Attachment 550156 Details for Bug 668130 – sci-biology:goby-cpp-1.9.8.1:20181009-050936.log

sci-biology:goby-cpp-1.9.8.1:20181009-050936.log

sci-biology:goby-cpp-1.9.8.1:20181009-050936.log (text/plain), 41.40 KB, created by Toralf Förster on 2018-10-09 08:26:46 UTC

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Creator: Toralf Förster

Created: 2018-10-09 08:26:46 UTC

Size: 41.40 KB

patch

obsolete

> * Package:    sci-biology/goby-cpp-1.9.8.1
> * Repository: gentoo
> * Maintainer: sci-biology@gentoo.org
> * USE:        abi_x86_64 amd64 elibc_glibc kernel_linux policykit userland_GNU
> * FEATURES:   network-sandbox preserve-libs sandbox userpriv usersandbox
>>>> Unpacking source...
>>>> Unpacking goby_1.9.8.1-cpp.zip to /var/tmp/portage/sci-biology/goby-cpp-1.9.8.1/work
>>>> Source unpacked in /var/tmp/portage/sci-biology/goby-cpp-1.9.8.1/work
>>>> Preparing source in /var/tmp/portage/sci-biology/goby-cpp-1.9.8.1/work/goby_1.9.8.1/cpp ...
> * Running eautoreconf in '/var/tmp/portage/sci-biology/goby-cpp-1.9.8.1/work/goby_1.9.8.1/cpp' ...
> * Running libtoolize --install --copy --force --automake ...
> [ ok ]
> * Running aclocal -I m4 ...
> [ ok ]
> * Running autoconf --force ...
> [ ok ]
> * Running autoheader ...
> [ ok ]
> * Running automake --add-missing --copy --foreign --force-missing ...
> [ ok ]
> * Running elibtoolize in: goby_1.9.8.1/cpp/
> *   Applying portage/1.2.0 patch ...
> *   Applying sed/1.5.6 patch ...
> *   Applying as-needed/2.4.3 patch ...
>>>> Source prepared.
>>>> Configuring source in /var/tmp/portage/sci-biology/goby-cpp-1.9.8.1/work/goby_1.9.8.1/cpp ...
> * econf: updating goby_1.9.8.1/cpp/config.sub with /usr/share/gnuconfig/config.sub
> * econf: updating goby_1.9.8.1/cpp/config.guess with /usr/share/gnuconfig/config.guess
>./configure --prefix=/usr --build=x86_64-pc-linux-gnu --host=x86_64-pc-linux-gnu --mandir=/usr/share/man --infodir=/usr/share/info --datadir=/usr/share --sysconfdir=/etc --localstatedir=/var/lib --disable-dependency-tracking --libdir=/usr/lib64
>configure: loading site script /usr/share/config.site
>checking build system type... x86_64-pc-linux-gnu
>checking host system type... x86_64-pc-linux-gnu
>checking target system type... x86_64-pc-linux-gnu
>checking for a BSD-compatible install... /usr/lib/portage/python3.6/ebuild-helpers/xattr/install -c
>checking whether build environment is sane... yes
>checking for a thread-safe mkdir -p... /bin/mkdir -p
>checking for gawk... gawk
>checking whether make sets $(MAKE)... yes
>checking whether make supports nested variables... yes
>checking for x86_64-pc-linux-gnu-g++... x86_64-pc-linux-gnu-g++
>checking whether the C++ compiler works... yes
>checking for C++ compiler default output file name... a.out
>checking for suffix of executables... 
