prokka (homebrew/science/prokka) on macOS 10.11.6 - Homebrew build logs

# prokka - 2016-10-04_22-08-37.txt

Homebrew build logs for homebrew/science/prokka on macOS 10.11.6
Build date: 2016-10-04 22:08:37

00.config.out

HOMEBREW_VERSION: 1.0.6
ORIGIN: https://github.com/Homebrew/brew.git
HEAD: 35ee2831086e923e7fcaf75fb440b01312e3f9c5
Last commit: 2 days ago
Core tap ORIGIN: https://github.com/Homebrew/homebrew-core
Core tap HEAD: bd4a5e88436985d05b1e2b5d82b96b02297636ef
Core tap last commit: 8 hours ago
HOMEBREW_PREFIX: /usr/local
HOMEBREW_REPOSITORY: /usr/local/Homebrew
HOMEBREW_CELLAR: /usr/local/Cellar
HOMEBREW_BOTTLE_DOMAIN: https://homebrew.bintray.com
CPU: quad-core 64-bit ivybridge
Homebrew Ruby: 2.0.0-p648
Clang: 8.0 build 800
Git: 2.8.4 => /Applications/Xcode.app/Contents/Developer/usr/bin/git
Perl: /usr/bin/perl
Python: /Users/philliptbrooks/anaconda/bin/python => /Users/philliptbrooks/anaconda/bin/python3.5
Ruby: /usr/bin/ruby => /System/Library/Frameworks/Ruby.framework/Versions/2.0/usr/bin/ruby
Java: 1.6.0_65-b14-468
macOS: 10.11.6-x86_64
Xcode: 8.0
CLT: 7.3.1.0.1.1461711523
X11: 2.7.8 => /opt/X11

00.doctor.out

Please note that these warnings are just used to help the Homebrew maintainers
with debugging if you file an issue. If everything you use Homebrew for is
working fine: please don't worry and just ignore them. Thanks!

Warning: Anaconda is known to frequently break Homebrew builds, including Vim and
MacVim, due to bundling many duplicates of system and Homebrew-available
tools.

If you encounter a build failure please temporarily remove Anaconda
from your $PATH and attempt the build again prior to reporting the
failure to us. Thanks!

Warning: python is symlinked to python3
This will confuse build scripts and in general lead to subtle breakage.

Warning: "config" scripts exist outside your system or Homebrew directories.
`./configure` scripts often look for *-config scripts to determine if
software packages are installed, and what additional flags to use when
compiling and linking.

Having additional scripts in your path can confuse software installed via
Homebrew if the config script overrides a system or Homebrew provided
script of the same name. We found the following "config" scripts:
    /Users/philliptbrooks/anaconda/bin/curl-config
    /Users/philliptbrooks/anaconda/bin/freetype-config
    /Users/philliptbrooks/anaconda/bin/libdynd-config
    /Users/philliptbrooks/anaconda/bin/libpng-config
    /Users/philliptbrooks/anaconda/bin/libpng16-config
    /Users/philliptbrooks/anaconda/bin/python3-config
    /Users/philliptbrooks/anaconda/bin/python3.5-config
    /Users/philliptbrooks/anaconda/bin/python3.5m-config
    /Users/philliptbrooks/anaconda/bin/xml2-config
    /Users/philliptbrooks/anaconda/bin/xslt-config

Warning: Your XQuartz (2.7.8) is outdated.
Please install XQuartz 2.7.9 (or delete it):
  https://xquartz.macosforge.org

Warning: Unbrewed dylibs were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.

Unexpected dylibs:
    /usr/local/lib/libtcl8.6.dylib
    /usr/local/lib/libtk8.6.dylib

Warning: Unbrewed header files were found in /usr/local/include.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.

Unexpected header files:
    /usr/local/include/fakemysql.h
    /usr/local/include/fakepq.h
    /usr/local/include/fakesql.h
    /usr/local/include/itcl.h
    /usr/local/include/itcl2TclOO.h
    /usr/local/include/itclDecls.h
    /usr/local/include/itclInt.h
    /usr/local/include/itclIntDecls.h
    /usr/local/include/itclMigrate2TclCore.h
    /usr/local/include/itclTclIntStubsFcn.h
    /usr/local/include/mysqlStubs.h
    /usr/local/include/odbcStubs.h
    /usr/local/include/pqStubs.h
    /usr/local/include/tcl.h
    /usr/local/include/tclDecls.h
    /usr/local/include/tclOO.h
    /usr/local/include/tclOODecls.h
    /usr/local/include/tclPlatDecls.h
    /usr/local/include/tclThread.h
    /usr/local/include/tclTomMath.h
    /usr/local/include/tclTomMathDecls.h
    /usr/local/include/tdbc.h
    /usr/local/include/tdbcDecls.h
    /usr/local/include/tdbcInt.h
    /usr/local/include/tk.h
    /usr/local/include/tkDecls.h
    /usr/local/include/tkPlatDecls.h

Warning: Unbrewed .pc files were found in /usr/local/lib/pkgconfig.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.

