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-bui...@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)
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