>checking whether we are cross compiling... no
>checking for suffix of object files... o
>checking whether we are using the GNU C++ compiler... yes
>checking whether x86_64-pc-linux-gnu-g++ accepts -g... yes
>checking whether make supports the include directive... yes (GNU style)
>checking dependency style of x86_64-pc-linux-gnu-g++... none
>checking for x86_64-pc-linux-gnu-gcc... x86_64-pc-linux-gnu-gcc
>checking whether we are using the GNU C compiler... yes
>checking whether x86_64-pc-linux-gnu-gcc accepts -g... yes
>checking for x86_64-pc-linux-gnu-gcc option to accept ISO C89... none needed
>checking whether x86_64-pc-linux-gnu-gcc understands -c and -o together... yes
>checking dependency style of x86_64-pc-linux-gnu-gcc... none
>checking how to print strings... printf
>checking for a sed that does not truncate output... /bin/sed
>checking for grep that handles long lines and -e... /bin/grep
>checking for egrep... /bin/grep -E
>checking for fgrep... /bin/grep -F
>checking for ld used by x86_64-pc-linux-gnu-gcc... /usr/x86_64-pc-linux-gnu/bin/ld
>checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld) is GNU ld... yes
>checking for BSD- or MS-compatible name lister (nm)... /usr/bin/x86_64-pc-linux-gnu-nm -B
>checking the name lister (/usr/bin/x86_64-pc-linux-gnu-nm -B) interface... BSD nm
>checking whether ln -s works... yes
>checking the maximum length of command line arguments... 1572864
>checking how to convert x86_64-pc-linux-gnu file names to x86_64-pc-linux-gnu format... func_convert_file_noop
>checking how to convert x86_64-pc-linux-gnu file names to toolchain format... func_convert_file_noop
>checking for /usr/x86_64-pc-linux-gnu/bin/ld option to reload object files... -r
>checking for x86_64-pc-linux-gnu-objdump... x86_64-pc-linux-gnu-objdump
>checking how to recognize dependent libraries... pass_all
>checking for x86_64-pc-linux-gnu-dlltool... no
>checking for dlltool... no
>checking how to associate runtime and link libraries... printf %s\n
>checking for x86_64-pc-linux-gnu-ar... x86_64-pc-linux-gnu-ar
>checking for archiver @FILE support... @
>checking for x86_64-pc-linux-gnu-strip... x86_64-pc-linux-gnu-strip
>checking for x86_64-pc-linux-gnu-ranlib... x86_64-pc-linux-gnu-ranlib
>checking command to parse /usr/bin/x86_64-pc-linux-gnu-nm -B output from x86_64-pc-linux-gnu-gcc object... ok
>checking for sysroot... no
>checking for a working dd... /bin/dd
>checking how to truncate binary pipes... /bin/dd bs=4096 count=1
>checking for x86_64-pc-linux-gnu-mt... no
>checking for mt... no
>checking if : is a manifest tool... no
>checking how to run the C preprocessor... x86_64-pc-linux-gnu-gcc -E
>checking for ANSI C header files... yes
>checking for sys/types.h... yes
>checking for sys/stat.h... yes
>checking for stdlib.h... yes
>checking for string.h... yes
>checking for memory.h... yes
>checking for strings.h... yes
>checking for inttypes.h... yes
>checking for stdint.h... yes
>checking for unistd.h... yes
>checking for dlfcn.h... yes
>checking for objdir... .libs
>checking if x86_64-pc-linux-gnu-gcc supports -fno-rtti -fno-exceptions... no
>checking for x86_64-pc-linux-gnu-gcc option to produce PIC... -fPIC -DPIC
>checking if x86_64-pc-linux-gnu-gcc PIC flag -fPIC -DPIC works... yes
>checking if x86_64-pc-linux-gnu-gcc static flag -static works... yes
>checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... yes
>checking if x86_64-pc-linux-gnu-gcc supports -c -o file.o... (cached) yes
>checking whether the x86_64-pc-linux-gnu-gcc linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
>checking whether -lc should be explicitly linked in... no
>checking dynamic linker characteristics... GNU/Linux ld.so
>checking how to hardcode library paths into programs... immediate
>checking whether stripping libraries is possible... yes
>checking if libtool supports shared libraries... yes
>checking whether to build shared libraries... yes
>checking whether to build static libraries... yes
>checking how to run the C++ preprocessor... x86_64-pc-linux-gnu-g++ -E
>checking for ld used by x86_64-pc-linux-gnu-g++... /usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64
>checking if the linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) is GNU ld... yes
>checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
>checking for x86_64-pc-linux-gnu-g++ option to produce PIC... -fPIC -DPIC
>checking if x86_64-pc-linux-gnu-g++ PIC flag -fPIC -DPIC works... yes
>checking if x86_64-pc-linux-gnu-g++ static flag -static works... yes
>checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... yes
>checking if x86_64-pc-linux-gnu-g++ supports -c -o file.o... (cached) yes
>checking whether the x86_64-pc-linux-gnu-g++ linker (/usr/x86_64-pc-linux-gnu/bin/ld -m elf_x86_64) supports shared libraries... yes
>checking dynamic linker characteristics... (cached) GNU/Linux ld.so
>checking how to hardcode library paths into programs... immediate
>checking for stdbool.h that conforms to C99... no
>checking for _Bool... no
>checking for ANSI C header files... (cached) yes
>checking for an ANSI C-conforming const... yes
>checking for inline... inline
>checking for off_t... yes
>checking for size_t... yes
>checking size of unsigned long... 8
>checking size of unsigned long long... 8
>checking fcntl.h usability... yes
>checking fcntl.h presence... yes
>checking for fcntl.h... yes
>checking malloc.h usability... yes
>checking malloc.h presence... yes
>checking for malloc.h... yes
>checking for getcwd... yes
>checking for memset... yes
>checking for putenv... yes
>checking for realpath... yes
>checking for setenv... yes
>checking for strerror... yes
>checking for stdlib.h... (cached) yes
>checking for GNU libc compatible malloc... yes
>checking for stdlib.h... (cached) yes
>checking for GNU libc compatible realloc... yes
>checking whether lstat correctly handles trailing slash... yes
>checking whether stat accepts an empty string... no
>checking whether lstat correctly handles trailing slash... (cached) yes
>checking for x86_64-pc-linux-gnu-pkg-config... /usr/bin/x86_64-pc-linux-gnu-pkg-config
>checking pkg-config is at least version 0.9.0... yes
>checking for protobuf >= 2.4.1... yes
>checking for libpcrecpp >= 8.10... yes
>checking that generated files are newer than configure... done
>configure: creating ./config.status
>config.status: creating Makefile
>config.status: creating src/Makefile
>config.status: creating goby.pc
>config.status: creating config.h
>config.status: executing depfiles commands
>config.status: executing libtool commands
>>>> Source configured.
