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bcgsc / orca

:whale: Genomics Research Container Architecture
http://www.bcgsc.ca/services/orca
GNU General Public License v3.0
48 stars 13 forks source link

mira: exp_flexer.cc #20

Open tmozgach opened 7 years ago

tmozgach commented 7 years ago 
==> Installing homebrew/science/mira
==> Downloading https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira-4.0.2.tar.bz2
==> Downloading from https://superb-dca2.dl.sourceforge.net/project/mira-assembler/MIRA/stable/mira-4.0.2.tar.bz2
######################################################################## 100.0%
==> ./configure --prefix=/home/linuxbrew/.linuxbrew/Cellar/mira/4.0.2 --with-expat=/home/linuxbrew/.linuxbrew/opt/expat --with-expat-lib=-L/home/linuxbrew/.linuxbrew/opt/exp
==> make LIBS='-lboost_regex-mt -lboost_system-mt -lboost_filesystem-mt -lboost_iostreams-mt -lboost_thread-mt -lexpat -lz'
Last 15 lines from /home/linuxbrew/.cache/Homebrew/Logs/mira/02.make:
In file included from exp_flexer.cc:323:0:
/home/linuxbrew/.linuxbrew/include/FlexLexer.h:156:8: error: candidate is: void EXPFlexLexer::yy_init_buffer(yy_buffer_state*, std::istream&)
   void yy_init_buffer( yy_buffer_state* b, std::istream& s );
        ^
make[5]: *** [exp_flexer.o] Error 1
make[5]: Leaving directory `/tmp/mira-20170816-8616-4nd1wo/mira-4.0.2/src/io'
make[4]: *** [all] Error 2
make[4]: Leaving directory `/tmp/mira-20170816-8616-4nd1wo/mira-4.0.2/src/io'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/tmp/mira-20170816-8616-4nd1wo/mira-4.0.2/src'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/tmp/mira-20170816-8616-4nd1wo/mira-4.0.2/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/tmp/mira-20170816-8616-4nd1wo/mira-4.0.2'
make: *** [all] Error 2

READ THIS: https://github.com/Linuxbrew/brew/blob/master/docs/Troubleshooting.md#troubleshooting
Please do not report this issue to Homebrew/brew or Homebrew/core, which support macOS only.

These open issues may also help:
mira: Add desc and rename google-perftools https://github.com/Homebrew/homebrew-science/pull/5522
mira: exp_flexer.cc:766:9: error: no match for 'operator=' https://github.com/Homebrew/homebrew-science/issues/3424
mira error quirks.C:56:5: error: 'cout' is not a member of 'std' https://github.com/Homebrew/homebrew-science/issues/2268
sjackman commented 7 years ago

Please report the output of …

brew install mira
brew gist-logs mira
tmozgach commented 7 years ago

@sjackman 

==> Installing homebrew/science/mira
==> Downloading https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira-4.0.2.tar.bz2
==> Downloading from https://versaweb.dl.sourceforge.net/project/mira-assembler/MIRA/stable/mira-4.0.2.tar.bz2
######################################################################## 100.0%
==> ./configure --prefix=/home/linuxbrew/.linuxbrew/Cellar/mira/4.0.2 --with-expat=/home/linuxbrew/.linuxbrew/opt/expat --with-expat-lib=
==> make LIBS='-lboost_regex-mt -lboost_system-mt -lboost_filesystem-mt -lboost_iostreams-mt -lboost_thread-mt -lexpat -lz'
Last 15 lines from /home/linuxbrew/.cache/Homebrew/Logs/mira/02.make:
/home/linuxbrew/.linuxbrew/include/FlexLexer.h:156:8: error: candidate is: void EXPFlexLexer::yy_init_buffer(yy_buffer_state*, std::istream&)
   void yy_init_buffer( yy_buffer_state* b, std::istream& s );
        ^
make[5]: *** [exp_flexer.o] Error 1
make[5]: *** Waiting for unfinished jobs....
make[5]: Leaving directory `/tmp/mira-20170817-9768-z9zd2l/mira-4.0.2/src/io'
make[4]: *** [all] Error 2
make[4]: Leaving directory `/tmp/mira-20170817-9768-z9zd2l/mira-4.0.2/src/io'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/tmp/mira-20170817-9768-z9zd2l/mira-4.0.2/src'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/tmp/mira-20170817-9768-z9zd2l/mira-4.0.2/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/tmp/mira-20170817-9768-z9zd2l/mira-4.0.2'
make: *** [all] Error 2

