某大学内でサーバを建ててあれこれやっているが、外部からアクセスできるようには、なかなかさせてもらえないので、学外にサーバを建てることにした。
といっても、物理サーバを管理することもできないので、レンタルサーバでお茶を濁す。
とにかく料金が安く、sshでそこそこ自由度の高いvalue serverに白羽の矢を立て、早速お試し開始。
とにかくpython3が走らないとお話にならないのだが、一応いんすとーるされてはいるようだ。
でもpip3が使えなくてライブラリが入れられないので、pyenv-virtualenvを入れよう・・・なんかドツボにハマっていきそうな予感。
$ git clone https://github.com/yyuu/pyenv.git ~/.pyenv Initialized empty Git repository in /virtual/hoge/.pyenv/.git/ remote: Enumerating objects: 63, done. remote: Counting objects: 100% (63/63), done. remote: Compressing objects: 100% (37/37), done. remote: Total 16547 (delta 25), reused 46 (delta 20), pack-reused 16484 Receiving objects: 100% (16547/16547), 3.21 MiB | 2.81 MiB/s, done. Resolving deltas: 100% (11217/11217), done. $ echo 'export PYENV_ROOT="$HOME/.pyenv"' >> ~/.bashrc $ echo 'export PATH="$PYENV_ROOT/bin:$PATH"' >> ~/.bashrc $ echo 'eval "$(pyenv init -)"' >> ~/.bashrc $ source .bashrc $ pyenv --version pyenv 1.2.8-5-gec9fb54 $ pyenv install 3.6.1 Downloading Python-3.6.1.tar.xz... -> https://www.python.org/ftp/python/3.6.1/Python-3.6.1.tar.xz Installing Python-3.6.1... Installed Python-3.6.1 to /virtual/hoge/.pyenv/versions/3.6.1 $ pyenv global 3.6.1 $ pyenv rehash $ python Python 3.6.1 (default, Nov 26 2018, 19:58:29) [GCC 4.4.7 20120313 (Red Hat 4.4.7-18)] on linux Type "help", "copyright", "credits" or "license" for more information. >>>
ここまではまあなんとか。
virtualenvを入れよう。そのために今後のことも考えてhomebrewを入れちゃおう。
$ sh -c "$(curl -fsSL https://raw.githubusercontent.com/Linuxbrew/install/master/install.sh)"
==> Select the Linuxbrew installation directory
- Enter your password to install to /home/linuxbrew/.linuxbrew (recommended)
- Press Control-D to install to /virtual/hoge/.linuxbrew
- Press Control-C to cancel installation
Sorry, user hoge may not run sudo on s2.
==> This script will install:
......
......
- Run `brew help` to get started
- Further documentation:
https://docs.brew.sh
Warning: /virtual/hoge/.linuxbrew/bin is not in your PATH.なんとも不穏な終わり方。
とりあえず
$ test -d ~/.linuxbrew && PATH="$HOME/.linuxbrew/bin:$HOME/.linuxbrew/sbin:$PATH" $ test -d /home/linuxbrew/.linuxbrew && PATH="/home/linuxbrew/.linuxbrew/bin:/home/linuxbrew/.linuxbrew/sbin:$PATH" $ test -r ~/.bash_profile && echo "export PATH='$(brew --prefix)/bin:$(brew --prefix)/sbin'":'"$PATH"' >>~/.bash_profile $ echo "export PATH='$(brew --prefix)/bin:$(brew --prefix)/sbin'":'"$PATH"' >>~/.profile $ brew install hello ==> Installing dependencies for curl: patchelf, zlib, binutils, linux-headers, glibc, m4, gmp, mpfr, libmpc, isl@0.18, gcc, openssl and pkg-config ==> Installing curl dependency: patchelf ==> Downloading https://linuxbrew.bintray.com/bottles/patchelf-0.9_1.x86_64_linu Updating Homebrew... ######################################################################## 100.0% ==> Pouring patchelf-0.9_1.x86_64_linux.bottle.tar.gz Warning: The post-install step did not complete successfully You can try again using `brew postinstall patchelf` ==> Summary 🍺 /virtual/hoge/.linuxbrew/Cellar/patchelf/0.9_1: 6 files, 1.2MB ==> Installing curl dependency: zlib ==> Downloading https://linuxbrew.bintray.com/bottles/zlib-1.2.11.x86_64_linux.b ######################################################################## 100.0% ==> Pouring zlib-1.2.11.x86_64_linux.bottle.tar.gz Warning: The post-install step did not complete successfully You can try again using `brew postinstall zlib` ==> Summary 🍺 /virtual/hoge/.linuxbrew/Cellar/zlib/1.2.11: 12 files, 423.5KB ==> Installing curl dependency: binutils ==> Downloading https://linuxbrew.bintray.com/bottles/binutils-2.31.1_2.x86_64_l ######################################################################## 100.0% ==> Pouring binutils-2.31.1_2.x86_64_linux.bottle.tar.gz Warning: The post-install step did not complete successfully You can try again using `brew postinstall binutils` ==> Summary 🍺 /virtual/hoge/.linuxbrew/Cellar/binutils/2.31.1_2: 4,638 files, 294MB ==> Installing curl dependency: linux-headers ==> Downloading https://linuxbrew.bintray.com/bottles/linux-headers-4.4.80.x86_6 ######################################################################## 100.0% ==> Pouring linux-headers-4.4.80.x86_64_linux.bottle.tar.gz Warning: The post-install step did not complete successfully You can try again using `brew postinstall linux-headers` ==> Summary 🍺 /virtual/hoge/.linuxbrew/Cellar/linux-headers/4.4.80: 772 files, 3.7MB ==> Installing curl dependency: glibc ==> Downloading https://ftp.gnu.org/gnu/glibc/glibc-2.23.tar.gz ######################################################################## 100.0% ==> ../configure --disable-debug --disable-dependency-tracking --disable-silent- Last 15 lines from /virtual/hoge/.cache/Homebrew/Logs/glibc/01.configure: checking version of gmake... 3.81, ok checking for gnumsgfmt... no checking for gmsgfmt... no checking for msgfmt... msgfmt checking version of msgfmt... 0.17, ok checking for makeinfo... no checking for sed... sed checking version of sed... 4.2.1, ok checking for gawk... gawk checking version of gawk... 3.1.7, ok checking if gcc -B/virtual/hoge/.linuxbrew/opt/binutils/bin/ is sufficient to build libc... no checking for nm... nm configure: error: *** These critical programs are missing or too old: compiler *** Check the INSTALL file for required versions. Error: parent directory is world writable but not sticky Please report this bug: https://github.com/Linuxbrew/brew/wiki/troubleshooting /usr/local/rvm/rubies/ruby-2.3.7/lib/ruby/2.3.0/tmpdir.rb:93:in `ensure in mktmpdir' /usr/local/rvm/rubies/ruby-2.3.7/lib/ruby/2.3.0/tmpdir.rb:95:in `mktmpdir' /virtual/hoge/.linuxbrew/Homebrew/Library/Homebrew/utils/fork.rb:28:in `safe_fork' /virtual/hoge/.linuxbrew/Homebrew/Library/Homebrew/formula_installer.rb:744:in `build' /virtual/hoge/.linuxbrew/Homebrew/Library/Homebrew/formula_installer.rb:318:in `install' /virtual/hoge/.linuxbrew/Homebrew/Library/Homebrew/formula_installer.rb:595:in `install_dependency' /virtual/hoge/.linuxbrew/Homebrew/Library/Homebrew/formula_installer.rb:549:in `block in install_dependencies' /virtual/hoge/.linuxbrew/Homebrew/Library/Homebrew/formula_installer.rb:549:in `each' /virtual/hoge/.linuxbrew/Homebrew/Library/Homebrew/formula_installer.rb:549:in `install_dependencies' /virtual/hoge/.linuxbrew/Homebrew/Library/Homebrew/formula_installer.rb:256:in `install' /virtual/hoge/.linuxbrew/Homebrew/Library/Homebrew/cmd/install.rb:329:in `install_formula' /virtual/hoge/.linuxbrew/Homebrew/Library/Homebrew/cmd/install.rb:259:in `block in install' /virtual/hoge/.linuxbrew/Homebrew/Library/Homebrew/cmd/install.rb:257:in `each' /virtual/hoge/.linuxbrew/Homebrew/Library/Homebrew/cmd/install.rb:257:in `install' /virtual/hoge/.linuxbrew/Homebrew/Library/Homebrew/brew.rb:89:in `<main>' 以下繰り返し・・・