>>>> Compiling source in /var/tmp/portage/sci-biology/goby-cpp-1.9.8.1/work/goby_1.9.8.1/cpp ...
>make -j1 
>make  all-recursive
>make[1]: Entering directory '/var/tmp/portage/sci-biology/goby-cpp-1.9.8.1/work/goby_1.9.8.1/cpp'
>Making all in .
>make[2]: Entering directory '/var/tmp/portage/sci-biology/goby-cpp-1.9.8.1/work/goby_1.9.8.1/cpp'
>make[2]: Leaving directory '/var/tmp/portage/sci-biology/goby-cpp-1.9.8.1/work/goby_1.9.8.1/cpp'
>Making all in src
>make[2]: Entering directory '/var/tmp/portage/sci-biology/goby-cpp-1.9.8.1/work/goby_1.9.8.1/cpp/src'
>echo '#define BUILD_TIMESTAMP "'`date "+%G%m%d%k%M%S"`'"' > goby/timestamp.h
>make  all-am
>make[3]: Entering directory '/var/tmp/portage/sci-biology/goby-cpp-1.9.8.1/work/goby_1.9.8.1/cpp/src'
>x86_64-pc-linux-gnu-g++ -DHAVE_CONFIG_H -I. -I..    -pthread   -O2 -pipe -march=native -c -o GobyAlignmentStats.o GobyAlignmentStats.cc
>In file included from GobyAlignmentStats.cc:41:
>goby/Alignments.pb.h:17:2: error: #error This file was generated by an older version of protoc which is
> #error This file was generated by an older version of protoc which is
>  ^~~~~
>goby/Alignments.pb.h:18:2: error: #error incompatible with your Protocol Buffer headers. Please
> #error incompatible with your Protocol Buffer headers.  Please
>  ^~~~~
>goby/Alignments.pb.h:19:2: error: #error regenerate this file with a newer version of protoc.
> #error regenerate this file with a newer version of protoc.
>  ^~~~~
>In file included from GobyAlignmentStats.cc:41:
>goby/Alignments.pb.h: In member function âvoid goby::SequenceVariation::clear_from()â:
>goby/Alignments.pb.h:2055:47: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (from_ != &::google::protobuf::internal::kEmptyString) {
>                                               ^~~~~~~~~~~~
>goby/Alignments.pb.h:2055:47: note: suggested alternative: âGetEmptyStringâ
>   if (from_ != &::google::protobuf::internal::kEmptyString) {
>                                               ^~~~~~~~~~~~
>                                               GetEmptyString
>goby/Alignments.pb.h: In member function âvoid goby::SequenceVariation::set_from(const string&)â:
>goby/Alignments.pb.h:2065:47: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (from_ == &::google::protobuf::internal::kEmptyString) {
>                                               ^~~~~~~~~~~~
>goby/Alignments.pb.h:2065:47: note: suggested alternative: âGetEmptyStringâ
>   if (from_ == &::google::protobuf::internal::kEmptyString) {
>                                               ^~~~~~~~~~~~
>                                               GetEmptyString
>goby/Alignments.pb.h: In member function âvoid goby::SequenceVariation::set_from(const char*)â:
>goby/Alignments.pb.h:2072:47: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (from_ == &::google::protobuf::internal::kEmptyString) {
>                                               ^~~~~~~~~~~~
>goby/Alignments.pb.h:2072:47: note: suggested alternative: âGetEmptyStringâ
>   if (from_ == &::google::protobuf::internal::kEmptyString) {
>                                               ^~~~~~~~~~~~
>                                               GetEmptyString
>goby/Alignments.pb.h: In member function âvoid goby::SequenceVariation::set_from(const char*, size_t)â:
>goby/Alignments.pb.h:2079:47: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (from_ == &::google::protobuf::internal::kEmptyString) {
>                                               ^~~~~~~~~~~~
>goby/Alignments.pb.h:2079:47: note: suggested alternative: âGetEmptyStringâ
>   if (from_ == &::google::protobuf::internal::kEmptyString) {
>                                               ^~~~~~~~~~~~
>                                               GetEmptyString
>goby/Alignments.pb.h: In member function âstd::__cxx11::string* goby::SequenceVariation::mutable_from()â:
>goby/Alignments.pb.h:2086:47: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (from_ == &::google::protobuf::internal::kEmptyString) {
>                                               ^~~~~~~~~~~~
>goby/Alignments.pb.h:2086:47: note: suggested alternative: âGetEmptyStringâ
>   if (from_ == &::google::protobuf::internal::kEmptyString) {
>                                               ^~~~~~~~~~~~
>                                               GetEmptyString
>goby/Alignments.pb.h: In member function âstd::__cxx11::string* goby::SequenceVariation::release_from()â:
>goby/Alignments.pb.h:2093:47: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (from_ == &::google::protobuf::internal::kEmptyString) {
>                                               ^~~~~~~~~~~~
>goby/Alignments.pb.h:2093:47: note: suggested alternative: âGetEmptyStringâ
>   if (from_ == &::google::protobuf::internal::kEmptyString) {
>                                               ^~~~~~~~~~~~
>                                               GetEmptyString
>goby/Alignments.pb.h:2097:72: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>  from_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
>                                                                     ^~~~~~~~~~~~
>
>goby/Alignments.pb.h:2097:72: note: suggested alternative: âGetEmptyStringâ
>  from_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