READ THIS: https://github.com/Linuxbrew/brew/blob/master/docs/Troubleshooting.md#troubleshooting
Please do not report this issue to Homebrew/brew or Homebrew/core, which support macOS only.

These open issues may also help:
mira: Add desc and rename google-perftools https://github.com/Homebrew/homebrew-science/pull/5522
mira: exp_flexer.cc:766:9: error: no match for 'operator=' https://github.com/Homebrew/homebrew-science/issues/3424
mira error quirks.C:56:5: error: 'cout' is not a member of 'std' https://github.com/Homebrew/homebrew-science/issues/2268
==> Installing discovardenovo from homebrew/science
==> Installing dependencies for homebrew/science/discovardenovo: patchelf, jemalloc
==> Installing homebrew/science/discovardenovo dependency: patchelf
==> Downloading https://linuxbrew.bintray.com/bottles/patchelf-0.9_1.x86_64_linux.bottle.tar.gz
######################################################################## 100.0%
==> Pouring patchelf-0.9_1.x86_64_linux.bottle.tar.gz
🍺  /home/linuxbrew/.linuxbrew/Cellar/patchelf/0.9_1: 6 files, 1.1MB
==> Installing homebrew/science/discovardenovo dependency: jemalloc
==> Downloading https://linuxbrew.bintray.com/bottles/jemalloc-5.0.1.x86_64_linux.bottle.tar.gz
######################################################################## 100.0%
==> Pouring jemalloc-5.0.1.x86_64_linux.bottle.tar.gz
🍺  /home/linuxbrew/.linuxbrew/Cellar/jemalloc/5.0.1: 16 files, 37.5MB
==> Installing homebrew/science/discovardenovo
==> Downloading ftp://ftp.broadinstitute.org/pub/crd/DiscovarDeNovo/latest_source_code/discovardenovo-52488.tar.gz
######################################################################## 100.0%
==> ./configure --disable-silent-rules --prefix=/home/linuxbrew/.linuxbrew/Cellar/discovardenovo/52488
==> make install
brew gist-logs mira
^Z
[2]+  Stopped                 brew install discovardenovo
linuxbrew@ca3f712735e3:~$ brew gist-logs cpanm
Error: No logs.
linuxbrew@ca3f712735e3:~$ brew install mira
Error: Another active Homebrew update process is already in progress.
Please wait for it to finish or terminate it to continue.
==> Installing mira from homebrew/science
==> Installing dependencies for homebrew/science/mira: ncurses, readline, sqlite, gdbm, zlib, openssl, berkeley-db@4, bzip2, python, boost, xz, libunwind, google-perftools, libxml2, docbook, libbsd, expat, gettext, m4, flex
==> Installing homebrew/science/mira dependency: ncurses
==> Downloading https://linuxbrew.bintray.com/bottles/ncurses-6.0_3.x86_64_linux.bottle.tar.gz
######################################################################## 100.0%
==> Pouring ncurses-6.0_3.x86_64_linux.bottle.tar.gz
🍺  /home/linuxbrew/.linuxbrew/Cellar/ncurses/6.0_3: 3,526 files, 16.4MB
==> Installing homebrew/science/mira dependency: readline
==> Downloading https://linuxbrew.bintray.com/bottles/readline-7.0.3_1.x86_64_linux.bottle.tar.gz
######################################################################## 100.0%
==> Pouring readline-7.0.3_1.x86_64_linux.bottle.tar.gz
🍺  /home/linuxbrew/.linuxbrew/Cellar/readline/7.0.3_1: 46 files, 1.7MB
==> Installing homebrew/science/mira dependency: sqlite
==> Downloading https://linuxbrew.bintray.com/bottles/sqlite-3.20.0.x86_64_linux.bottle.tar.gz
######################################################################## 100.0%
==> Pouring sqlite-3.20.0.x86_64_linux.bottle.tar.gz
🍺  /home/linuxbrew/.linuxbrew/Cellar/sqlite/3.20.0: 12 files, 18.9MB
==> Installing homebrew/science/mira dependency: gdbm
==> Downloading https://linuxbrew.bintray.com/bottles/gdbm-1.13_1.x86_64_linux.bottle.tar.gz
######################################################################## 100.0%
==> Pouring gdbm-1.13_1.x86_64_linux.bottle.tar.gz
🍺  /home/linuxbrew/.linuxbrew/Cellar/gdbm/1.13_1: 37 files, 2.0MB
==> Installing homebrew/science/mira dependency: zlib
==> Downloading https://linuxbrew.bintray.com/bottles/zlib-1.2.11.x86_64_linux.bottle.tar.gz
######################################################################## 100.0%
==> Pouring zlib-1.2.11.x86_64_linux.bottle.tar.gz
🍺  /home/linuxbrew/.linuxbrew/Cellar/zlib/1.2.11: 12 files, 391.8KB
==> Installing homebrew/science/mira dependency: openssl
==> Downloading https://linuxbrew.bintray.com/bottles/openssl-1.0.2l.x86_64_linux.bottle.tar.gz
######################################################################## 100.0%
==> Pouring openssl-1.0.2l.x86_64_linux.bottle.tar.gz
==> Downloading https://curl.haxx.se/ca/cacert-2017-01-18.pem
######################################################################## 100.0%
==> Caveats
A CA file has been bootstrapped using certificates from the SystemRoots
keychain. To add additional certificates (e.g. the certificates added in
the System keychain), place .pem files in
  /home/linuxbrew/.linuxbrew/etc/openssl/certs

