioc-rhdf5 which boils down to some code in
|   src/Makevars
| which throws an error:
| 
| 
| $ echo 'Rhdf5lib::pkgconfig("PKG_CXX_LIBS")'| R --vanilla --slave
| Error in system.file("lib", package = "Rhdf5lib", mustWork = TRUE) : 
|   no file found
| Calls: <Anonymous> -> Sys.getenv -> system.file
| Execution halted

Something is not right. From

  https://github.com/grimbough/Rhdf5lib/blob/master/R/zzz.R#L15-L18

we have
  
  pkgconfig <- function(opt = c("PKG_CXX_LIBS", "PKG_C_LIBS")) {
    
      path <- Sys.getenv(
          x = "RHDF5LIB_RPATH",
          unset = system.file("lib", package="Rhdf5lib", mustWork=TRUE)
      )
    
      #... more stuff omitted ...

So if the env.var is missing (as in your case) it assumes it has
a "lib" directory installed in the package.  I read this as the
package maintainer/author assuming the package would always
install with a lib dir.  Does it?  I see no `inst/dir` in the
sources.

You could bypass the issue for now, it seems, by setting the
variable it wants to use: RHDF5LIB_RPATH.

(All this untested as I'm at work...)

Dirk
 

-- 
http://dirk.eddelbuettel.com | @eddelbuettel | edd@debian.org