きたきた。
Error: parent directory is world writable but not sticky
ってなんなんよ。
どうやらインストールに使うtmpディレクトリに -t属性をつけとけってことらしいのだが、
$ sudo chmod +t /private/tmp
というような処置をしろという記述はあちらこちらで見かけるがsudoできんし。
$ brew doctor
というコマンドで調べると
Warning: /export/tmp is world-writable but does not have the sticky bit set. Please execute `sudo chmod +t /export/tmp` in your Terminal. If you don't have administrative privileges on this machine, create a directory and set the HOMEBREW_TEMP environment variable, for example: install -d -m 1755 ~/tmp echo 'export HOMEBREW_TEMP=~/tmp' >> ~/.bash_profile
と出ている。これやっとけばいいのか。
$ install -d -m 1755 ~/tmp $ echo 'export HOMEBREW_TEMP=~/tmp' >> ~/.bash_profile $ source .bash_profile
こうすると、今度は
$ brew install hello ==> Installing dependencies for curl: glibc, m4, gmp, mpfr, libmpc, isl@0.18, gcc, openssl and pkg-config ==> Installing curl dependency: glibc ==> Downloading https://ftp.gnu.org/gnu/glibc/glibc-2.23.tar.gz Already downloaded: /virtual/hoge/.cache/Homebrew/downloads/3c17421daad583cfd4fad587b8e1260f19385344f309d7ae11e0c2bb6b75d801--glibc-2.23.tar.gz Updating Homebrew... ==> ../configure --disable-debug --disable-dependency-tracking --disable-silent-rules --prefix=/virtual/hoge/.linuxbrew/Cellar/ Last 15 lines from /virtual/hoge/.cache/Homebrew/Logs/glibc/01.configure: checking version of gmake... 3.81, ok checking for gnumsgfmt... no checking for gmsgfmt... no checking for msgfmt... msgfmt checking version of msgfmt... 0.17, ok checking for makeinfo... no checking for sed... sed checking version of sed... 4.2.1, ok checking for gawk... gawk checking version of gawk... 3.1.7, ok checking if gcc -B/virtual/hoge/.linuxbrew/opt/binutils/bin/ is sufficient to build libc... no checking for nm... nm configure: error: *** These critical programs are missing or too old: compiler *** Check the INSTALL file for required versions.
gccが古いぞゴルァ。
開発環境 - Heavy Watal
まずglibc抜きでgccを入れてそのgccでglibcをコンパイルなんだと。
$ HOMEBREW_BUILD_FROM_SOURCE=1 brew install gcc --without-glibc
==> Installing dependencies for curl: openssl and pkg-config
==> Installing curl dependency: openssl
==> Downloading https://www.openssl.org/source/openssl-1.0.2p.tar.gz
Already downloaded: /virtual/hoge/.cache/Homebrew/downloads/6d2f0aa30538560efe2aae756229a9ced40e636a70083696fb1bceb6c1a7564c--openssl-1.0.2p.tar.gz
==> perl ./Configure --prefix=/virtual/hoge/.linuxbrew/Cellar/openssl/1.0.2p --openssldir=/virtual/hoge/.linuxbrew/etc/ope
Updating Homebrew...
==> make depend
==> make
==> make test
==> make install MANDIR=/virtual/hoge/.linuxbrew/Cellar/openssl/1.0.2p/share/man MANSUFFIX=ssl
==> 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
/virtual/hoge/.linuxbrew/etc/openssl/certs
and run
/virtual/hoge/.linuxbrew/opt/openssl/bin/c_rehash
==> Summary
🍺 /virtual/hoge/.linuxbrew/Cellar/openssl/1.0.2p: 1,792 files, 14.1MB, built in 5 minutes 34 seconds
==> Installing curl dependency: pkg-config
==> Downloading https://pkgconfig.freedesktop.org/releases/pkg-config-0.29.2.tar.gz
Already downloaded: /virtual/hoge/.cache/Homebrew/downloads/5bdbf3b3fdadaf72744884b98b74a2ff887bd63a20b246f811a222a146ad7b64--pkg-config-0.29.2.tar.gz
==> ./configure --prefix=/virtual/hoge/.linuxbrew/Cellar/pkg-config/0.29.2_1 --disable-host-tool --with-internal-glib --with-pc
==> make
==> make check
==> make install
🍺 /virtual/hoge/.linuxbrew/Cellar/pkg-config/0.29.2_1: 11 files, 727.0KB, built in 58 seconds
==> Installing curl
==> Downloading https://curl.haxx.se/download/curl-7.62.0.tar.bz2
######################################################################## 100.0%
==> ./configure --disable-silent-rules --prefix=/virtual/hoge/.linuxbrew/Cellar/curl/7.62.0 --with-ssl=/virtual/hoge/.linu
==> make install
🍺 /virtual/hoge/.linuxbrew/Cellar/curl/7.62.0: 445 files, 3.6MB, built in 1 minute 16 seconds
==> Caveats
==> openssl
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
/virtual/hoge/.linuxbrew/etc/openssl/certs
and run
/virtual/hoge/.linuxbrew/opt/openssl/bin/c_rehash
==> Installing dependencies for git: gpatch, ncurses, gettext, bzip2, pcre2, libbsd and expat
==> Installing git dependency: gpatch
==> Downloading https://ftp.gnu.org/gnu/patch/patch-2.7.6.tar.xz
######################################################################## 100.0%
==> ./configure --prefix=/virtual/hoge/.linuxbrew/Cellar/gpatch/2.7.6
==> make install
🍺 /virtual/hoge/.linuxbrew/Cellar/gpatch/2.7.6: 10 files, 373.5KB, built in 1 minute 7 seconds
==> Installing git dependency: ncurses
==> Downloading https://ftp.gnu.org/gnu/ncurses/ncurses-6.1.tar.gz
######################################################################## 100.0%
==> ./configure --prefix=/virtual/hoge/.linuxbrew/Cellar/ncurses/6.1 --enable-pc-files --with-pkg-config-libdir=/virtual/notagu
==> make install
🍺 /virtual/hoge/.linuxbrew/Cellar/ncurses/6.1: 3,878 files, 9MB, built in 1 minute 2 seconds
==> Installing git dependency: gettext
==> Downloading https://ftp.gnu.org/gnu/gettext/gettext-0.19.8.1.tar.xz
######################################################################## 100.0%
==> Downloading http://xmlsoft.org/sources/libxml2-2.9.7.tar.gz
######################################################################## 100.0%
==> ./configure --prefix=/virtual/hoge/.linuxbrew/Cellar/gettext/0.19.8.1_1/libexec --without-python --without-lzma
==> make install
==> ./configure --disable-silent-rules --prefix=/virtual/hoge/.linuxbrew/Cellar/gettext/0.19.8.1_1 --with-included-glib --with
==> make
==> make install
==> Caveats
Emacs Lisp files have been installed to:
/virtual/hoge/.linuxbrew/share/emacs/site-lisp/gettext
==> Summary
🍺 /virtual/hoge/.linuxbrew/Cellar/gettext/0.19.8.1_1: 2,204 files, 28.9MB, built in 4 minutes 55 seconds
==> Installing git dependency: bzip2
==> Downloading https://ftp.osuosl.org/pub/clfs/conglomeration/bzip2/bzip2-1.0.6.tar.gz
