Jupyter NotebookでRを動かしたい。

Question

前提・実現したいこと

anacondaでpythonを触っていたが、Rも同様なことができると知ったので、ネットで探してやってみようと思ったが、最初の必要なパッケージをインストーるするところでつまずいてしまってわからなくなってしまった。

発生している問題・エラーメッセージ

エラーメッセージ

• installing source package ‘ps’ ...

** パッケージ ‘ps’ の解凍および MD5 サムの検証に成功しました
** libs
x86_64-apple-darwin13.4.0-clang -march=core2 -mtune=haswell -mssse3 -ftree-vectorize -fPIC -fPIE -fstack-protector-strong -O2 -pipe -I/anaconda3/include -fdebug-prefix-map==/usr/local/src/conda/- -fdebug-prefix-map==/usr/local/src/conda-prefix -Wall px.c -o px
ld: warning: ignoring file /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libSystem.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/lib/libSystem.tbd
Undefined symbols for architecture x86_64:
"___error", referenced from:
_echo_from_fd in px-29b3f4.o
"___stack_chk_fail", referenced from:
_cat2 in px-29b3f4.o
_cat in px-29b3f4.o
_echo_from_fd in px-29b3f4.o
_main in px-29b3f4.o
"___stack_chk_guard", referenced from:
_cat2 in px-29b3f4.o
_cat in px-29b3f4.o
_echo_from_fd in px-29b3f4.o
_main in px-29b3f4.o
"___stderrp", referenced from:
_usage in px-29b3f4.o
_cat2 in px-29b3f4.o
_cat in px-29b3f4.o
_write_to_fd in px-29b3f4.o
_echo_from_fd in px-29b3f4.o
_main in px-29b3f4.o
"___stdoutp", referenced from:
_echo_from_fd in px-29b3f4.o
_main in px-29b3f4.o
"_close", referenced from:
_cat in px-29b3f4.o
"_exit", referenced from:
_cat2 in px-29b3f4.o
_cat in px-29b3f4.o
"_fflush", referenced from:
_echo_from_fd in px-29b3f4.o
_main in px-29b3f4.o
"_fprintf", referenced from:
_cat2 in px-29b3f4.o
_cat in px-29b3f4.o
_write_to_fd in px-29b3f4.o
_echo_from_fd in px-29b3f4.o
_main in px-29b3f4.o
"_fputs", referenced from:
_main in px-29b3f4.o
"_fwrite", referenced from:
_usage in px-29b3f4.o
_main in px-29b3f4.o
"_getenv", referenced from:
_main in px-29b3f4.o
"_open", referenced from:
_cat in px-29b3f4.o
"_printf", referenced from:
_main in px-29b3f4.o
"_puts", referenced from:
_main in px-29b3f4.o
"_read", referenced from:
_cat2 in px-29b3f4.o
_cat in px-29b3f4.o
_echo_from_fd in px-29b3f4.o
"_sleep", referenced from:
_main in px-29b3f4.o
"_sscanf", referenced from:
_main in px-29b3f4.o
"_strcmp", referenced from:
_main in px-29b3f4.o
"_strerror", referenced from:
_echo_from_fd in px-29b3f4.o
"_strlen", referenced from:
_write_to_fd in px-29b3f4.o
_echo_from_fd in px-29b3f4.o
_main in px-29b3f4.o
"_usleep", referenced from:
_main in px-29b3f4.o
"_write", referenced from:
_cat2 in px-29b3f4.o
_cat in px-29b3f4.o
_write_to_fd in px-29b3f4.o
_echo_from_fd in px-29b3f4.o
_main in px-29b3f4.o
(maybe you meant: _write_to_fd)
ld: symbol(s) not found for architecture x86_64
clang-4.0: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [Makevars:11: px] Error 1
ERROR: compilation failed for package ‘ps’

• removing ‘/anaconda3/lib/R/library/ps’
• installing source package ‘fs’ ...

** パッケージ ‘fs’ の解凍および MD5 サムの検証に成功しました
中略
ERROR: compilation failed for package ‘fs’

• removing ‘/anaconda3/lib/R/library/fs’
• installing source package ‘git2r’ ...

