[Debian-med-packaging] Bug#789985: FTBFS: IRanges_defines.h: fatal error: S4Vectors_defines.h: No such file or directory

[Chris West (Faux)]

Package: r-bioc-shortread
Version: 1.22.0-1
Severity: serious
Justification: fails to build from source (but built successfully in the past)
User: reproducible-builds at lists.alioth.debian.org
Usertags: ftbfs

Dear Maintainer,

The package fails to build:

config.status: creating src/Makevars
** libs
make[1]: Entering directory '/tmp/buildd/r-bioc-shortread-1.22.0/src'
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG   -I"/usr/lib/R/site-library/IRanges/include" -I"/usr/lib/R/site-library/XVector/include" -I"/usr/lib/R/site-library/Biostrings/include"  -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -D_FORTIFY_SOURCE=2 -g  -c Biostrings_stubs.c -o Biostrings_stubs.o
In file included from /usr/lib/R/site-library/Biostrings/include/Biostrings_defines.h:18:0,
                 from /usr/lib/R/site-library/Biostrings/include/Biostrings_interface.h:114,
                 from /usr/lib/R/site-library/Biostrings/include/_Biostrings_stubs.c:1,
                 from Biostrings_stubs.c:1:
/usr/lib/R/site-library/IRanges/include/IRanges_defines.h:18:31: fatal error: S4Vectors_defines.h: No such file or directory
 #include "S4Vectors_defines.h"
                               ^
compilation terminated.
/usr/lib/R/etc/Makeconf:134: recipe for target 'Biostrings_stubs.o' failed


Maybe this is a bug in r-bioc-biostrings, or r-bioc-iranges?

The same bug affects at least r-bioc-genomicalignments, r-bioc-rtracklayer, and r-bioc-variantannotation.
(all same maintainer)

Full build log:
https://reproducible.debian.net/rb-pkg/testing/amd64/r-bioc-shortread.html

-- System Information:
Debian Release: stretch/sid
  APT prefers unstable
  APT policy: (500, 'unstable'), (1, 'experimental')
Architecture: amd64 (x86_64)

Kernel: Linux 3.19.0-21-generic (SMP w/8 CPU cores)
Locale: LANG=en_GB.UTF-8, LC_CTYPE=en_GB.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)