######################################################################## 100.0%
==> make install PREFIX=/virtual/hoge/.linuxbrew/Cellar/bzip2/1.0.6_1
==> make -f Makefile-libbz2_so clean
==> make -f Makefile-libbz2_so
🍺 /virtual/hoge/.linuxbrew/Cellar/bzip2/1.0.6_1: 30 files, 551.5KB, built in 8 seconds
==> Installing git dependency: pcre2
==> Downloading https://ftp.pcre.org/pub/pcre/pcre2-10.32.tar.bz2
######################################################################## 100.0%
==> ./configure --prefix=/virtual/hoge/.linuxbrew/Cellar/pcre2/10.32 --enable-pcre2-16 --enable-pcre2-32 --enable-pcre2grep-lib
==> make
==> make install
🍺 /virtual/hoge/.linuxbrew/Cellar/pcre2/10.32: 228 files, 6.1MB, built in 31 seconds
==> Installing git dependency: libbsd
==> Downloading https://libbsd.freedesktop.org/releases/libbsd-0.8.3.tar.xz
######################################################################## 100.0%
==> ./configure --disable-silent-rules --prefix=/virtual/hoge/.linuxbrew/Cellar/libbsd/0.8.3
==> make install
Last 15 lines from /virtual/hoge/.cache/Homebrew/Logs/libbsd/02.make:
make[1]: *** [nlist.lo] Error 1
make[1]: *** [pidfile.lo] Error 1
make[1]: *** [progname.lo] Error 1
In file included from ../include/bsd/libutil.h:46,
from ../include/bsd/stdlib.h:37,
from radixsort.c:57:
../include/bsd/stdio.h:52: error: wrong number of arguments specified for ‘deprecated’ attribute
In file included from ../include/bsd/libutil.h:46,
from ../include/bsd/stdlib.h:37,
from reallocf.c:30:
../include/bsd/stdio.h:52: error: wrong number of arguments specified for ‘deprecated’ attribute
make[1]: *** [radixsort.lo] Error 1
make[1]: *** [reallocf.lo] Error 1
make[1]: Leaving directory `/virtual/hoge/tmp/libbsd-20181126-45023-81u4p4/libbsd-0.8.3/src'
make: *** [install-recursive] Error 1
READ THIS: https://github.com/Linuxbrew/brew/wiki/troubleshooting
Please do not report this issue to Homebrew/brew or Homebrew/core,
which support macOS only."
Initialized empty Git repository in /virtual/hoge/.linuxbrew/Homebrew/.git/
usage: git ls-remote [--heads] [--tags] [-u <exec> | --upload-pack <exec>] <repository> <refs>...
error: unknown option `shallow-since='
usage: git fetch [<options>] [<repository> [<refspec>...]]
or: git fetch [<options>] <group>
or: git fetch --multiple [<options>] [<repository> | <group>]...
or: git fetch --all [<options>]
-v, --verbose be more verbose
-q, --quiet be more quiet
--all fetch from all remotes
-a, --append append to .git/FETCH_HEAD instead of overwriting
--upload-pack <PATH> path to upload pack on remote end
-f, --force force overwrite of local branch
-m, --multiple fetch from multiple remotes
-t, --tags fetch all tags and associated objects
-n do not fetch all tags (--no-tags)
-p, --prune prune tracking branches no longer on remote
--dry-run dry run
-k, --keep keep downloaded pack
-u, --update-head-ok allow updating of HEAD ref
--progress force progress reporting
--depth <DEPTH> deepen history of shallow clone
==> Installing dependencies for gcc: m4, gmp, mpfr, libmpc and isl@0.18
==> Installing gcc dependency: m4
==> Downloading https://ftp.gnu.org/gnu/m4/m4-1.4.18.tar.xz
Already downloaded: /virtual/hoge/.cache/Homebrew/downloads/bb74c92bda9bdc32be0653ca50751920ff35cfe8f329499d0bea86fbe66ce580--m4-1.4.18.tar.xz
==> ./configure --prefix=/virtual/hoge/.linuxbrew/Cellar/m4/1.4.18
==> make
==> make install
🍺 /virtual/hoge/.linuxbrew/Cellar/m4/1.4.18: 13 files, 633.6KB, built in 1 minute
==> Installing gcc dependency: gmp
==> Downloading https://gmplib.org/download/gmp/gmp-6.1.2.tar.xz
######################################################################## 100.0%
==> ./configure --prefix=/virtual/hoge/.linuxbrew/Cellar/gmp/6.1.2_2 --enable-cxx --with-pic
==> make
==> make check
==> make install
🍺 /virtual/hoge/.linuxbrew/Cellar/gmp/6.1.2_2: 20 files, 3.7MB, built in 2 minutes 3 seconds
==> Installing gcc dependency: mpfr
==> Downloading https://ftp.gnu.org/gnu/mpfr/mpfr-4.0.1.tar.xz
######################################################################## 100.0%
==> ./configure --prefix=/virtual/hoge/.linuxbrew/Cellar/mpfr/4.0.1 --disable-silent-rules
==> make
==> make check
==> make install
🍺 /virtual/hoge/.linuxbrew/Cellar/mpfr/4.0.1: 29 files, 5MB, built in 50 seconds
==> Installing gcc dependency: libmpc
==> Downloading https://ftp.gnu.org/gnu/mpc/mpc-1.1.0.tar.gz
######################################################################## 100.0%
==> ./configure --prefix=/virtual/hoge/.linuxbrew/Cellar/libmpc/1.1.0 --with-gmp=/virtual/hoge/.linuxbrew/opt/gmp --with-m
==> make
==> make check
==> make install
🍺 /virtual/hoge/.linuxbrew/Cellar/libmpc/1.1.0: 13 files, 489.3KB, built in 26 seconds
==> Installing gcc dependency: isl@0.18
==> Downloading http://isl.gforge.inria.fr/isl-0.18.tar.xz
######################################################################## 100.0%
==> ./configure --disable-silent-rules --prefix=/virtual/hoge/.linuxbrew/Cellar/isl@0.18/0.18 --with-gmp=system --with-gmp-pref
==> make check
==> make install
==> Caveats
isl@0.18 is keg-only, which means it was not symlinked into /virtual/hoge/.linuxbrew,
because this is an alternate version of another formula.
For compilers to find isl@0.18 you may need to set:
export LDFLAGS="-L/virtual/hoge/.linuxbrew/opt/isl@0.18/lib"
export CPPFLAGS="-I/virtual/hoge/.linuxbrew/opt/isl@0.18/include"
For pkg-config to find isl@0.18 you may need to set:
export PKG_CONFIG_PATH="/virtual/hoge/.linuxbrew/opt/isl@0.18/lib/pkgconfig"
==> Summary
🍺 /virtual/hoge/.linuxbrew/Cellar/isl@0.18/0.18: 81 files, 5.1MB, built in 59 seconds
==> Installing gcc --without-glibc
==> Downloading https://ftp.gnu.org/gnu/gcc/gcc-5.5.0/gcc-5.5.0.tar.xz
######################################################################## 100.0%
==> ../configure --with-isl=/virtual/hoge/.linuxbrew/opt/isl@0.18 --with-bugurl=https://github.com/Linuxbrew/homebrew-core/issu
==> make
==> make install-strip
==> Creating the GCC specs file: /virtual/hoge/.linuxbrew/Cellar/gcc/5.5.0_4/lib/gcc/x86_64-unknown-linux-gnu/5.5.0/specs
🍺 /virtual/hoge/.linuxbrew/Cellar/gcc/5.5.0_4: 1,352 files, 167.5MB, built in 18 minutes 18 seconds
==> Caveats
==> isl@0.18
isl@0.18 is keg-only, which means it was not symlinked into /virtual/hoge/.linuxbrew,
because this is an alternate version of another formula.
