from /var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/2.0.1/cpp/src/goby/Alignments.h:32, from /var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/2.0.1/cpp/src/GobyAlignmentStats.cc:43: /var/tmp/portage/sci-biology/goby-cpp-2.0.1/work/2.0.1/cpp/src/goby/ICBFileInputStream.h:156:31: error: ‘scoped_array’ in namespace ‘google::protobuf’ does not name a template type google::protobuf::scoped_array<google::protobuf::uint8> buffer_; ^~~~~~~~~~~~ make[3]: *** [Makefile:684: GobyAlignmentStats.o] Error 1 ------------------------------------------------------------------- This is an unstable amd64 chroot image at a tinderbox (==build bot) name: 17.0-no-multilib_20180707-104832 ------------------------------------------------------------------- gcc-config -l: [1] x86_64-pc-linux-gnu-7.3.0 * Available Python interpreters, in order of preference: [1] python3.5 [2] python2.7 (fallback) Available Ruby profiles: [1] ruby23 (with Rubygems) * emerge -qpv sci-biology/goby-cpp [ebuild N ] sci-biology/goby-cpp-2.0.1 USE="-static-libs"
Created attachment 538766 [details] emerge-info.txt
Created attachment 538768 [details] emerge-history.txt
Created attachment 538770 [details] environment
Created attachment 538772 [details] etc.portage.tbz2
Created attachment 538774 [details] logs.tbz2
Created attachment 538776 [details] sci-biology:goby-cpp-2.0.1:20180708-113345.log
Created attachment 538778 [details] temp.tbz2
Same here. Maybe it is not compatible with dev-libs/protobuf-3? I was designed for protobuf-2.4.1 as https://github.com/CampagneLaboratory/goby3/blob/master/cpp/README.txt says. I wonder if there is a newer version. Here is the old 1 and 2 version repo: https://github.com/CampagneLaboratory/goby Here is version 3 repo: https://github.com/CampagneLaboratory/goby3 Seems last release of goby bundle was 2.3.6: http://chagall.med.cornell.edu/goby/releases/CHANGES.txt . But there is no corresponding goby-cpp release tarball?
In sci-biology/goby-3 upstream they switched from ant to maven.
Package removed.
