問題
% brew update
出力結果
error: unable to unlink old 'Library/ENV/scm/git' (Permission denied)
error: unable to unlink old 'Library/Homebrew/manpages/brew.1.md' (Permission denied)
Error: Failure while executing: git pull --ff --no-rebase --quiet origin refs/heads/master:refs/remotes/origin/master
解決方法
$ sudo chown -R `whoami` /usr/local
$ cd /usr/local
$ git reset --hard origin/master
再実行
% brew update
出力結果
==> New Formulae
homebrew/binary/chronograf homebrew/science/minimap homebrew/versions/antlr3
homebrew/binary/rebol-core homebrew/science/msieve homebrew/versions/apache-spark131
homebrew/binary/rebol-view homebrew/science/multi-worm-tracker homebrew/versions/apache-spark141
homebrew/science/abacas homebrew/science/ncbi-c++-toolkit homebrew/versions/astyle204
homebrew/science/ace-corrector homebrew/science/nccmp homebrew/versions/boot2docker162
homebrew/science/andi homebrew/science/nip2 homebrew/versions/docker162
homebrew/science/arrayfire homebrew/science/opencv3 homebrew/versions/docker171
homebrew/science/art homebrew/science/oswitch homebrew/versions/elasticsearch17
homebrew/science/ascii_plots homebrew/science/pathd8 homebrew/versions/erlang-r17
homebrew/science/astral homebrew/science/paxtools homebrew/versions/freetds091
homebrew/science/bcalm homebrew/science/phipack homebrew/versions/gdal111
homebrew/science/bioformats-cpp homebrew/science/phyutility homebrew/versions/gegl02
homebrew/science/biointerchange homebrew/science/pilercr homebrew/versions/go14
homebrew/science/biopp homebrew/science/pilon homebrew/versions/gradle24
homebrew/science/blaze-lib homebrew/science/poretools homebrew/versions/gradle26
homebrew/science/boost-compute homebrew/science/psmc homebrew/versions/gradle27
homebrew/science/circlator homebrew/science/quest homebrew/versions/gradle28
homebrew/science/clinfo homebrew/science/r8s homebrew/versions/influxdb08
homebrew/science/cmdstan homebrew/science/rna-star homebrew/versions/iojs
homebrew/science/cryptoverif homebrew/science/rnammer homebrew/versions/jruby168
homebrew/science/datamash homebrew/science/simulate-pcr homebrew/versions/jruby1721
homebrew/science/dazz_db homebrew/science/sortmerna homebrew/versions/jruby9000
homebrew/science/dextractor homebrew/science/spici homebrew/versions/jython253
homebrew/science/dida homebrew/science/suite-sparse421 homebrew/versions/libxc21
homebrew/science/ea-utils homebrew/science/superlu43 homebrew/versions/libxml278
homebrew/science/exabayes homebrew/science/transdecoder homebrew/versions/lz4r117
homebrew/science/gap homebrew/science/transpose homebrew/versions/mapnik2
homebrew/science/graphlan homebrew/science/transrate-tools homebrew/versions/mysql56
homebrew/science/gubbins homebrew/science/ucto homebrew/versions/nasm21106
homebrew/science/hisat2 homebrew/science/vcflib homebrew/versions/nifi021
homebrew/science/humann2 homebrew/science/vips7 homebrew/versions/node012
homebrew/science/iva homebrew/science/vsearch homebrew/versions/node4-lts
homebrew/science/libcerf homebrew/science/wfdb homebrew/versions/protobuf260
homebrew/science/libfolia homebrew/science/xcdf homebrew/versions/saxon6
homebrew/science/mash homebrew/science/yass homebrew/versions/selenium-server-standalone245
homebrew/science/metaphlan homebrew/versions/android-ndk-r10d homebrew/versions/zeromq405
homebrew/science/minced homebrew/versions/ansible18
==> Updated Formulae
homebrew/binary/adobe-air-sdk homebrew/science/gmsh homebrew/science/p4est homebrew/science/veclibfort
homebrew/binary/adobe-air-sdk-flex homebrew/science/gmt homebrew/science/parmetis homebrew/science/vips
homebrew/binary/ddptools homebrew/science/gmt4 homebrew/science/pastix homebrew/science/vislcg3
homebrew/binary/eventstore homebrew/science/gnudatalanguage homebrew/science/pathvisio homebrew/science/vtk
homebrew/binary/mpress homebrew/science/grabix homebrew/science/petsc homebrew/science/vtk5
homebrew/binary/perforce homebrew/science/graph-tool homebrew/science/piler homebrew/science/wcslib
homebrew/binary/perforce-proxy homebrew/science/gromacs homebrew/science/prank homebrew/science/wcstools
homebrew/binary/perforce-server homebrew/science/h5utils homebrew/science/prokka homebrew/science/wxmaxima
homebrew/binary/subgit homebrew/science/harvest-tools homebrew/science/proverif homebrew/science/xmgredit
homebrew/science/abinit homebrew/science/hdf5 homebrew/science/pspp homebrew/science/xmi-msim
homebrew/science/abyss homebrew/science/healpix homebrew/science/pulseview homebrew/science/xrmc
homebrew/science/adam homebrew/science/hisat homebrew/science/pymol homebrew/science/yaggo