and run
  /home/linuxbrew/.linuxbrew/opt/openssl/bin/c_rehash

==> Summary
🍺  /home/linuxbrew/.linuxbrew/Cellar/openssl/1.0.2l: 1,716 files, 14.5MB
==> Installing homebrew/science/mira dependency: berkeley-db@4
==> Downloading https://linuxbrew.bintray.com/bottles/berkeley-db@4-4.8.30.x86_64_linux.bottle.tar.gz
######################################################################## 100.0%
==> Pouring berkeley-db@4-4.8.30.x86_64_linux.bottle.tar.gz
==> Caveats
This formula is keg-only, which means it was not symlinked into /home/linuxbrew/.linuxbrew,
because this is an alternate version of another formula.

If you need to have this software first in your PATH run:
  echo 'export PATH="/home/linuxbrew/.linuxbrew/opt/berkeley-db@4/bin:$PATH"' >> ~/.bash_profile

For compilers to find this software you may need to set:
    LDFLAGS:  -L/home/linuxbrew/.linuxbrew/opt/berkeley-db@4/lib
    CPPFLAGS: -I/home/linuxbrew/.linuxbrew/opt/berkeley-db@4/include

==> Summary
🍺  /home/linuxbrew/.linuxbrew/Cellar/berkeley-db@4/4.8.30: 4,596 files, 82MB
==> Installing homebrew/science/mira dependency: bzip2
==> Downloading https://linuxbrew.bintray.com/bottles/bzip2-1.0.6_1.x86_64_linux.bottle.tar.gz
######################################################################## 100.0%
==> Pouring bzip2-1.0.6_1.x86_64_linux.bottle.tar.gz
🍺  /home/linuxbrew/.linuxbrew/Cellar/bzip2/1.0.6_1: 30 files, 1.5MB
==> Installing homebrew/science/mira dependency: python
==> Downloading https://linuxbrew.bintray.com/bottles/python-2.7.13_1.x86_64_linux.bottle.tar.gz
######################################################################## 100.0%
==> Pouring python-2.7.13_1.x86_64_linux.bottle.tar.gz
==> /home/linuxbrew/.linuxbrew/Cellar/python/2.7.13_1/bin/python2 -s setup.py --no-user-cfg install --force --verbose --single-version-externa
==> /home/linuxbrew/.linuxbrew/Cellar/python/2.7.13_1/bin/python2 -s setup.py --no-user-cfg install --force --verbose --single-version-externa
==> /home/linuxbrew/.linuxbrew/Cellar/python/2.7.13_1/bin/python2 -s setup.py --no-user-cfg install --force --verbose --single-version-externa
sh: 1: python: not found
sh: 1: python: not found
==> Caveats
This formula installs a python2 executable to /home/linuxbrew/.linuxbrew/bin.
If you wish to have this formula's python executable in your PATH then add
the following to ~/.bash_profile:
  export PATH="/home/linuxbrew/.linuxbrew/opt/python/libexec/bin:$PATH"

Pip and setuptools have been installed. To update them