** パッケージ ‘git2r’ の解凍および MD5 サムの検証に成功しました
checking build system type... x86_64-apple-darwin18.7.0
checking host system type... x86_64-apple-darwin18.7.0
checking for gcc... x86_64-apple-darwin13.4.0-clang
checking whether the C compiler works... no
configure: error: in /private/var/folders/1j/ykvjgzl54qd3mffmxmk191c40000gn/T/Rtmpuqstls/R.INSTALLb9a7ee0f365/git2r': configure: error: C compiler cannot create executables See config.log' for more details
ERROR: configuration failed for package ‘git2r’

• removing ‘/anaconda3/lib/R/library/git2r’

• installing source package ‘pbdZMQ’ ...

** パッケージ ‘pbdZMQ’ の解凍および MD5 サムの検証に成功しました
checking for pkg-config... no

****************** Results of pbdZMQ package configure *****************

GET_PKG_CONFIG = no
GET_SYSTEM_ZMQ = no
PKG_CONFIG =
SYSTEM_ZMQ_INCLUDEDIR =
SYSTEM_ZMQ_LIBDIR =
ENABLE_INTERNAL_ZMQ = no
INTERNAL_ZMQ_INCLUDEDIR = ./zmqsrc/include
INTERNAL_ZMQ_LIBDIR = ./
EXTERNAL_ZMQ_INCLUDE =
EXTERNAL_ZMQ_LDFLAGS =
ZMQ_INCLUDE = -I./zmqsrc/include
ZMQ_LDFLAGS = -L./ -lzmq
EXT_LIBS = $(R_ZMQ)
ZMQ_POLLER = select

---

configure: creating ./config.status
config.status: creating src/Makevars
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/build_zmq
configure: creating ./config.status
config.status: creating src/Makevars
config.status: creating src/build_zmq
config.status: creating R/zzz.r
** libs
( sh ./chmod_zmq.inc; cd zmqsrc; sh ../build_zmq )
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... config/install-sh -c -d
checking for gawk... no
checking for mawk... no
checking for nawk... no
checking for awk... awk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking whether UID '501' is supported by ustar format... yes
checking whether GID '20' is supported by ustar format... yes
checking how to create a ustar tar archive... gnutar
checking whether make supports nested variables... (cached) yes
checking for gcc... x86_64-apple-darwin13.4.0-clang
checking whether the C compiler works... no
configure: error: in /private/var/folders/1j/ykvjgzl54qd3mffmxmk191c40000gn/T/Rtmp0l1kTW/R.INSTALLba9a4f57d766/pbdZMQ/src/zmqsrc': configure: error: C compiler cannot create executables See config.log' for more details
make[1]: Entering directory '/private/var/folders/1j/ykvjgzl54qd3mffmxmk191c40000gn/T/Rtmp0l1kTW/R.INSTALLba9a4f57d766/pbdZMQ/src/zmqsrc'
make[1]: *** No targets specified and no makefile found. Stop.
make[1]: Leaving directory '/private/var/folders/1j/ykvjgzl54qd3mffmxmk191c40000gn/T/Rtmp0l1kTW/R.INSTALLba9a4f57d766/pbdZMQ/src/zmqsrc'
make[1]: Entering directory '/private/var/folders/1j/ykvjgzl54qd3mffmxmk191c40000gn/T/Rtmp0l1kTW/R.INSTALLba9a4f57d766/pbdZMQ/src/zmqsrc'
make[1]: *** No rule to make target 'install'. Stop.
make[1]: Leaving directory '/private/var/folders/1j/ykvjgzl54qd3mffmxmk191c40000gn/T/Rtmp0l1kTW/R.INSTALLba9a4f57d766/pbdZMQ/src/zmqsrc'
make: *** [Makevars:52: libzmq] Error 2
ERROR: compilation failed for package ‘pbdZMQ’

• removing ‘/anaconda3/lib/R/library/pbdZMQ’
• restoring previous ‘/anaconda3/lib/R/library/pbdZMQ’
• installing source package ‘uuid’ ...