For compilers to find isl@0.18 you may need to set:
export LDFLAGS="-L/virtual/hoge/.linuxbrew/opt/isl@0.18/lib"
export CPPFLAGS="-I/virtual/hoge/.linuxbrew/opt/isl@0.18/include"
For pkg-config to find isl@0.18 you may need to set:
export PKG_CONFIG_PATH="/virtual/hoge/.linuxbrew/opt/isl@0.18/lib/pkgconfig"まだなんかエラー出てるな。
ここでためにしなんかインストールしてみる。
$ brew install samtools
==> Downloading https://www.kernel.org/pub/software/scm/git/git-2.19.1.tar.xz
Already downloaded: /virtual/hoge/.cache/Homebrew/downloads/6d97b8dc5e65b0074703493a78fad9f1118ea2438a9112e32d3e727a5e52685a--git-2.19.1.tar.xz
Updating Homebrew...
==> make install prefix=/virtual/hoge/.linuxbrew/Cellar/git/2.19.1 sysconfdir=/virtual/hoge/.linuxbrew/etc CC=gcc-5 CFLAGS
Last 15 lines from /virtual/hoge/.cache/Homebrew/Logs/git/01.make:
gcc-5 -I. -DHAVE_SYSINFO -DGIT_HOST_CPU="\"x86_64\"" -DUSE_LIBPCRE2 -I/virtual/hoge/.linuxbrew/opt/pcre2/include -DHAVE_ALLOCA_H -DUSE_CURL_FOR_IMAP_SEND -I/virtual/hoge/.linuxbrew/opt/openssl/include -DSHA1_DC -DSHA1DC_NO_STANDARD_INCLUDES -DSHA1DC_INIT_SAFE_HASH_DEFAULT=0 -DSHA1DC_CUSTOM_INCLUDE_SHA1_C="\"cache.h\"" -DSHA1DC_CUSTOM_INCLUDE_UBC_CHECK_C="\"git-compat-util.h\"" -DHAVE_PATHS_H -DHAVE_DEV_TTY -DHAVE_CLOCK_GETTIME -DHAVE_CLOCK_MONOTONIC -DHAVE_GETDELIM '-DPROCFS_EXECUTABLE_PATH="/proc/self/exe"' -DFREAD_READS_DIRECTORIES -DNO_STRLCPY -DSHELL_PATH='"/bin/sh"' -DPAGER_ENV='"LESS=FRX LV=-c"' -o t/helper/test-fake-ssh t/helper/test-fake-ssh.o common-main.o libgit.a xdiff/lib.a libgit.a xdiff/lib.a -lpcre2-8 -L/virtual/hoge/.linuxbrew/opt/pcre2/lib -Wl,-rpath,/virtual/hoge/.linuxbrew/opt/pcre2/lib -lz -lpthread -lrt
gcc-5 -I. -DHAVE_SYSINFO -DGIT_HOST_CPU="\"x86_64\"" -DUSE_LIBPCRE2 -I/virtual/hoge/.linuxbrew/opt/pcre2/include -DHAVE_ALLOCA_H -DUSE_CURL_FOR_IMAP_SEND -I/virtual/hoge/.linuxbrew/opt/openssl/include -DSHA1_DC -DSHA1DC_NO_STANDARD_INCLUDES -DSHA1DC_INIT_SAFE_HASH_DEFAULT=0 -DSHA1DC_CUSTOM_INCLUDE_SHA1_C="\"cache.h\"" -DSHA1DC_CUSTOM_INCLUDE_UBC_CHECK_C="\"git-compat-util.h\"" -DHAVE_PATHS_H -DHAVE_DEV_TTY -DHAVE_CLOCK_GETTIME -DHAVE_CLOCK_MONOTONIC -DHAVE_GETDELIM '-DPROCFS_EXECUTABLE_PATH="/proc/self/exe"' -DFREAD_READS_DIRECTORIES -DNO_STRLCPY -DSHELL_PATH='"/bin/sh"' -DPAGER_ENV='"LESS=FRX LV=-c"' -o t/helper/test-line-buffer t/helper/test-line-buffer.o common-main.o libgit.a xdiff/lib.a vcs-svn/lib.a libgit.a xdiff/lib.a -lpcre2-8 -L/virtual/hoge/.linuxbrew/opt/pcre2/lib -Wl,-rpath,/virtual/hoge/.linuxbrew/opt/pcre2/lib -lz -lpthread -lrt
gcc-5 -I. -DHAVE_SYSINFO -DGIT_HOST_CPU="\"x86_64\"" -DUSE_LIBPCRE2 -I/virtual/hoge/.linuxbrew/opt/pcre2/include -DHAVE_ALLOCA_H -DUSE_CURL_FOR_IMAP_SEND -I/virtual/hoge/.linuxbrew/opt/openssl/include -DSHA1_DC -DSHA1DC_NO_STANDARD_INCLUDES -DSHA1DC_INIT_SAFE_HASH_DEFAULT=0 -DSHA1DC_CUSTOM_INCLUDE_SHA1_C="\"cache.h\"" -DSHA1DC_CUSTOM_INCLUDE_UBC_CHECK_C="\"git-compat-util.h\"" -DHAVE_PATHS_H -DHAVE_DEV_TTY -DHAVE_CLOCK_GETTIME -DHAVE_CLOCK_MONOTONIC -DHAVE_GETDELIM '-DPROCFS_EXECUTABLE_PATH="/proc/self/exe"' -DFREAD_READS_DIRECTORIES -DNO_STRLCPY -DSHELL_PATH='"/bin/sh"' -DPAGER_ENV='"LESS=FRX LV=-c"' -o t/helper/test-parse-options t/helper/test-parse-options.o common-main.o libgit.a xdiff/lib.a libgit.a xdiff/lib.a -lpcre2-8 -L/virtual/hoge/.linuxbrew/opt/pcre2/lib -Wl,-rpath,/virtual/hoge/.linuxbrew/opt/pcre2/lib -lz -lpthread -lrt
gcc-5 -I. -DHAVE_SYSINFO -DGIT_HOST_CPU="\"x86_64\"" -DUSE_LIBPCRE2 -I/virtual/hoge/.linuxbrew/opt/pcre2/include -DHAVE_ALLOCA_H -DUSE_CURL_FOR_IMAP_SEND -I/virtual/hoge/.linuxbrew/opt/openssl/include -DSHA1_DC -DSHA1DC_NO_STANDARD_INCLUDES -DSHA1DC_INIT_SAFE_HASH_DEFAULT=0 -DSHA1DC_CUSTOM_INCLUDE_SHA1_C="\"cache.h\"" -DSHA1DC_CUSTOM_INCLUDE_UBC_CHECK_C="\"git-compat-util.h\"" -DHAVE_PATHS_H -DHAVE_DEV_TTY -DHAVE_CLOCK_GETTIME -DHAVE_CLOCK_MONOTONIC -DHAVE_GETDELIM '-DPROCFS_EXECUTABLE_PATH="/proc/self/exe"' -DFREAD_READS_DIRECTORIES -DNO_STRLCPY -DSHELL_PATH='"/bin/sh"' -DPAGER_ENV='"LESS=FRX LV=-c"' -o t/helper/test-pkt-line t/helper/test-pkt-line.o common-main.o libgit.a xdiff/lib.a libgit.a xdiff/lib.a -lpcre2-8 -L/virtual/hoge/.linuxbrew/opt/pcre2/lib -Wl,-rpath,/virtual/hoge/.linuxbrew/opt/pcre2/lib -lz -lpthread -lrt
