Shaun Jackman

``` /bin/bash ../libtool --tag=CXX --mode=link g++-4.8 -pthread -fopenmp -fpermissive -std=c++11 -Wextra -Wall -Wsign-promo -Woverloaded-virtual -Wendif-labels -Wno-unused -Wno-deprecated -Wno-long-long -Wno-parentheses -Wno-unused-parameter -fno-nonansi-builtins -mieee-fp -fno-strict-aliasing -iquote . -ggdb -DNDEBUG -o DiscovarDeNovo DiscovarDeNovo.o...

This is a bit of a shot in the dark, but can you try… ```ruby # Fix error: undefined reference to `digraphE::O(int) const' depends_on "binutils" => :build unless OS.mac? ```

We may have to drop `discovardenovo` if we're unable to find a fix.

I did manage to compile discovardenovo once with GCC 4.9: ``` /gsc/btl/linuxbrew/Cellar/discovardenovo/52488/INSTALL_RECEIPT.json ``` I can't unfortunately tell you what I did to get it to compile. =/

Please report the output of … ```sh brew install mira brew gist-logs mira ```

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"`

``` 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...

Let's first try updating `blasr` to the most recent version, 4.0.0.

This may be caused by the upgrade from Python 3.6 to Python 3.7.

I've removed `htseq` with PR https://github.com/bcgsc/orca/pull/61. Still be worth looking into the build failure, but not a priority.