>                                                                     ^~~~~~~~~~~~
>                                                                     GetEmptyString
>goby/Alignments.pb.h: In member function âvoid goby::SequenceVariation::clear_to()â:
>goby/Alignments.pb.h:2113:45: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (to_ != &::google::protobuf::internal::kEmptyString) {
>                                             ^~~~~~~~~~~~
>goby/Alignments.pb.h:2113:45: note: suggested alternative: âGetEmptyStringâ
>   if (to_ != &::google::protobuf::internal::kEmptyString) {
>                                             ^~~~~~~~~~~~
>                                             GetEmptyString
>goby/Alignments.pb.h: In member function âvoid goby::SequenceVariation::set_to(const string&)â:
>goby/Alignments.pb.h:2123:45: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (to_ == &::google::protobuf::internal::kEmptyString) {
>                                             ^~~~~~~~~~~~
>goby/Alignments.pb.h:2123:45: note: suggested alternative: âGetEmptyStringâ
>   if (to_ == &::google::protobuf::internal::kEmptyString) {
>                                             ^~~~~~~~~~~~
>                                             GetEmptyString
>goby/Alignments.pb.h: In member function âvoid goby::SequenceVariation::set_to(const char*)â:
>goby/Alignments.pb.h:2130:45: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (to_ == &::google::protobuf::internal::kEmptyString) {
>                                             ^~~~~~~~~~~~
>goby/Alignments.pb.h:2130:45: note: suggested alternative: âGetEmptyStringâ
>   if (to_ == &::google::protobuf::internal::kEmptyString) {
>                                             ^~~~~~~~~~~~
>                                             GetEmptyString
>goby/Alignments.pb.h: In member function âvoid goby::SequenceVariation::set_to(const char*, size_t)â:
>goby/Alignments.pb.h:2137:45: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (to_ == &::google::protobuf::internal::kEmptyString) {
>                                             ^~~~~~~~~~~~
>goby/Alignments.pb.h:2137:45: note: suggested alternative: âGetEmptyStringâ
>   if (to_ == &::google::protobuf::internal::kEmptyString) {
>                                             ^~~~~~~~~~~~
>                                             GetEmptyString
>goby/Alignments.pb.h: In member function âstd::__cxx11::string* goby::SequenceVariation::mutable_to()â:
>goby/Alignments.pb.h:2144:45: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (to_ == &::google::protobuf::internal::kEmptyString) {
>                                             ^~~~~~~~~~~~
>goby/Alignments.pb.h:2144:45: note: suggested alternative: âGetEmptyStringâ
>   if (to_ == &::google::protobuf::internal::kEmptyString) {
>                                             ^~~~~~~~~~~~
>                                             GetEmptyString
>goby/Alignments.pb.h: In member function âstd::__cxx11::string* goby::SequenceVariation::release_to()â:
>goby/Alignments.pb.h:2151:45: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (to_ == &::google::protobuf::internal::kEmptyString) {
>                                             ^~~~~~~~~~~~
>goby/Alignments.pb.h:2151:45: note: suggested alternative: âGetEmptyStringâ
>   if (to_ == &::google::protobuf::internal::kEmptyString) {
>                                             ^~~~~~~~~~~~
>                                             GetEmptyString
>goby/Alignments.pb.h:2155:70: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>    to_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
>                                                                     ^~~~~~~~~~~~
>
>goby/Alignments.pb.h:2155:70: note: suggested alternative: âGetEmptyStringâ
>    to_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
>                                                                     ^~~~~~~~~~~~
>                                                                     GetEmptyString
>goby/Alignments.pb.h: In member function âvoid goby::SequenceVariation::clear_to_quality()â:
>goby/Alignments.pb.h:2215:53: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (to_quality_ != &::google::protobuf::internal::kEmptyString) {
>                                                     ^~~~~~~~~~~~
>goby/Alignments.pb.h:2215:53: note: suggested alternative: âGetEmptyStringâ
>   if (to_quality_ != &::google::protobuf::internal::kEmptyString) {
>                                                     ^~~~~~~~~~~~
>                                                     GetEmptyString
>goby/Alignments.pb.h: In member function âvoid goby::SequenceVariation::set_to_quality(const string&)â:
>goby/Alignments.pb.h:2225:53: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (to_quality_ == &::google::protobuf::internal::kEmptyString) {
>                                                     ^~~~~~~~~~~~
>goby/Alignments.pb.h:2225:53: note: suggested alternative: âGetEmptyStringâ
>   if (to_quality_ == &::google::protobuf::internal::kEmptyString) {
>                                                     ^~~~~~~~~~~~
>                                                     GetEmptyString
>goby/Alignments.pb.h: In member function âvoid goby::SequenceVariation::set_to_quality(const char*)â:
