[Debian-med-packaging] Bug#755335: r-bioc-genomicfeatures: FTBFS: in 'GenomicFeatures' methods for export not found: findSpliceOverlaps

[David Suárez]

Source: r-bioc-genomicfeatures
Version: 1.14.2-1
Severity: serious
Tags: jessie sid
User: debian-qa at lists.debian.org
Usertags: qa-ftbfs-20140718 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):
>  fakeroot debian/rules binary
> test -x debian/rules
> dh_testroot
> dh_prep 
> dh_installdirs -A 
> mkdir -p "."
> dh_installdirs		usr/lib/R/site-library
> echo "R:Depends=r-base-core (>= 3.1.1-1)" >> debian/r-bioc-genomicfeatures.substvars
> if test -f /usr/bin/xvfb-run; then 			\
> 		 xvfb-run -a 			\
> 			R CMD INSTALL -l /«PKGBUILDDIR»/debian/r-bioc-genomicfeatures/usr/lib/R/site-library --clean     \
> 				 . ;	\
> 	else							\
> 		 R CMD INSTALL -l /«PKGBUILDDIR»/debian/r-bioc-genomicfeatures/usr/lib/R/site-library 	\
> 				--clean  . ;\
> 	fi
> * installing *source* package 'GenomicFeatures' ...
> ** R
> ** inst
> ** preparing package for lazy loading
> code for methods in class "TranscriptDb" was not checked for suspicious field assignments (recommended package 'codetools' not available?)
> ** help
> *** installing help indices
> ** building package indices
> ** testing if installed package can be loaded
> Warning: no function found corresponding to methods exports from 'GenomicFeatures' for: 'findSpliceOverlaps'
> Error in loadNamespace(package, c(which.lib.loc, lib.loc)) : 
>   in 'GenomicFeatures' methods for export not found: findSpliceOverlaps
> Error: loading failed
> Execution halted
> ERROR: loading failed
> * removing '/«PKGBUILDDIR»/debian/r-bioc-genomicfeatures/usr/lib/R/site-library/GenomicFeatures'
> make: *** [R_any_arch] Error 1

The full build log is available from:
   http://aws-logs.debian.net/ftbfs-logs/2014/07/18/r-bioc-genomicfeatures_1.14.2-1_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.