gcc-5 -I. -DHAVE_SYSINFO -DGIT_HOST_CPU="\"x86_64\"" -DUSE_LIBPCRE2 -I/virtual/hoge/.linuxbrew/opt/pcre2/include -DHAVE_ALLOCA_H -DUSE_CURL_FOR_IMAP_SEND -I/virtual/hoge/.linuxbrew/opt/openssl/include -DSHA1_DC -DSHA1DC_NO_STANDARD_INCLUDES -DSHA1DC_INIT_SAFE_HASH_DEFAULT=0 -DSHA1DC_CUSTOM_INCLUDE_SHA1_C="\"cache.h\"" -DSHA1DC_CUSTOM_INCLUDE_UBC_CHECK_C="\"git-compat-util.h\"" -DHAVE_PATHS_H -DHAVE_DEV_TTY -DHAVE_CLOCK_GETTIME -DHAVE_CLOCK_MONOTONIC -DHAVE_GETDELIM '-DPROCFS_EXECUTABLE_PATH="/proc/self/exe"' -DFREAD_READS_DIRECTORIES -DNO_STRLCPY -DSHELL_PATH='"/bin/sh"' -DPAGER_ENV='"LESS=FRX LV=-c"' -o t/helper/test-svn-fe t/helper/test-svn-fe.o common-main.o libgit.a xdiff/lib.a vcs-svn/lib.a libgit.a xdiff/lib.a -lpcre2-8 -L/virtual/hoge/.linuxbrew/opt/pcre2/lib -Wl,-rpath,/virtual/hoge/.linuxbrew/opt/pcre2/lib -lz -lpthread -lrt
gcc-5 -I. -DHAVE_SYSINFO -DGIT_HOST_CPU="\"x86_64\"" -DUSE_LIBPCRE2 -I/virtual/hoge/.linuxbrew/opt/pcre2/include -DHAVE_ALLOCA_H -DUSE_CURL_FOR_IMAP_SEND -I/virtual/hoge/.linuxbrew/opt/openssl/include -DSHA1_DC -DSHA1DC_NO_STANDARD_INCLUDES -DSHA1DC_INIT_SAFE_HASH_DEFAULT=0 -DSHA1DC_CUSTOM_INCLUDE_SHA1_C="\"cache.h\"" -DSHA1DC_CUSTOM_INCLUDE_UBC_CHECK_C="\"git-compat-util.h\"" -DHAVE_PATHS_H -DHAVE_DEV_TTY -DHAVE_CLOCK_GETTIME -DHAVE_CLOCK_MONOTONIC -DHAVE_GETDELIM '-DPROCFS_EXECUTABLE_PATH="/proc/self/exe"' -DFREAD_READS_DIRECTORIES -DNO_STRLCPY -DSHELL_PATH='"/bin/sh"' -DPAGER_ENV='"LESS=FRX LV=-c"' -o t/helper/test-tool t/helper/test-tool.o common-main.o t/helper/test-chmtime.o t/helper/test-config.o t/helper/test-ctype.o t/helper/test-date.o t/helper/test-delta.o t/helper/test-drop-caches.o t/helper/test-dump-cache-tree.o t/helper/test-dump-split-index.o t/helper/test-example-decorate.o t/helper/test-genrandom.o t/helper/test-hashmap.o t/helper/test-index-version.o t/helper/test-json-writer.o t/helper/test-lazy-init-name-hash.o t/helper/test-match-trees.o t/helper/test-mergesort.o t/helper/test-mktemp.o t/helper/test-online-cpus.o t/helper/test-path-utils.o t/helper/test-prio-queue.o t/helper/test-read-cache.o t/helper/test-ref-store.o t/helper/test-regex.o t/helper/test-repository.o t/helper/test-revision-walking.o t/helper/test-run-command.o t/helper/test-scrap-cache-tree.o t/helper/test-sha1-array.o t/helper/test-sha1.o t/helper/test-sigchain.o t/helper/test-strcmp-offset.o t/helper/test-string-list.o t/helper/test-submodule-config.o t/helper/test-subprocess.o t/helper/test-urlmatch-normalization.o t/helper/test-wildmatch.o t/helper/test-write-cache.o libgit.a xdiff/lib.a libgit.a xdiff/lib.a -lpcre2-8 -L/virtual/hoge/.linuxbrew/opt/pcre2/lib -Wl,-rpath,/virtual/hoge/.linuxbrew/opt/pcre2/lib -lz -lpthread -lrt
/virtual/hoge/.linuxbrew/bin/ld: //virtual/hoge/.linuxbrew/lib/libbsd.so.0: undefined reference to `getauxval@GLIBC_2.16'
/virtual/hoge/.linuxbrew/bin/ld: /virtual/hoge/.linuxbrew/lib/libexpat.so: undefined reference to `memcpy@GLIBC_2.14'
collect2: error: ld returned 1 exit status
make: *** [git-http-push] Error 1
make: *** Waiting for unfinished jobs....
/virtual/hoge/.linuxbrew/bin/ld: //virtual/hoge/.linuxbrew/lib/libbsd.so.0: undefined reference to `getauxval@GLIBC_2.16'
/virtual/hoge/.linuxbrew/bin/ld: /virtual/hoge/.linuxbrew/lib/libexpat.so: undefined reference to `memcpy@GLIBC_2.14'
collect2: error: ld returned 1 exit status
make: *** [git-remote-http] Error 1
READ THIS: https://github.com/Linuxbrew/brew/wiki/troubleshooting
Please do not report this issue to Homebrew/brew or Homebrew/core,
which support macOS only."
These open issues may also help:
git: add caveat explaining Net::SMTP::SSL module https://github.com/Homebrew/homebrew-core/pull/33557
Initialized empty Git repository in /virtual/hoge/.linuxbrew/Homebrew/.git/
usage: git ls-remote [--heads] [--tags] [-u <exec> | --upload-pack <exec>] <repository> <refs>...
error: unknown option `shallow-since='
usage: git fetch [<options>] [<repository> [<refspec>...]]
or: git fetch [<options>] <group>
or: git fetch --multiple [<options>] [<repository> | <group>]...