Unexpected .pc files:
    /usr/local/lib/pkgconfig/tcl.pc
    /usr/local/lib/pkgconfig/tk.pc

Warning: Unbrewed static libraries were found in /usr/local/lib.
If you didn't put them there on purpose they could cause problems when
building Homebrew formulae, and may need to be deleted.

Unexpected static libraries:
    /usr/local/lib/libtclstub8.6.a
    /usr/local/lib/libtkstub8.6.a

00.tap.out

Formula: prokka
Tap: homebrew/science
Path: /usr/local/Homebrew/Library/Taps/homebrew/homebrew-science/prokka.rb

post_install.01.prokka

2016-10-04 22:08:37 -0400

/usr/local/Cellar/prokka/HEAD-1caf239_1/bin/prokka
--setupdb

[22:08:37] Appending to PATH: /usr/local/Cellar/prokka/HEAD-1caf239_1/bin/../binaries/darwin
[22:08:37] Appending to PATH: /usr/local/Cellar/prokka/HEAD-1caf239_1/bin/../binaries/darwin/../common
[22:08:37] Appending to PATH: /usr/local/Cellar/prokka/HEAD-1caf239_1/bin
[22:08:37] Cleaning databases in /usr/local/Cellar/prokka/HEAD-1caf239_1/bin/../db
[22:08:37] Cleaning complete.
[22:08:37] Looking for 'makeblastdb' - found /usr/local/bin/makeblastdb
[22:08:37] Determined makeblastdb version is 2.4
[22:08:37] Making kingdom BLASTP database: /usr/local/Cellar/prokka/HEAD-1caf239_1/bin/../db/kingdom/Archaea/sprot
[22:08:37] Running: makeblastdb -hash_index -dbtype prot -in \/usr\/local\/Cellar\/prokka\/HEAD\-1caf239_1\/bin\/\.\.\/db\/kingdom\/Archaea\/sprot -logfile /dev/null
[22:08:38] Making kingdom BLASTP database: /usr/local/Cellar/prokka/HEAD-1caf239_1/bin/../db/kingdom/Bacteria/sprot
[22:08:38] Running: makeblastdb -hash_index -dbtype prot -in \/usr\/local\/Cellar\/prokka\/HEAD\-1caf239_1\/bin\/\.\.\/db\/kingdom\/Bacteria\/sprot -logfile /dev/null
[22:08:40] Making kingdom BLASTP database: /usr/local/Cellar/prokka/HEAD-1caf239_1/bin/../db/kingdom/Mitochondria/sprot
[22:08:40] Running: makeblastdb -hash_index -dbtype prot -in \/usr\/local\/Cellar\/prokka\/HEAD\-1caf239_1\/bin\/\.\.\/db\/kingdom\/Mitochondria\/sprot -logfile /dev/null
[22:08:40] Making kingdom BLASTP database: /usr/local/Cellar/prokka/HEAD-1caf239_1/bin/../db/kingdom/Viruses/sprot
[22:08:40] Running: makeblastdb -hash_index -dbtype prot -in \/usr\/local\/Cellar\/prokka\/HEAD\-1caf239_1\/bin\/\.\.\/db\/kingdom\/Viruses\/sprot -logfile /dev/null
[22:08:41] Making genus BLASTP database: /usr/local/Cellar/prokka/HEAD-1caf239_1/bin/../db/genus/Enterococcus
[22:08:41] Running: makeblastdb -hash_index -dbtype prot -in \/usr\/local\/Cellar\/prokka\/HEAD\-1caf239_1\/bin\/\.\.\/db\/genus\/Enterococcus -logfile /dev/null
[22:08:41] Making genus BLASTP database: /usr/local/Cellar/prokka/HEAD-1caf239_1/bin/../db/genus/Escherichia
[22:08:41] Running: makeblastdb -hash_index -dbtype prot -in \/usr\/local\/Cellar\/prokka\/HEAD\-1caf239_1\/bin\/\.\.\/db\/genus\/Escherichia -logfile /dev/null
[22:08:42] Making genus BLASTP database: /usr/local/Cellar/prokka/HEAD-1caf239_1/bin/../db/genus/Staphylococcus