>goby/Alignments.pb.h:2232:53: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (to_quality_ == &::google::protobuf::internal::kEmptyString) {
>                                                     ^~~~~~~~~~~~
>goby/Alignments.pb.h:2232:53: note: suggested alternative: âGetEmptyStringâ
>   if (to_quality_ == &::google::protobuf::internal::kEmptyString) {
>                                                     ^~~~~~~~~~~~
>                                                     GetEmptyString
>goby/Alignments.pb.h: In member function âvoid goby::SequenceVariation::set_to_quality(const void*, size_t)â:
>goby/Alignments.pb.h:2239:53: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (to_quality_ == &::google::protobuf::internal::kEmptyString) {
>                                                     ^~~~~~~~~~~~
>goby/Alignments.pb.h:2239:53: note: suggested alternative: âGetEmptyStringâ
>   if (to_quality_ == &::google::protobuf::internal::kEmptyString) {
>                                                     ^~~~~~~~~~~~
>                                                     GetEmptyString
>goby/Alignments.pb.h: In member function âstd::__cxx11::string* goby::SequenceVariation::mutable_to_quality()â:
>goby/Alignments.pb.h:2246:53: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (to_quality_ == &::google::protobuf::internal::kEmptyString) {
>                                                     ^~~~~~~~~~~~
>goby/Alignments.pb.h:2246:53: note: suggested alternative: âGetEmptyStringâ
>   if (to_quality_ == &::google::protobuf::internal::kEmptyString) {
>                                                     ^~~~~~~~~~~~
>                                                     GetEmptyString
>goby/Alignments.pb.h: In member function âstd::__cxx11::string* goby::SequenceVariation::release_to_quality()â:
>goby/Alignments.pb.h:2253:53: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (to_quality_ == &::google::protobuf::internal::kEmptyString) {
>                                                     ^~~~~~~~~~~~
>goby/Alignments.pb.h:2253:53: note: suggested alternative: âGetEmptyStringâ
>   if (to_quality_ == &::google::protobuf::internal::kEmptyString) {
>                                                     ^~~~~~~~~~~~
>                                                     GetEmptyString
>goby/Alignments.pb.h:2257:78: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
> ality_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
>                                                                     ^~~~~~~~~~~~
>
>goby/Alignments.pb.h:2257:78: note: suggested alternative: âGetEmptyStringâ
> ality_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
>                                                                     ^~~~~~~~~~~~
>                                                                     GetEmptyString
>goby/Alignments.pb.h: In member function âvoid goby::AlignmentHeader::clear_aligner_name()â:
>goby/Alignments.pb.h:2583:55: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (aligner_name_ != &::google::protobuf::internal::kEmptyString) {
>                                                       ^~~~~~~~~~~~
>goby/Alignments.pb.h:2583:55: note: suggested alternative: âGetEmptyStringâ
>   if (aligner_name_ != &::google::protobuf::internal::kEmptyString) {
>                                                       ^~~~~~~~~~~~
>                                                       GetEmptyString
>goby/Alignments.pb.h: In member function âvoid goby::AlignmentHeader::set_aligner_name(const string&)â:
>goby/Alignments.pb.h:2593:55: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (aligner_name_ == &::google::protobuf::internal::kEmptyString) {
>                                                       ^~~~~~~~~~~~
>goby/Alignments.pb.h:2593:55: note: suggested alternative: âGetEmptyStringâ
>   if (aligner_name_ == &::google::protobuf::internal::kEmptyString) {
>                                                       ^~~~~~~~~~~~
>                                                       GetEmptyString
>goby/Alignments.pb.h: In member function âvoid goby::AlignmentHeader::set_aligner_name(const char*)â:
>goby/Alignments.pb.h:2600:55: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (aligner_name_ == &::google::protobuf::internal::kEmptyString) {
>                                                       ^~~~~~~~~~~~
>goby/Alignments.pb.h:2600:55: note: suggested alternative: âGetEmptyStringâ
>   if (aligner_name_ == &::google::protobuf::internal::kEmptyString) {
>                                                       ^~~~~~~~~~~~
>                                                       GetEmptyString
>goby/Alignments.pb.h: In member function âvoid goby::AlignmentHeader::set_aligner_name(const char*, size_t)â:
>goby/Alignments.pb.h:2607:55: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (aligner_name_ == &::google::protobuf::internal::kEmptyString) {
>                                                       ^~~~~~~~~~~~
>goby/Alignments.pb.h:2607:55: note: suggested alternative: âGetEmptyStringâ
>   if (aligner_name_ == &::google::protobuf::internal::kEmptyString) {
>                                                       ^~~~~~~~~~~~
>                                                       GetEmptyString
