[Debian-med-packaging] Bug#871333: r-bioc-rtracklayer: FTBFS: Error: package or namespace load failed for 'rtracklayer' in dyn.load(file, DLLpath = DLLpath, ...):

[Lucas Nussbaum]

Source: r-bioc-rtracklayer
Version: 1.34.1-1
Severity: serious
Tags: buster sid
User: debian-qa at lists.debian.org
Usertags: qa-ftbfs-20170807 qa-ftbfs
Justification: FTBFS on amd64

Hi,

During a rebuild of all packages in sid, your package failed to build on
amd64.

Relevant part (hopefully):
> make[1]: Entering directory '/<<PKGBUILDDIR>>/src'
> make[1]: Leaving directory '/<<PKGBUILDDIR>>/src'
> installing to /<<PKGBUILDDIR>>/debian/r-bioc-rtracklayer/usr/lib/R/site-library/rtracklayer/libs
> ** R
> ** data
> ** demo
> ** inst
> ** preparing package for lazy loading
> Warning: undefined slot classes in definition of "UCSCTableQuery": track(class "characterORNULL"), table(class "characterORNULL"), outputType(class "characterORNULL"), NAMES(class "characterORNULL"), intersectTrack(class "characterORNULL")
> Warning: undefined slot classes in definition of "Bed15TrackLine": expNames(class "characterORNULL")
> Creating a generic function for 'offset' from package 'stats' in package 'rtracklayer'
> Creating a generic function from function 'uri' in package 'rtracklayer'
> ** help
> *** installing help indices
> ** building package indices
> ** installing vignettes
> ** testing if installed package can be loaded
> Error: package or namespace load failed for 'rtracklayer' in dyn.load(file, DLLpath = DLLpath, ...):
>  unable to load shared object '/<<PKGBUILDDIR>>/debian/r-bioc-rtracklayer/usr/lib/R/site-library/rtracklayer/libs/rtracklayer.so':
>   /<<PKGBUILDDIR>>/debian/r-bioc-rtracklayer/usr/lib/R/site-library/rtracklayer/libs/rtracklayer.so: undefined symbol: append_string_to_CharAEAE
> Error: loading failed
> Execution halted
> ERROR: loading failed
> * removing '/<<PKGBUILDDIR>>/debian/r-bioc-rtracklayer/usr/lib/R/site-library/rtracklayer'
> dh_auto_install: R CMD INSTALL -l /<<PKGBUILDDIR>>/debian/r-bioc-rtracklayer/usr/lib/R/site-library --clean . "--built-timestamp='Sun, 04 Dec 2016 21:53:17 +0100'" returned exit code 1
> debian/rules:4: recipe for target 'binary' failed
> make: *** [binary] Error 25

The full build log is available from:
   http://aws-logs.debian.net/2017/08/07/r-bioc-rtracklayer_1.34.1-1_unstable.log

A list of current common problems and possible solutions is available at
http://wiki.debian.org/qa.debian.org/FTBFS . You're welcome to contribute!

About the archive rebuild: The rebuild was done on EC2 VM instances from
Amazon Web Services, using a clean, minimal and up-to-date chroot. Every
failed build was retried once to eliminate random failures.