or: git fetch --all [<options>]
-v, --verbose be more verbose
-q, --quiet be more quiet
--all fetch from all remotes
-a, --append append to .git/FETCH_HEAD instead of overwriting
--upload-pack <PATH> path to upload pack on remote end
-f, --force force overwrite of local branch
-m, --multiple fetch from multiple remotes
-t, --tags fetch all tags and associated objects
-n do not fetch all tags (--no-tags)
-p, --prune prune tracking branches no longer on remote
--dry-run dry run
-k, --keep keep downloaded pack
-u, --update-head-ok allow updating of HEAD ref
--progress force progress reporting
--depth <DEPTH> deepen history of shallow clone
==> Installing dependencies for samtools: xz and htslib
==> Installing samtools dependency: xz
==> Downloading https://linuxbrew.bintray.com/bottles/xz-5.2.4.x86_64_linux.bottle.tar.gz
######################################################################## 100.0%
==> Pouring xz-5.2.4.x86_64_linux.bottle.tar.gz
🍺 /virtual/hoge/.linuxbrew/Cellar/xz/5.2.4: 99 files, 3.3MB
==> Installing samtools dependency: htslib
==> Downloading https://linuxbrew.bintray.com/bottles/htslib-1.9.x86_64_linux.bottle.tar.gz
######################################################################## 100.0%
==> Pouring htslib-1.9.x86_64_linux.bottle.tar.gz
🍺 /virtual/hoge/.linuxbrew/Cellar/htslib/1.9: 163 files, 21.2MB
==> Installing samtools
==> Downloading https://linuxbrew.bintray.com/bottles/samtools-1.9.x86_64_linux.bottle.tar.gz
######################################################################## 100.0%
==> Pouring samtools-1.9.x86_64_linux.bottle.tar.gz
🍺 /virtual/hoge/.linuxbrew/Cellar/samtools/1.9: 29 files, 837.5KB
[hoge@s2 ~]$ samtools
samtools: /lib64/libm.so.6: version `GLIBC_2.23' not found (required by /virtual/hoge/.linuxbrew/lib/libhts.so.2)
samtools: /lib64/libc.so.6: version `GLIBC_2.15' not found (required by /virtual/hoge/.linuxbrew/lib/libhts.so.2)
samtools: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /virtual/hoge/.linuxbrew/lib/libhts.so.2)
samtools: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by /virtual/hoge/.linuxbrew/lib/liblzma.so.5)
samtools: /lib64/libc.so.6: version `GLIBC_2.17' not found (required by /virtual/hoge/.linuxbrew/lib/liblzma.so.5)なんかインストールはできたがやはりGLIBC_2.23が無いと言って走らない。
$ brew install glibc
==> Downloading https://www.kernel.org/pub/software/scm/git/git-2.19.1.tar.xz
Already downloaded: /virtual/hoge/.cache/Homebrew/downloads/6d97b8dc5e65b0074703493a78fad9f1118ea2438a9112e32d3e727a5e52685a--git-2.19.1.tar.xz
Updating Homebrew...
==> make install prefix=/virtual/hoge/.linuxbrew/Cellar/git/2.19.1 sysconfdir=/virtual/hoge/.linuxbrew/etc CC=gcc-5 CFLAGS
Last 15 lines from /virtual/hoge/.cache/Homebrew/Logs/git/01.make:
ln -s git git-bisect--helper 2>/dev/null || \
cp git git-bisect--helper
/virtualrm -f git-blame && \
ln git git-blame 2>/dev/null || \
ln -s git git-blame 2>/dev/null || \
/ cp git git-blame
hoge/.linuxbrew/bin/ld: //virtual/hoge/.linuxbrew/lib/libbsd.so.0: undefined reference to `getauxval@GLIBC_2.16'
/virtual/hoge/.linuxbrew/bin/ld: /virtual/hoge/.linuxbrew/lib/libexpat.so: undefined reference to `memcpy@GLIBC_2.14'
collect2: error: ld returned 1 exit status
/virtual/hoge/.linuxbrew/bin/ld: //virtual/hoge/.linuxbrew/lib/libbsd.so.0: undefined reference to `getauxval@GLIBC_2.16'
/virtual/hoge/.linuxbrew/bin/ld: /virtual/hoge/.linuxbrew/lib/libexpat.so: undefined reference to `memcpy@GLIBC_2.14'
collect2: error: ld returned 1 exit status
make: *** [git-http-push] Error 1
make: *** Waiting for unfinished jobs....
make: *** [git-remote-http] Error 1
READ THIS: https://github.com/Linuxbrew/brew/wiki/troubleshooting
Please do not report this issue to Homebrew/brew or Homebrew/core,
which support macOS only."
These open issues may also help:
git: add caveat explaining Net::SMTP::SSL module https://github.com/Homebrew/homebrew-core/pull/33557
Initialized empty Git repository in /virtual/hoge/.linuxbrew/Homebrew/.git/
usage: git ls-remote [--heads] [--tags] [-u <exec> | --upload-pack <exec>] <repository> <refs>...
error: unknown option `shallow-since='
usage: git fetch [<options>] [<repository> [<refspec>...]]
or: git fetch [<options>] <group>
or: git fetch --multiple [<options>] [<repository> | <group>]...
or: git fetch --all [<options>]
-v, --verbose be more verbose
-q, --quiet be more quiet
--all fetch from all remotes
-a, --append append to .git/FETCH_HEAD instead of overwriting
--upload-pack <PATH> path to upload pack on remote end
-f, --force force overwrite of local branch
-m, --multiple fetch from multiple remotes
-t, --tags fetch all tags and associated objects
-n do not fetch all tags (--no-tags)
-p, --prune prune tracking branches no longer on remote
--dry-run dry run
-k, --keep keep downloaded pack
-u, --update-head-ok allow updating of HEAD ref
--progress force progress reporting
--depth <DEPTH> deepen history of shallow clone
==> Downloading https://ftp.gnu.org/gnu/glibc/glibc-2.23.tar.gz
Already downloaded: /virtual/hoge/.cache/Homebrew/downloads/3c17421daad583cfd4fad587b8e1260f19385344f309d7ae11e0c2bb6b75d801--glibc-2.23.tar.gz
==> ../configure --disable-debug --disable-dependency-tracking --disable-silent-rules --prefix=/virtual/hoge/.linuxbrew/Cellar/
==> make
==> make install
==> Installing locale data for en_US.UTF-8
==> /virtual/hoge/.linuxbrew/Cellar/glibc/2.23/bin/localedef -i en_US -f UTF-8 en_US.UTF-8
🍺 /virtual/hoge/.linuxbrew/Cellar/glibc/2.23: 1,405 files, 42.2MB, built in 4 minutes 48 secondsglibcをインストールするのにglibcがないと言われてもなあ。
しかし、これでglibcは更新できたようで
$ samtools
Program: samtools (Tools for alignments in the SAM format)
Version: 1.9 (using htslib 1.9)
Usage: samtools <command> [options]
Commands:
-- Indexing
dict create a sequence dictionary file
faidx index/extract FASTA
fqidx index/extract FASTQ
index index alignment
-- Editing
calmd recalculate MD/NM tags and '=' bases
fixmate fix mate information
reheader replace BAM header
targetcut cut fosmid regions (for fosmid pool only)
addreplacerg adds or replaces RG tags
markdup mark duplicates
-- File operations
collate shuffle and group alignments by name
cat concatenate BAMs
merge merge sorted alignments
mpileup multi-way pileup