>goby/Alignments.pb.h: In member function âstd::__cxx11::string* goby::AlignmentHeader::mutable_aligner_name()â:
>goby/Alignments.pb.h:2614:55: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (aligner_name_ == &::google::protobuf::internal::kEmptyString) {
>                                                       ^~~~~~~~~~~~
>goby/Alignments.pb.h:2614:55: note: suggested alternative: âGetEmptyStringâ
>   if (aligner_name_ == &::google::protobuf::internal::kEmptyString) {
>                                                       ^~~~~~~~~~~~
>                                                       GetEmptyString
>goby/Alignments.pb.h: In member function âstd::__cxx11::string* goby::AlignmentHeader::release_aligner_name()â:
>goby/Alignments.pb.h:2621:55: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (aligner_name_ == &::google::protobuf::internal::kEmptyString) {
>                                                       ^~~~~~~~~~~~
>goby/Alignments.pb.h:2621:55: note: suggested alternative: âGetEmptyStringâ
>   if (aligner_name_ == &::google::protobuf::internal::kEmptyString) {
>                                                       ^~~~~~~~~~~~
>                                                       GetEmptyString
>goby/Alignments.pb.h:2625:80: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
> _name_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
>                                                                     ^~~~~~~~~~~~
>
>goby/Alignments.pb.h:2625:80: note: suggested alternative: âGetEmptyStringâ
> _name_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
>                                                                     ^~~~~~~~~~~~
>                                                                     GetEmptyString
>goby/Alignments.pb.h: In member function âvoid goby::AlignmentHeader::clear_aligner_version()â:
>goby/Alignments.pb.h:2641:58: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (aligner_version_ != &::google::protobuf::internal::kEmptyString) {
>                                                          ^~~~~~~~~~~~
>goby/Alignments.pb.h:2641:58: note: suggested alternative: âGetEmptyStringâ
>   if (aligner_version_ != &::google::protobuf::internal::kEmptyString) {
>                                                          ^~~~~~~~~~~~
>                                                          GetEmptyString
>goby/Alignments.pb.h: In member function âvoid goby::AlignmentHeader::set_aligner_version(const string&)â:
>goby/Alignments.pb.h:2651:58: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (aligner_version_ == &::google::protobuf::internal::kEmptyString) {
>                                                          ^~~~~~~~~~~~
>goby/Alignments.pb.h:2651:58: note: suggested alternative: âGetEmptyStringâ
>   if (aligner_version_ == &::google::protobuf::internal::kEmptyString) {
>                                                          ^~~~~~~~~~~~
>                                                          GetEmptyString
>goby/Alignments.pb.h: In member function âvoid goby::AlignmentHeader::set_aligner_version(const char*)â:
>goby/Alignments.pb.h:2658:58: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (aligner_version_ == &::google::protobuf::internal::kEmptyString) {
>                                                          ^~~~~~~~~~~~
>goby/Alignments.pb.h:2658:58: note: suggested alternative: âGetEmptyStringâ
>   if (aligner_version_ == &::google::protobuf::internal::kEmptyString) {
>                                                          ^~~~~~~~~~~~
>                                                          GetEmptyString
>goby/Alignments.pb.h: In member function âvoid goby::AlignmentHeader::set_aligner_version(const char*, size_t)â:
>goby/Alignments.pb.h:2665:58: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (aligner_version_ == &::google::protobuf::internal::kEmptyString) {
>                                                          ^~~~~~~~~~~~
>goby/Alignments.pb.h:2665:58: note: suggested alternative: âGetEmptyStringâ
>   if (aligner_version_ == &::google::protobuf::internal::kEmptyString) {
>                                                          ^~~~~~~~~~~~
>                                                          GetEmptyString
>goby/Alignments.pb.h: In member function âstd::__cxx11::string* goby::AlignmentHeader::mutable_aligner_version()â:
>goby/Alignments.pb.h:2672:58: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (aligner_version_ == &::google::protobuf::internal::kEmptyString) {
>                                                          ^~~~~~~~~~~~
>goby/Alignments.pb.h:2672:58: note: suggested alternative: âGetEmptyStringâ
>   if (aligner_version_ == &::google::protobuf::internal::kEmptyString) {
>                                                          ^~~~~~~~~~~~
>                                                          GetEmptyString
>goby/Alignments.pb.h: In member function âstd::__cxx11::string* goby::AlignmentHeader::release_aligner_version()â:
>goby/Alignments.pb.h:2679:58: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (aligner_version_ == &::google::protobuf::internal::kEmptyString) {
>                                                          ^~~~~~~~~~~~
>goby/Alignments.pb.h:2679:58: note: suggested alternative: âGetEmptyStringâ