homebrew/science/alembic homebrew/science/hopdm homebrew/science/qr_mumps homebrew/science/yaha
homebrew/science/alpscore homebrew/science/htsbox homebrew/science/qrupdate homebrew/versions/bind99
homebrew/science/armadillo homebrew/science/hwloc homebrew/science/qualimap homebrew/versions/elasticsearch14
homebrew/science/arpack homebrew/science/hypre homebrew/science/quast homebrew/versions/gcc49
homebrew/science/asl homebrew/science/igv homebrew/science/r homebrew/versions/gcc5
homebrew/science/astrometry-net homebrew/science/insighttoolkit homebrew/science/r-gui homebrew/versions/glfw3
homebrew/science/atomic-pseudopotential-engine homebrew/science/inter-views homebrew/science/radx homebrew/versions/gnupg21
homebrew/science/bali-phy homebrew/science/ipopt homebrew/science/readseq homebrew/versions/gnutls34
homebrew/science/bam-readcount homebrew/science/kallisto homebrew/science/repeatmodeler homebrew/versions/hdf4
homebrew/science/bamtools homebrew/science/kent-tools homebrew/science/root homebrew/versions/jenkins-lts
homebrew/science/bamutil homebrew/science/lammps homebrew/science/root6 homebrew/versions/jetty76
homebrew/science/barrnap homebrew/science/last homebrew/science/rstudio-server homebrew/versions/libmongoclient-legacy
homebrew/science/bedtools homebrew/science/libmatio homebrew/science/sailfish homebrew/versions/libpng12
homebrew/science/bioawk homebrew/science/libpll homebrew/science/salmon homebrew/versions/llvm36
homebrew/science/biobloomtools homebrew/science/libsigrokdecode homebrew/science/sambamba homebrew/versions/lua53
homebrew/science/blasr homebrew/science/lighter homebrew/science/samblaster homebrew/versions/mongodb26
homebrew/science/blast homebrew/science/links-scaffolder homebrew/science/scalapack homebrew/versions/mysql55
homebrew/science/bowtie homebrew/science/lumpy-sv homebrew/science/seqdb homebrew/versions/nettle3
homebrew/science/bowtie2 homebrew/science/madlib homebrew/science/sfscode homebrew/versions/node010
homebrew/science/bpipe homebrew/science/mathgl homebrew/science/slepc homebrew/versions/node08
homebrew/science/butterflow homebrew/science/maxima homebrew/science/snid homebrew/versions/openssl098
homebrew/science/cantera homebrew/science/mbsystem homebrew/science/snp_sites homebrew/versions/openssl101
homebrew/science/cd-hit homebrew/science/megahit homebrew/science/snpeff homebrew/versions/play13
homebrew/science/cdo homebrew/science/metis4 homebrew/science/spades homebrew/versions/postgresql8
homebrew/science/cdsclient homebrew/science/mhap homebrew/science/sratoolkit homebrew/versions/postgresql9
homebrew/science/ceres-solver homebrew/science/mlst homebrew/science/statismo homebrew/versions/postgresql91
homebrew/science/clustal-omega homebrew/science/mumps homebrew/science/stringtie homebrew/versions/postgresql92
homebrew/science/daligner homebrew/science/nanopolish homebrew/science/suite-sparse homebrew/versions/postgresql93
homebrew/science/dealii homebrew/science/ncview homebrew/science/sumo homebrew/versions/redis26
homebrew/science/dgtal homebrew/science/netcdf homebrew/science/sundials homebrew/versions/redis28
homebrew/science/diamond homebrew/science/neuron homebrew/science/superlu homebrew/versions/ruby187
homebrew/science/ds9 homebrew/science/nextflow homebrew/science/superlu_dist homebrew/versions/ruby193
homebrew/science/dsk homebrew/science/nonpareil homebrew/science/swetest homebrew/versions/ruby20
homebrew/science/etsf_io homebrew/science/novoalign homebrew/science/swrcfit homebrew/versions/ruby21
homebrew/science/fermikit homebrew/science/octave homebrew/science/ticcutils homebrew/versions/tomcat6
homebrew/science/fgsl homebrew/science/openblas homebrew/science/timbl homebrew/versions/tomcat7
homebrew/science/flann homebrew/science/opencascade homebrew/science/tisean homebrew/versions/v8-315
homebrew/science/flint homebrew/science/opencv homebrew/science/trans-abyss peco/peco/peco (installed)
homebrew/science/fwdpp homebrew/science/openfst homebrew/science/trilinos
homebrew/science/genometools homebrew/science/openimageio homebrew/science/ucsc-genome-browser
homebrew/science/getdp homebrew/science/osgearth homebrew/science/vcftools
==> Renamed Formulae
homebrew/science/gal-sim -> homebrew/science/galsim
==> Deleted Formulae
homebrew/binary/consul homebrew/science/coinutils homebrew/versions/allegro5
homebrew/binary/exercism homebrew/science/fast-statistical-alignment homebrew/versions/mapnik071
homebrew/binary/packer homebrew/science/z3 homebrew/versions/plowshare3