[22:08:42] Running: makeblastdb -hash_index -dbtype prot -in \/usr\/local\/Cellar\/prokka\/HEAD\-1caf239_1\/bin\/\.\.\/db\/genus\/Staphylococcus -logfile /dev/null
[22:08:43] Looking for 'hmmpress' - found /usr/local/bin/hmmpress
[22:08:43] Determined hmmpress version is 3.1
[22:08:43] Pressing HMM database: /usr/local/Cellar/prokka/HEAD-1caf239_1/bin/../db/hmm/HAMAP.hmm
[22:08:43] Running: hmmpress \/usr\/local\/Cellar\/prokka\/HEAD\-1caf239_1\/bin\/\.\.\/db\/hmm\/HAMAP\.hmm
Working...    done.
Pressed and indexed 1463 HMMs (1463 names).
Models pressed into binary file:   /usr/local/Cellar/prokka/HEAD-1caf239_1/bin/../db/hmm/HAMAP.hmm.h3m
SSI index for binary model file:   /usr/local/Cellar/prokka/HEAD-1caf239_1/bin/../db/hmm/HAMAP.hmm.h3i
Profiles (MSV part) pressed into:  /usr/local/Cellar/prokka/HEAD-1caf239_1/bin/../db/hmm/HAMAP.hmm.h3f
Profiles (remainder) pressed into: /usr/local/Cellar/prokka/HEAD-1caf239_1/bin/../db/hmm/HAMAP.hmm.h3p
[22:08:44] Looking for 'cmpress' - found /usr/local/bin/cmpress
[22:08:44] Determined cmpress version is 1.1
[22:08:44] Pressing CM database: /usr/local/Cellar/prokka/HEAD-1caf239_1/bin/../db/cm/Viruses
[22:08:44] Running: cmpress \/usr\/local\/Cellar\/prokka\/HEAD\-1caf239_1\/bin\/\.\.\/db\/cm\/Viruses
Working...    done.
Pressed and indexed 142 CMs and p7 HMM filters (142 names and 142 accessions).
Covariance models and p7 filters pressed into binary file:  /usr/local/Cellar/prokka/HEAD-1caf239_1/bin/../db/cm/Viruses.i1m
SSI index for binary covariance model file:                 /usr/local/Cellar/prokka/HEAD-1caf239_1/bin/../db/cm/Viruses.i1i
Optimized p7 filter profiles (MSV part)  pressed into:      /usr/local/Cellar/prokka/HEAD-1caf239_1/bin/../db/cm/Viruses.i1f
Optimized p7 filter profiles (remainder) pressed into:      /usr/local/Cellar/prokka/HEAD-1caf239_1/bin/../db/cm/Viruses.i1p
[22:08:45] Pressing CM database: /usr/local/Cellar/prokka/HEAD-1caf239_1/bin/../db/cm/Bacteria
[22:08:45] Running: cmpress \/usr\/local\/Cellar\/prokka\/HEAD\-1caf239_1\/bin\/\.\.\/db\/cm\/Bacteria
Working...    done.
Pressed and indexed 564 CMs and p7 HMM filters (564 names and 564 accessions).
Covariance models and p7 filters pressed into binary file:  /usr/local/Cellar/prokka/HEAD-1caf239_1/bin/../db/cm/Bacteria.i1m
SSI index for binary covariance model file:                 /usr/local/Cellar/prokka/HEAD-1caf239_1/bin/../db/cm/Bacteria.i1i
Optimized p7 filter profiles (MSV part)  pressed into:      /usr/local/Cellar/prokka/HEAD-1caf239_1/bin/../db/cm/Bacteria.i1f
Optimized p7 filter profiles (remainder) pressed into:      /usr/local/Cellar/prokka/HEAD-1caf239_1/bin/../db/cm/Bacteria.i1p
[22:08:45] Looking for databases in: /usr/local/Cellar/prokka/HEAD-1caf239_1/bin/../db
[22:08:45] * Kingdoms: Archaea Bacteria Mitochondria Viruses
[22:08:45] * Genera: Enterococcus Escherichia Staphylococcus
[22:08:45] * HMMs: HAMAP
[22:08:45] * CMs: Bacteria Viruses