>   if (aligner_version_ == &::google::protobuf::internal::kEmptyString) {
>                                                          ^~~~~~~~~~~~
>                                                          GetEmptyString
>goby/Alignments.pb.h:2683:83: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
> rsion_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
>                                                                     ^~~~~~~~~~~~
>
>goby/Alignments.pb.h:2683:83: note: suggested alternative: âGetEmptyStringâ
> rsion_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
>                                                                     ^~~~~~~~~~~~
>                                                                     GetEmptyString
>goby/Alignments.pb.h: In member function âvoid goby::AlignmentHeader::clear_version()â:
>goby/Alignments.pb.h:2699:50: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (version_ != &::google::protobuf::internal::kEmptyString) {
>                                                  ^~~~~~~~~~~~
>goby/Alignments.pb.h:2699:50: note: suggested alternative: âGetEmptyStringâ
>   if (version_ != &::google::protobuf::internal::kEmptyString) {
>                                                  ^~~~~~~~~~~~
>                                                  GetEmptyString
>goby/Alignments.pb.h: In member function âvoid goby::AlignmentHeader::set_version(const string&)â:
>goby/Alignments.pb.h:2709:50: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (version_ == &::google::protobuf::internal::kEmptyString) {
>                                                  ^~~~~~~~~~~~
>goby/Alignments.pb.h:2709:50: note: suggested alternative: âGetEmptyStringâ
>   if (version_ == &::google::protobuf::internal::kEmptyString) {
>                                                  ^~~~~~~~~~~~
>                                                  GetEmptyString
>goby/Alignments.pb.h: In member function âvoid goby::AlignmentHeader::set_version(const char*)â:
>goby/Alignments.pb.h:2716:50: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (version_ == &::google::protobuf::internal::kEmptyString) {
>                                                  ^~~~~~~~~~~~
>goby/Alignments.pb.h:2716:50: note: suggested alternative: âGetEmptyStringâ
>   if (version_ == &::google::protobuf::internal::kEmptyString) {
>                                                  ^~~~~~~~~~~~
>                                                  GetEmptyString
>goby/Alignments.pb.h: In member function âvoid goby::AlignmentHeader::set_version(const char*, size_t)â:
>goby/Alignments.pb.h:2723:50: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (version_ == &::google::protobuf::internal::kEmptyString) {
>                                                  ^~~~~~~~~~~~
>goby/Alignments.pb.h:2723:50: note: suggested alternative: âGetEmptyStringâ
>   if (version_ == &::google::protobuf::internal::kEmptyString) {
>                                                  ^~~~~~~~~~~~
>                                                  GetEmptyString
>goby/Alignments.pb.h: In member function âstd::__cxx11::string* goby::AlignmentHeader::mutable_version()â:
>goby/Alignments.pb.h:2730:50: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (version_ == &::google::protobuf::internal::kEmptyString) {
>                                                  ^~~~~~~~~~~~
>goby/Alignments.pb.h:2730:50: note: suggested alternative: âGetEmptyStringâ
>   if (version_ == &::google::protobuf::internal::kEmptyString) {
>                                                  ^~~~~~~~~~~~
>                                                  GetEmptyString
>goby/Alignments.pb.h: In member function âstd::__cxx11::string* goby::AlignmentHeader::release_version()â:
>goby/Alignments.pb.h:2737:50: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (version_ == &::google::protobuf::internal::kEmptyString) {
>                                                  ^~~~~~~~~~~~
>goby/Alignments.pb.h:2737:50: note: suggested alternative: âGetEmptyStringâ
>   if (version_ == &::google::protobuf::internal::kEmptyString) {
>                                                  ^~~~~~~~~~~~
>                                                  GetEmptyString
>goby/Alignments.pb.h:2741:75: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
> rsion_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
>                                                                     ^~~~~~~~~~~~
>
>goby/Alignments.pb.h:2741:75: note: suggested alternative: âGetEmptyStringâ
> rsion_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
>                                                                     ^~~~~~~~~~~~
>                                                                     GetEmptyString
>goby/Alignments.pb.h: In member function âvoid goby::IdentifierInfo::clear_name()â:
>goby/Alignments.pb.h:2834:47: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (name_ != &::google::protobuf::internal::kEmptyString) {
>                                               ^~~~~~~~~~~~
>goby/Alignments.pb.h:2834:47: note: suggested alternative: âGetEmptyStringâ
>   if (name_ != &::google::protobuf::internal::kEmptyString) {
>                                               ^~~~~~~~~~~~
>                                               GetEmptyString