  pip2 install --upgrade pip setuptools

You can install Python packages with
  pip2 install <package>

They will install into the site-package directory
  /home/linuxbrew/.linuxbrew/lib/python2.7/site-packages

See: https://docs.brew.sh/Homebrew-and-Python.html

Python modules have been installed and Homebrew's site-packages is not
in your Python sys.path, so you will not be able to import the modules
this formula installed. If you plan to develop with these modules,
please run:
  mkdir -p 
  echo 'import site; site.addsitedir("/home/linuxbrew/.linuxbrew/lib/python2.7/site-packages")' >> homebrew.pth
==> Summary
🍺  /home/linuxbrew/.linuxbrew/Cellar/python/2.7.13_1: 2,957 files, 70.7MB
==> Installing homebrew/science/mira dependency: boost
==> Downloading https://linuxbrew.bintray.com/bottles/boost-1.64.0_1.x86_64_linux.bottle.tar.gz
######################################################################## 100.0%
==> Pouring boost-1.64.0_1.x86_64_linux.bottle.tar.gz
🍺  /home/linuxbrew/.linuxbrew/Cellar/boost/1.64.0_1: 12,685 files, 189.4MB
==> Installing homebrew/science/mira dependency: xz
==> Downloading https://linuxbrew.bintray.com/bottles/xz-5.2.3.x86_64_linux.bottle.tar.gz
######################################################################## 100.0%
==> Pouring xz-5.2.3.x86_64_linux.bottle.tar.gz
🍺  /home/linuxbrew/.linuxbrew/Cellar/xz/5.2.3: 99 files, 1.7MB
==> Installing homebrew/science/mira dependency: libunwind
==> Downloading https://linuxbrew.bintray.com/bottles/libunwind-1.2.x86_64_linux.bottle.1.tar.gz
######################################################################## 100.0%
==> Pouring libunwind-1.2.x86_64_linux.bottle.1.tar.gz
🍺  /home/linuxbrew/.linuxbrew/Cellar/libunwind/1.2: 42 files, 535.8KB
==> Installing homebrew/science/mira dependency: google-perftools
==> Downloading https://linuxbrew.bintray.com/bottles/gperftools-2.6.1.x86_64_linux.bottle.tar.gz
######################################################################## 100.0%
==> Pouring gperftools-2.6.1.x86_64_linux.bottle.tar.gz
🍺  /home/linuxbrew/.linuxbrew/Cellar/gperftools/2.6.1: 110 files, 33.8MB
==> Installing homebrew/science/mira dependency: libxml2
==> Downloading https://linuxbrew.bintray.com/bottles/libxml2-2.9.4_3.x86_64_linux.bottle.tar.gz
######################################################################## 100.0%
==> Pouring libxml2-2.9.4_3.x86_64_linux.bottle.tar.gz
sh: 1: python: not found
sh: 1: python: not found
==> Caveats