sort sort alignment file
split splits a file by read group
quickcheck quickly check if SAM/BAM/CRAM file appears intact
fastq converts a BAM to a FASTQ
fasta converts a BAM to a FASTA
-- Statistics
bedcov read depth per BED region
depth compute the depth
flagstat simple stats
idxstats BAM index stats
phase phase heterozygotes
stats generate stats (former bamcheck)
-- Viewing
flags explain BAM flags
tview text alignment viewer
view SAM<->BAM<->CRAM conversion
depad convert padded BAM to unpadded BAMちゃんと走るようになった。
さて、gccもバージョンを上げておくか。
$ brew remove gcc Uninstalling /virtual/hoge/.linuxbrew/Cellar/gcc/5.5.0_4... (1,352 files, 167.5MB) $ brew install gcc ==> Installing dependencies for git: gcc ==> Installing git dependency: gcc ==> Downloading https://linuxbrew.bintray.com/bottles/gcc-5.5.0_4.x86_64_linux.bottle.2.tar.gz Updating Homebrew... ######################################################################## 100.0% ==> Pouring gcc-5.5.0_4.x86_64_linux.bottle.2.tar.gz ==> Creating the GCC specs file: /virtual/hoge/.linuxbrew/Cellar/gcc/5.5.0_4/bin/../lib/gcc/x86_64-unknown-linux-gnu/5.5.0/spec 🍺 /virtual/hoge/.linuxbrew/Cellar/gcc/5.5.0_4: 1,361 files, 169.8MB ==> Installing git ==> Downloading https://www.kernel.org/pub/software/scm/git/git-2.19.1.tar.xz Already downloaded: /virtual/hoge/.cache/Homebrew/downloads/6d97b8dc5e65b0074703493a78fad9f1118ea2438a9112e32d3e727a5e52685a--git-2.19.1.tar.xz ==> make install prefix=/virtual/hoge/.linuxbrew/Cellar/git/2.19.1 sysconfdir=/virtual/hoge/.linuxbrew/etc CC=gcc-5 CFLAGS ==> make ==> make test ==> make CC=gcc-5 CFLAGS= LDFLAGS= ==> Downloading https://www.kernel.org/pub/software/scm/git/git-manpages-2.19.1.tar.xz ==> Downloading from https://mirrors.edge.kernel.org/pub/software/scm/git/git-manpages-2.19.1.tar.xz ######################################################################## 100.0% ==> Downloading https://www.kernel.org/pub/software/scm/git/git-htmldocs-2.19.1.tar.xz ==> Downloading from https://mirrors.edge.kernel.org/pub/software/scm/git/git-htmldocs-2.19.1.tar.xz ######################################################################## 100.0% ==> Caveats Bash completion has been installed to: /virtual/hoge/.linuxbrew/etc/bash_completion.d Emacs Lisp files have been installed to: /virtual/hoge/.linuxbrew/share/emacs/site-lisp/git ==> Summary 🍺 /virtual/hoge/.linuxbrew/Cellar/git/2.19.1: 1,439 files, 42.8MB, built in 35 seconds ==> Caveats ==> git Bash completion has been installed to: /virtual/hoge/.linuxbrew/etc/bash_completion.d Emacs Lisp files have been installed to: /virtual/hoge/.linuxbrew/share/emacs/site-lisp/git Initialized empty Git repository in /virtual/hoge/.linuxbrew/Homebrew/.git/ remote: Enumerating objects: 233, done. remote: Counting objects: 100% (233/233), done. remote: Compressing objects: 100% (152/152), done. remote: Total 125562 (delta 149), reused 115 (delta 78), pack-reused 125329 Receiving objects: 100% (125562/125562), 28.79 MiB | 15.12 MiB/s, done. Resolving deltas: 100% (92006/92006), done. From https://github.com/Linuxbrew/brew * [new branch] gh-pages -> origin/gh-pages * [new branch] master -> origin/master remote: Total 0 (delta 0), reused 0 (delta 0), pack-reused 0 * [new tag] 1.0.0 -> 1.0.0 * [new tag] 1.0.1 -> 1.0.1 * [new tag] 1.0.2 -> 1.0.2 * [new tag] 1.0.3 -> 1.0.3 * [new tag] 1.0.4 -> 1.0.4 * [new tag] 1.0.5 -> 1.0.5 * [new tag] 1.0.6 -> 1.0.6 * [new tag] 1.0.7 -> 1.0.7 * [new tag] 1.0.8 -> 1.0.8 * [new tag] 1.0.9 -> 1.0.9 * [new tag] 1.1.0 -> 1.1.0 * [new tag] 1.1.0.1 -> 1.1.0.1 * [new tag] 1.1.1 -> 1.1.1 * [new tag] 1.1.10 -> 1.1.10 * [new tag] 1.1.11 -> 1.1.11 * [new tag] 1.1.12 -> 1.1.12 * [new tag] 1.1.13 -> 1.1.13 * [new tag] 1.1.2 -> 1.1.2 * [new tag] 1.1.2.1 -> 1.1.2.1 * [new tag] 1.1.3 -> 1.1.3 * [new tag] 1.1.4 -> 1.1.4 * [new tag] 1.1.5 -> 1.1.5 * [new tag] 1.1.6 -> 1.1.6 * [new tag] 1.1.7 -> 1.1.7 * [new tag] 1.1.8 -> 1.1.8 * [new tag] 1.1.9 -> 1.1.9 * [new tag] 1.2.0 -> 1.2.0 * [new tag] 1.2.1 -> 1.2.1 * [new tag] 1.2.2 -> 1.2.2 * [new tag] 1.2.3 -> 1.2.3 * [new tag] 1.2.4 -> 1.2.4 * [new tag] 1.2.5 -> 1.2.5 * [new tag] 1.2.6 -> 1.2.6 * [new tag] 1.2.7 -> 1.2.7 * [new tag] 1.2.8 -> 1.2.8 * [new tag] 1.3.0 -> 1.3.0 * [new tag] 1.3.1 -> 1.3.1 * [new tag] 1.3.2 -> 1.3.2 * [new tag] 1.3.3 -> 1.3.3 * [new tag] 1.3.4 -> 1.3.4 * [new tag] 1.3.5 -> 1.3.5 * [new tag] 1.3.6 -> 1.3.6 * [new tag] 1.3.7 -> 1.3.7 * [new tag] 1.3.8 -> 1.3.8 * [new tag] 1.3.9 -> 1.3.9 * [new tag] 1.4.0 -> 1.4.0 * [new tag] 1.4.1 -> 1.4.1 * [new tag] 1.4.2 -> 1.4.2 * [new tag] 1.4.3 -> 1.4.3 * [new tag] 1.5.0 -> 1.5.0 * [new tag] 1.5.1 -> 1.5.1 * [new tag] 1.5.10 -> 1.5.10 * [new tag] 1.5.11 -> 1.5.11 * [new tag] 1.5.12 -> 1.5.12 * [new tag] 1.5.13 -> 1.5.13 * [new tag] 1.5.14 -> 1.5.14 * [new tag] 1.5.2 -> 1.5.2 * [new tag] 1.5.3 -> 1.5.3 * [new tag] 1.5.4 -> 1.5.4 * [new tag] 1.5.5 -> 1.5.5 * [new tag] 1.5.6 -> 1.5.6 * [new tag] 1.5.7 -> 1.5.7 * [new tag] 1.5.8 -> 1.5.8 * [new tag] 1.5.9 -> 1.5.9 * [new tag] 1.6.0 -> 1.6.0 * [new tag] 1.6.1 -> 1.6.1 * [new tag] 1.6.10 -> 1.6.10 * [new tag] 1.6.11 -> 1.6.11 * [new tag] 1.6.12 -> 1.6.12 * [new tag] 1.6.13 -> 1.6.13 * [new tag] 1.6.14 -> 1.6.14 * [new tag] 1.6.15 -> 1.6.15 * [new tag] 1.6.16 -> 1.6.16 * [new tag] 1.6.17 -> 1.6.17 * [new tag] 1.6.2 -> 1.6.2 * [new tag] 1.6.3 -> 1.6.3 * [new tag] 1.6.4 -> 1.6.4 * [new tag] 1.6.5 -> 1.6.5 * [new tag] 1.6.6 -> 1.6.6 * [new tag] 1.6.7 -> 1.6.7 * [new tag] 1.6.8 -> 1.6.8 * [new tag] 1.6.9 -> 1.6.9 * [new tag] 1.7.0 -> 1.7.0 * [new tag] 1.7.1 -> 1.7.1 * [new tag] 1.7.2 -> 1.7.2 * [new tag] 1.7.3 -> 1.7.3 * [new tag] 1.7.4 -> 1.7.4 * [new tag] 1.7.5 -> 1.7.5 * [new tag] 1.7.6 -> 1.7.6 * [new tag] 1.7.7 -> 1.7.7 * [new tag] 1.8.0 -> 1.8.0 * [new tag] 1.8.1 -> 1.8.1 * [new tag] 1.8.2 -> 1.8.2 * [new tag] 1.8.3 -> 1.8.3 HEAD is now at 571347fa6 Merge tag Homebrew/1.8.4 into Linuxbrew/master Initialized empty Git repository in /virtual/hoge/.linuxbrew/Homebrew/Library/Taps/homebrew/homebrew-core/.git/ remote: Enumerating objects: 4911, done. remote: Counting objects: 100% (4911/4911), done. remote: Compressing objects: 100% (4707/4707), done. remote: Total 4911 (delta 49), reused 332 (delta 11), pack-reused 0 Receiving objects: 100% (4911/4911), 4.22 MiB | 8.56 MiB/s, done. Resolving deltas: 100% (49/49), done. From https://github.com/Linuxbrew/homebrew-core * [new branch] master -> origin/master HEAD is now at 8935061 amazon-ecs-cli: update 1.12.0 bottle for Linuxbrew. Warning: gcc 5.5.0_4 is already installed and up-to-date To reinstall 5.5.0_4, run `brew reinstall gcc`