>goby/Alignments.pb.h: In member function âvoid goby::IdentifierInfo::set_name(const string&)â:
>goby/Alignments.pb.h:2844:47: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (name_ == &::google::protobuf::internal::kEmptyString) {
>                                               ^~~~~~~~~~~~
>goby/Alignments.pb.h:2844:47: note: suggested alternative: âGetEmptyStringâ
>   if (name_ == &::google::protobuf::internal::kEmptyString) {
>                                               ^~~~~~~~~~~~
>                                               GetEmptyString
>goby/Alignments.pb.h: In member function âvoid goby::IdentifierInfo::set_name(const char*)â:
>goby/Alignments.pb.h:2851:47: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (name_ == &::google::protobuf::internal::kEmptyString) {
>                                               ^~~~~~~~~~~~
>goby/Alignments.pb.h:2851:47: note: suggested alternative: âGetEmptyStringâ
>   if (name_ == &::google::protobuf::internal::kEmptyString) {
>                                               ^~~~~~~~~~~~
>                                               GetEmptyString
>goby/Alignments.pb.h: In member function âvoid goby::IdentifierInfo::set_name(const char*, size_t)â:
>goby/Alignments.pb.h:2858:47: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (name_ == &::google::protobuf::internal::kEmptyString) {
>                                               ^~~~~~~~~~~~
>goby/Alignments.pb.h:2858:47: note: suggested alternative: âGetEmptyStringâ
>   if (name_ == &::google::protobuf::internal::kEmptyString) {
>                                               ^~~~~~~~~~~~
>                                               GetEmptyString
>goby/Alignments.pb.h: In member function âstd::__cxx11::string* goby::IdentifierInfo::mutable_name()â:
>goby/Alignments.pb.h:2865:47: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (name_ == &::google::protobuf::internal::kEmptyString) {
>                                               ^~~~~~~~~~~~
>goby/Alignments.pb.h:2865:47: note: suggested alternative: âGetEmptyStringâ
>   if (name_ == &::google::protobuf::internal::kEmptyString) {
>                                               ^~~~~~~~~~~~
>                                               GetEmptyString
>goby/Alignments.pb.h: In member function âstd::__cxx11::string* goby::IdentifierInfo::release_name()â:
>goby/Alignments.pb.h:2872:47: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>   if (name_ == &::google::protobuf::internal::kEmptyString) {
>                                               ^~~~~~~~~~~~
>goby/Alignments.pb.h:2872:47: note: suggested alternative: âGetEmptyStringâ
>   if (name_ == &::google::protobuf::internal::kEmptyString) {
>                                               ^~~~~~~~~~~~
>                                               GetEmptyString
>goby/Alignments.pb.h:2876:72: error: âkEmptyStringâ is not a member of âgoogle::protobuf::internalâ
>  name_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
>                                                                     ^~~~~~~~~~~~
>
>goby/Alignments.pb.h:2876:72: note: suggested alternative: âGetEmptyStringâ
>  name_ = const_cast< ::std::string*>(&::google::protobuf::internal::kEmptyString);
>                                                                     ^~~~~~~~~~~~
>                                                                     GetEmptyString
>In file included from goby/MessageChunks.h:42,
>                 from goby/Alignments.h:32,
>                 from GobyAlignmentStats.cc:42:
>goby/ICBFileInputStream.h: At global scope:
>goby/ICBFileInputStream.h:156:31: error: âscoped_arrayâ in namespace âgoogle::protobufâ does not name a template type
>             google::protobuf::scoped_array<google::protobuf::uint8> buffer_;
>                               ^~~~~~~~~~~~
>make[3]: *** [Makefile:662: GobyAlignmentStats.o] Error 1
>make[3]: Leaving directory '/var/tmp/portage/sci-biology/goby-cpp-1.9.8.1/work/goby_1.9.8.1/cpp/src'
>make[2]: *** [Makefile:468: all] Error 2
>make[2]: Leaving directory '/var/tmp/portage/sci-biology/goby-cpp-1.9.8.1/work/goby_1.9.8.1/cpp/src'
>make[1]: *** [Makefile:494: all-recursive] Error 1
>make[1]: Leaving directory '/var/tmp/portage/sci-biology/goby-cpp-1.9.8.1/work/goby_1.9.8.1/cpp'
>make: *** [Makefile:403: all] Error 2
> * ERROR: sci-biology/goby-cpp-1.9.8.1::gentoo failed (compile phase):
> *   emake failed
> * 
> * If you need support, post the output of `emerge --info '=sci-biology/goby-cpp-1.9.8.1::gentoo'`,
> * the complete build log and the output of `emerge -pqv '=sci-biology/goby-cpp-1.9.8.1::gentoo'`.
> * The complete build log is located at '/var/log/portage/sci-biology:goby-cpp-1.9.8.1:20181009-050936.log'.
> * For convenience, a symlink to the build log is located at '/var/tmp/portage/sci-biology/goby-cpp-1.9.8.1/temp/build.log'.
> * The ebuild environment file is located at '/var/tmp/portage/sci-biology/goby-cpp-1.9.8.1/temp/environment'.
> * Working directory: '/var/tmp/portage/sci-biology/goby-cpp-1.9.8.1/work/goby_1.9.8.1/cpp'
> * S: '/var/tmp/portage/sci-biology/goby-cpp-1.9.8.1/work/goby_1.9.8.1/cpp'

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Attachments on bug 668130: 550146 | 550148 | 550150 | 550152 | 550154 | 550156