Python modules have been installed and Homebrew's site-packages is not
in your Python sys.path, so you will not be able to import the modules
this formula installed. If you plan to develop with these modules,
please run:
  mkdir -p 
  echo 'import site; site.addsitedir("/home/linuxbrew/.linuxbrew/lib/python2.7/site-packages")' >> homebrew.pth
==> Summary
🍺  /home/linuxbrew/.linuxbrew/Cellar/libxml2/2.9.4_3: 282 files, 22.9MB
==> Installing homebrew/science/mira dependency: docbook
==> Downloading https://linuxbrew.bintray.com/bottles/docbook-5.0.x86_64_linux.bottle.3.tar.gz
######################################################################## 100.0%
==> Pouring docbook-5.0.x86_64_linux.bottle.3.tar.gz
==> xmlcatalog --noout --create /home/linuxbrew/.linuxbrew/etc/xml/catalog
==> xmlcatalog --noout --del file:///home/linuxbrew/.linuxbrew/Cellar/docbook/5.0/docbook/xml/4.2/catalog.xml /home/linuxbrew/.linuxbrew/etc/x
==> xmlcatalog --noout --add nextCatalog  file:///home/linuxbrew/.linuxbrew/Cellar/docbook/5.0/docbook/xml/4.2/catalog.xml /home/linuxbrew/.li
==> xmlcatalog --noout --del file:///home/linuxbrew/.linuxbrew/Cellar/docbook/5.0/docbook/xml/4.1.2/catalog.xml /home/linuxbrew/.linuxbrew/etc
==> xmlcatalog --noout --add nextCatalog  file:///home/linuxbrew/.linuxbrew/Cellar/docbook/5.0/docbook/xml/4.1.2/catalog.xml /home/linuxbrew/.
==> xmlcatalog --noout --del file:///home/linuxbrew/.linuxbrew/Cellar/docbook/5.0/docbook/xml/4.3/catalog.xml /home/linuxbrew/.linuxbrew/etc/x
==> xmlcatalog --noout --add nextCatalog  file:///home/linuxbrew/.linuxbrew/Cellar/docbook/5.0/docbook/xml/4.3/catalog.xml /home/linuxbrew/.li
==> xmlcatalog --noout --del file:///home/linuxbrew/.linuxbrew/Cellar/docbook/5.0/docbook/xml/4.4/catalog.xml /home/linuxbrew/.linuxbrew/etc/x
==> xmlcatalog --noout --add nextCatalog  file:///home/linuxbrew/.linuxbrew/Cellar/docbook/5.0/docbook/xml/4.4/catalog.xml /home/linuxbrew/.li
==> xmlcatalog --noout --del file:///home/linuxbrew/.linuxbrew/Cellar/docbook/5.0/docbook/xml/4.5/catalog.xml /home/linuxbrew/.linuxbrew/etc/x
==> xmlcatalog --noout --add nextCatalog  file:///home/linuxbrew/.linuxbrew/Cellar/docbook/5.0/docbook/xml/4.5/catalog.xml /home/linuxbrew/.li
==> xmlcatalog --noout --del file:///home/linuxbrew/.linuxbrew/Cellar/docbook/5.0/docbook/xml/5.0/catalog.xml /home/linuxbrew/.linuxbrew/etc/x
==> xmlcatalog --noout --add nextCatalog  file:///home/linuxbrew/.linuxbrew/Cellar/docbook/5.0/docbook/xml/5.0/catalog.xml /home/linuxbrew/.li
==> Caveats
To use the DocBook package in your XML toolchain,
you need to add the following to your ~/.bashrc:

export XML_CATALOG_FILES="/home/linuxbrew/.linuxbrew/etc/xml/catalog"