warningはあるもののようやくエラーが無くなったね。
やっと本来やりたかったところに戻ってきたよ。
$ brew install pyenv-virtualenv ==> Installing dependencies for pyenv-virtualenv: autoconf, readline and pyenv ==> Installing pyenv-virtualenv dependency: autoconf ==> Downloading https://linuxbrew.bintray.com/bottles/autoconf-2.69.x86_64_linux.bottle.4.tar.gz ######################################################################## 100.0% ==> Pouring autoconf-2.69.x86_64_linux.bottle.4.tar.gz ==> Caveats Emacs Lisp files have been installed to: /virtual/hoge/.linuxbrew/share/emacs/site-lisp/autoconf ==> Summary 🍺 /virtual/hoge/.linuxbrew/Cellar/autoconf/2.69: 70 files, 3MB ==> Installing pyenv-virtualenv dependency: readline ==> Downloading https://linuxbrew.bintray.com/bottles/readline-7.0.5.x86_64_linux.bottle.tar.gz ######################################################################## 100.0% ==> Pouring readline-7.0.5.x86_64_linux.bottle.tar.gz 🍺 /virtual/hoge/.linuxbrew/Cellar/readline/7.0.5: 46 files, 3.5MB ==> Installing pyenv-virtualenv dependency: pyenv ==> Installing dependencies for pyenv: gdbm, sqlite, libffi and python ==> Installing pyenv dependency: gdbm ==> Downloading https://linuxbrew.bintray.com/bottles/gdbm-1.18.1.x86_64_linux.bottle.tar.gz ######################################################################## 100.0% ==> Pouring gdbm-1.18.1.x86_64_linux.bottle.tar.gz 🍺 /virtual/hoge/.linuxbrew/Cellar/gdbm/1.18.1: 40 files, 1MB ==> Installing pyenv dependency: sqlite ==> Downloading https://linuxbrew.bintray.com/bottles/sqlite-3.25.3.x86_64_linux.bottle.tar.gz ######################################################################## 100.0% ==> Pouring sqlite-3.25.3.x86_64_linux.bottle.tar.gz 🍺 /virtual/hoge/.linuxbrew/Cellar/sqlite/3.25.3: 12 files, 4.4MB ==> Installing pyenv dependency: libffi ==> Downloading https://linuxbrew.bintray.com/bottles/libffi-3.2.1.x86_64_linux.bottle.tar.gz ######################################################################## 100.0% ==> Pouring libffi-3.2.1.x86_64_linux.bottle.tar.gz 🍺 /virtual/hoge/.linuxbrew/Cellar/libffi/3.2.1: 17 files, 362.4KB ==> Installing pyenv dependency: python ==> Downloading https://www.python.org/ftp/python/3.7.1/Python-3.7.1.tar.xz ######################################################################## 100.0% ==> ./configure --prefix=/virtual/hoge/.linuxbrew/Cellar/python/3.7.1 --enable-ipv6 --datarootdir=/virtual/hoge/.linuxbrew ==> make ==> make install PYTHONAPPSDIR=/virtual/hoge/.linuxbrew/Cellar/python/3.7.1 ==> Downloading https://files.pythonhosted.org/packages/26/e5/9897eee1100b166a61f91b68528cb692e8887300d9cbdaa1a349f6304b79/setuptool ######################################################################## 100.0% ==> Downloading https://files.pythonhosted.org/packages/45/ae/8a0ad77defb7cc903f09e551d88b443304a9bd6e6f124e75c0fbbf6de8f7/pip-18.1. ######################################################################## 100.0% ==> Downloading https://files.pythonhosted.org/packages/c2/00/21e3ecc8a9d484f9de995471c061aa3d8f02ae54bdfd9cbdddb59138c809/wheel-0.3 ######################################################################## 100.0% ==> /virtual/hoge/.linuxbrew/Cellar/python/3.7.1/bin/python3 -s setup.py --no-user-cfg install --force --verbose --install-scri ==> /virtual/hoge/.linuxbrew/Cellar/python/3.7.1/bin/python3 -s setup.py --no-user-cfg install --force --verbose --install-scri ==> /virtual/hoge/.linuxbrew/Cellar/python/3.7.1/bin/python3 -s setup.py --no-user-cfg install --force --verbose --install-scri ==> Caveats Python has been installed as /virtual/hoge/.linuxbrew/bin/python3 Unversioned symlinks `python`, `python-config`, `pip` etc. pointing to `python3`, `python3-config`, `pip3` etc., respectively, have been installed into /virtual/hoge/.linuxbrew/opt/python/libexec/bin If you need Homebrew's Python 2.7 run brew install python@2 You can install Python packages with pip3 install <package> They will install into the site-package directory /virtual/hoge/.linuxbrew/lib/python3.7/site-packages See: https://docs.brew.sh/Homebrew-and-Python ==> Summary 🍺 /virtual/hoge/.linuxbrew/Cellar/python/3.7.1: 8,084 files, 123.8MB, built in 3 minutes 18 seconds ==> Installing pyenv ==> Downloading https://linuxbrew.bintray.com/bottles/pyenv-1.2.8.x86_64_linux.bottle.tar.gz ######################################################################## 100.0% ==> Pouring pyenv-1.2.8.x86_64_linux.bottle.tar.gz 🍺 /virtual/hoge/.linuxbrew/Cellar/pyenv/1.2.8: 612 files, 2.9MB ==> Installing pyenv-virtualenv ==> Downloading https://github.com/pyenv/pyenv-virtualenv/archive/v1.1.3.tar.gz ==> Downloading from https://codeload.github.com/pyenv/pyenv-virtualenv/tar.gz/v1.1.3 #=#=-# # ==> ./install.sh ==> Caveats To enable auto-activation add to your profile: if which pyenv-virtualenv-init > /dev/null; then eval "$(pyenv virtualenv-init -)"; fi ==> Summary 🍺 /virtual/hoge/.linuxbrew/Cellar/pyenv-virtualenv/1.1.3: 20 files, 96.9KB, built in 5 seconds ==> Caveats ==> autoconf Emacs Lisp files have been installed to: /virtual/hoge/.linuxbrew/share/emacs/site-lisp/autoconf ==> python Python has been installed as /virtual/hoge/.linuxbrew/bin/python3 Unversioned symlinks `python`, `python-config`, `pip` etc. pointing to `python3`, `python3-config`, `pip3` etc., respectively, have been installed into /virtual/hoge/.linuxbrew/opt/python/libexec/bin If you need Homebrew's Python 2.7 run brew install python@2 You can install Python packages with pip3 install <package> They will install into the site-package directory /virtual/hoge/.linuxbrew/lib/python3.7/site-packages See: https://docs.brew.sh/Homebrew-and-Python ==> pyenv-virtualenv To enable auto-activation add to your profile: if which pyenv-virtualenv-init > /dev/null; then eval "$(pyenv virtualenv-init -)"; fi
よしよし。
