Bug#812294: bedtools: FTBFS with GCC 6: parse error in template argument

[Martin Michlmayr]

Package: bedtools
Version: 2.25.0-1
Severity: normal
User: debian-***@lists.debian.org
Usertags: ftbfs-gcc-6

This package fails to build with GCC 6. GCC 6 has not been released
yet, but it's expected that GCC 6 will become the default compiler for
stretch.

You can find a snapshot of GCC 6 in experimental. To build with
GCC 6, you can set CC=gcc-6 CXX=g++-6 explicitly.

You may be able to find out more about this issue at
https://gcc.gnu.org/gcc-6/changes.html

sbuild (Debian sbuild) 0.67.0 (26 Dec 2015) on dl580gen9-02.hlinux

...

- Building in src/utils/bedFile
* compiling bedFile.cpp
bedFile.h:799:47: error: parse error in template argument list
else if ( (bed.start < 0) || (bed.end < 0) ) {
^~~~~~~
bedFile.h:877:42: error: parse error in template argument list
if ( (bed.start < 0) || (bed.end < 0) ) {
^~~~~~~
bedFile.h:567:55: required from 'BedLineStatus BedFile::parseLine(T&, const std::vector<std::__cxx11::basic_string<char> >&) [with T = BED]'
bedFile.cpp:233:44: required from here
bedFile.h:799:47: error: 'end' is not a member template function
else if ( (bed.start < 0) || (bed.end < 0) ) {
~~~~~^~~~~~~~
bedFile.h:572:55: required from 'BedLineStatus BedFile::parseLine(T&, const std::vector<std::__cxx11::basic_string<char> >&) [with T = BED]'
bedFile.cpp:233:44: required from here
bedFile.h:877:42: error: 'end' is not a member template function
if ( (bed.start < 0) || (bed.end < 0) ) {
~~~~~^~~~~~~~
Makefile:22: recipe for target '../../../obj//bedFile.o' failed
make[2]: *** [../../../obj//bedFile.o] Error 1

[Michael Crusoe]

Control: forwarded -1 https://github.com/arq5x/bedtools2/issues/352

I have alerted upstream to the issue.

[Martin Michlmayr]

Post by Martin Michlmayr
Package: bedtools
Version: 2.25.0-1
Severity: normal

bedFile.h:799:47: error: parse error in template argument list
else if ( (bed.start < 0) || (bed.end < 0) ) {
^~~~~~~

The package builds fine with GCC 6 6-20160228-1. Since the package
itself didn't change, I guess that either a bug in GCC 6 got fixed or
possibly a header in another package.

Looks like a GCC 6 issue... I see upstream made some changes based on
your report. I guess they can revert the ((bed.end) change.

I'll leave this bug, but it compiles so feel free to close or to close
when you've spoken to upstream. Sorry for the noise!

[Martin Michlmayr]

Post by Martin Michlmayr
The package builds fine with GCC 6 6-20160228-1. Since the package
itself didn't change, I guess that either a bug in GCC 6 got fixed or
possibly a header in another package.
Looks like a GCC 6 issue... I see upstream made some changes based on
your report. I guess they can revert the ((bed.end) change.

Fedora mass rebuild reports at
https://lists.fedoraproject.org/archives/list/***@lists.fedoraproject.org/thread/DH7M2ADHM6XCRFTRRSKZD6MWFUJKHBZK/
says:

BEDTools-2.25.0-1.fc24.src.rpm
frepple-3.0-1.fc24.src.rpm

wrong parsing of template argument list http://gcc.gnu.org/PR10200 fixed
upstream and in gcc-6.0.0-0.11.fc24, will need more substantial
changes in GCC 7

[Michael Crusoe]

Thanks for the update; I've alerted upstream.

Post by Martin Michlmayr

Post by Martin Michlmayr
The package builds fine with GCC 6 6-20160228-1. Since the package
itself didn't change, I guess that either a bug in GCC 6 got fixed or
possibly a header in another package.
Looks like a GCC 6 issue... I see upstream made some changes based on
your report. I guess they can revert the ((bed.end) change.

Fedora mass rebuild reports at
BEDTools-2.25.0-1.fc24.src.rpm
frepple-3.0-1.fc24.src.rpm
wrong parsing of template argument list http://gcc.gnu.org/PR10200 fixed
upstream and in gcc-6.0.0-0.11.fc24, will need more substantial
changes in GCC 7
--
Martin Michlmayr
Linux for HPE Helion, Hewlett Packard Enterprise
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Debian-med-packaging mailing list
http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-packaging

[Martin Michlmayr]

Post by Michael Crusoe
Thanks for the update; I've alerted upstream.

Ok, so can we close this bug report?