==> Summary
🍺  /home/linuxbrew/.linuxbrew/Cellar/docbook/5.0: 181 files, 4.7MB
==> Installing homebrew/science/mira dependency: libbsd
==> Downloading https://linuxbrew.bintray.com/bottles/libbsd-0.8.3.x86_64_linux.bottle.tar.gz
######################################################################## 100.0%
==> Pouring libbsd-0.8.3.x86_64_linux.bottle.tar.gz
🍺  /home/linuxbrew/.linuxbrew/Cellar/libbsd/0.8.3: 82 files, 682.3KB
==> Installing homebrew/science/mira dependency: expat
==> Downloading https://linuxbrew.bintray.com/bottles/expat-2.2.3.x86_64_linux.bottle.tar.gz
######################################################################## 100.0%
==> Pouring expat-2.2.3.x86_64_linux.bottle.tar.gz
🍺  /home/linuxbrew/.linuxbrew/Cellar/expat/2.2.3: 16 files, 1.5MB
==> Installing homebrew/science/mira dependency: gettext
==> Downloading https://linuxbrew.bintray.com/bottles/gettext-0.19.8.1.x86_64_linux.bottle.tar.gz
######################################################################## 100.0%
==> Pouring gettext-0.19.8.1.x86_64_linux.bottle.tar.gz
==> Caveats

Emacs Lisp files have been installed to:
  /home/linuxbrew/.linuxbrew/share/emacs/site-lisp/gettext
==> Summary
🍺  /home/linuxbrew/.linuxbrew/Cellar/gettext/0.19.8.1: 1,932 files, 17.2MB
==> Installing homebrew/science/mira dependency: m4
==> Downloading https://linuxbrew.bintray.com/bottles/m4-1.4.18.x86_64_linux.bottle.tar.gz
######################################################################## 100.0%
==> Pouring m4-1.4.18.x86_64_linux.bottle.tar.gz
🍺  /home/linuxbrew/.linuxbrew/Cellar/m4/1.4.18: 13 files, 1.1MB
==> Installing homebrew/science/mira dependency: flex
==> Downloading https://linuxbrew.bintray.com/bottles/flex-2.6.4.x86_64_linux.bottle.tar.gz
######################################################################## 100.0%
==> Pouring flex-2.6.4.x86_64_linux.bottle.tar.gz
🍺  /home/linuxbrew/.linuxbrew/Cellar/flex/2.6.4: 47 files, 1.8MB
==> Installing homebrew/science/mira
==> Downloading https://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira-4.0.2.tar.bz2
==> Downloading from https://superb-dca2.dl.sourceforge.net/project/mira-assembler/MIRA/stable/mira-4.0.2.tar.bz2
######################################################################## 100.0%
==> ./configure --prefix=/home/linuxbrew/.linuxbrew/Cellar/mira/4.0.2 --with-expat=/home/linuxbrew/.linuxbrew/opt/expat --with-expat-lib=-L/ho
==> make LIBS='-lboost_regex-mt -lboost_system-mt -lboost_filesystem-mt -lboost_iostreams-mt -lboost_thread-mt -lexpat -lz'
Last 15 lines from /home/linuxbrew/.cache/Homebrew/Logs/mira/02.make:
/home/linuxbrew/.linuxbrew/include/FlexLexer.h:156:8: error: candidate is: void EXPFlexLexer::yy_init_buffer(yy_buffer_state*, std::istream&)
   void yy_init_buffer( yy_buffer_state* b, std::istream& s );
        ^
make[5]: *** [exp_flexer.o] Error 1
make[5]: *** Waiting for unfinished jobs....
make[5]: Leaving directory `/tmp/mira-20170817-11704-pww07j/mira-4.0.2/src/io'
make[4]: *** [all] Error 2
make[4]: Leaving directory `/tmp/mira-20170817-11704-pww07j/mira-4.0.2/src/io'
make[3]: *** [all-recursive] Error 1
make[3]: Leaving directory `/tmp/mira-20170817-11704-pww07j/mira-4.0.2/src'
make[2]: *** [all] Error 2
make[2]: Leaving directory `/tmp/mira-20170817-11704-pww07j/mira-4.0.2/src'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/tmp/mira-20170817-11704-pww07j/mira-4.0.2'
make: *** [all] Error 2

READ THIS: https://github.com/Linuxbrew/brew/blob/master/docs/Troubleshooting.md#troubleshooting
Please do not report this issue to Homebrew/brew or Homebrew/core, which support macOS only.

These open issues may also help:
mira: Add desc and rename google-perftools https://github.com/Homebrew/homebrew-science/pull/5522
mira: exp_flexer.cc:766:9: error: no match for 'operator=' https://github.com/Homebrew/homebrew-science/issues/3424
mira error quirks.C:56:5: error: 'cout' is not a member of 'std' https://github.com/Homebrew/homebrew-science/issues/2268
tmozgach commented 7 years ago

@sjackman brew gist-logs mira shows 

Error: GitHub 
The GitHub credentials in the macOS keychain may be invalid.
Clear them with:
  printf "protocol=https\nhost=github.com\n" | git credential-osxkeychain erase
Or create a personal access token:
  https://github.com/settings/tokens/new?scopes=gist,public_repo&description=Homebrew
and then set the token as: export HOMEBREW_GITHUB_API_TOKEN="your_new_token"

Should I set up it somehow?

sjackman commented 7 years ago

Yeah. Go to https://github.com/settings/tokens/new?scopes=gist,public_repo&description=Homebrew and then set the token as: export HOMEBREW_GITHUB_API_TOKEN="your_new_token"

tmozgach commented 7 years ago

@sjackman https://gist.github.com/ae544f58ac1f1fa9fcc53c9608d2cc77

sjackman commented 7 years ago 
g++-4.8 -DPACKAGE_NAME=\"mira\" -DPACKAGE_TARNAME=\"mira\" -DPACKAGE_VERSION=\"4.0.2\" -DPACKAGE_STRING=\"mira\ 4.0.2\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DPACKAGE=\"mira\" -DVERSION=\"4.0.2\" -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DENABLE64=1 -DHAVE_DLFCN_H=1 -DLT_OBJDIR=\".libs/\" -DYYTEXT_POINTER=1 -DSTDC_HEADERS=1 -DHAVE__BOOL=1 -DHAVE_STDBOOL_H=1 -Drestrict=__restrict -DHAVE_STDLIB_H=1 -DHAVE_MALLOC=1 -DHAVE_STDLIB_H=1 -DHAVE_REALLOC=1 -DLSTAT_FOLLOWS_SLASHED_SYMLINK=1 -DHAVE_STRFTIME=1 -DHAVE_MEMSET=1 -DHAVE_FSEEKO=1 -DHAVE_ISBLANK=1 -DHAVE_NAMESPACES=/\*\*/ -DHAVE_STD=/\*\*/ -DHAVE_STL=/\*\*/ -DHAVE_BOOST=/\*\*/ -DHAVE_BOOST_THREAD=/\*\*/ -DHAVE_BOOST_REGEX=/\*\*/ -DHAVE_BOOST_SYSTEM=/\*\*/ -DHAVE_BOOST_FILESYSTEM=/\*\*/ -DHAVE_BOOST_IOSTREAMS=/\*\*/ -DHAVE_LIBRT=1 -DBOUNDTRACKFLAG=1 -DBUGTRACKFLAG=1 -I.  -I../../src    -DPUBLICQUIET -DAJ_Linux64   -I/home/linuxbrew/.linuxbrew/Cellar/mira/4.0.2/include -O3 -funroll-loops -pthread -I/home/linuxbrew/.linuxbrew/opt/boost/include -I/home/linuxbrew/.linuxbrew/opt/expat/include -Werror=uninitialized -Werror=return-type -Werror=parentheses -std=c++0x -Werror=unused-value -c -o exp_flexer.o exp_flexer.cc
exp_flexer.cc: In member function ‘virtual int EXPFlexLexer::yylex()’:
exp_flexer.cc:766:9: error: no match for ‘operator=’ (operand types are ‘std::istream {aka std::basic_istream<char>}’ and ‘std::istream* {aka std::basic_istream<char>*}’)
    yyin = & std::cin;

https://gist.github.com/anonymous/ae544f58ac1f1fa9fcc53c9608d2cc77#file-02-make-L39

Can you please report this issue upstream to the developers of mira and report the version of MIRA, flex, bison, and GCC.

tmozgach commented 7 years ago

Wrote email to bach@chevreux.org bach@chevreux.org