** パッケージ ‘uuid’ の解凍および MD5 サムの検証に成功しました
checking for gcc... x86_64-apple-darwin13.4.0-clang
checking whether the C compiler works... no
configure: error: in /private/var/folders/1j/ykvjgzl54qd3mffmxmk191c40000gn/T/Rtmp1tfrQl/R.INSTALLbe02479f30fa/uuid': configure: error: C compiler cannot create executables See config.log' for more details
ERROR: configuration failed for package ‘uuid’

• removing ‘/anaconda3/lib/R/library/uuid’

ERROR: dependency ‘ps’ is not available for package ‘processx’

• removing ‘/anaconda3/lib/R/library/processx’

ERROR: dependencies ‘fs’, ‘git2r’ are not available for package ‘usethis’

• removing ‘/anaconda3/lib/R/library/usethis’
• installing source package ‘IRdisplay’ ...

** パッケージ ‘IRdisplay’ の解凍および MD5 サムの検証に成功しました
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded

• DONE (IRdisplay)

ERROR: dependency ‘processx’ is not available for package ‘xopen’

• removing ‘/anaconda3/lib/R/library/xopen’

ERROR: dependency ‘processx’ is not available for package ‘callr’

• removing ‘/anaconda3/lib/R/library/callr’

ERROR: dependency ‘callr’ is not available for package ‘pkgbuild’

• removing ‘/anaconda3/lib/R/library/pkgbuild’

ERROR: dependency ‘pkgbuild’ is not available for package ‘pkgload’

• removing ‘/anaconda3/lib/R/library/pkgload’

ERROR: dependencies ‘callr’, ‘pkgbuild’, ‘xopen’ are not available for package ‘rcmdcheck’

• removing ‘/anaconda3/lib/R/library/rcmdcheck’

ERROR: dependency ‘pkgload’ is not available for package ‘roxygen2’

• removing ‘/anaconda3/lib/R/library/roxygen2’

ERROR: dependencies ‘usethis’, ‘callr’, ‘git2r’, ‘pkgbuild’, ‘pkgload’, ‘rcmdcheck’, ‘roxygen2’ are not available for package ‘devtools’

• removing ‘/anaconda3/lib/R/library/devtools’

ダウンロードされたパッケージは、以下にあります
‘/private/var/folders/1j/ykvjgzl54qd3mffmxmk191c40000gn/T/RtmplYekNy/downloaded_packages’
'.Library' 中のパッケージの HTML 索引を更新します
Making 'packages.html' ... 完了
14 件の警告がありました (警告を見るには warnings() を使って下さい)

該当のソースコード

install.packages(c('repr', 'IRdisplay', 'evaluate', 'crayon', 'pbdZMQ', 'devtools', 'uuid', 'digest'))

試したこと

ここに問題に対して試したことを記載してください。

補足情報（FW/ツールのバージョンなど）

Mac OSX Mojave 10.14.6
anaconda、Rは最新にバージョンアップ済み
ここにより詳細な情報を記載してください。

Answer 1

以下が該当しませんでしょうか？

Qiita:install.packages("pander")にてx86_64-apple-darwin13.4.0-clang++: command not found出力時の対応方法

$ conda install clangxx_osx-64

因みに「apple-darwin13.4.0-clang」でググっただけです。

Comments

[hassyukidaruma]

それに関しては以前やってみたのですが、結果としては、うまくいかなかったです。
$ conda install clangxx_osx-64
Collecting package metadata (repodata.json): done
Solving environment: done

## Package Plan ##

environment location: /anaconda3

added / updated specs:
- clangxx_osx-64

The following packages will be downloaded:

package | build
---------------------------|-----------------
certifi-2019.9.11 | py37_0 154 KB
conda-4.7.12 | py37_0 3.0 MB
------------------------------------------------------------
Total: 3.1 MB

The following packages will be SUPERSEDED by a higher-priority channel:

certifi anaconda --> pkgs/main
conda anaconda --> pkgs/main
openssl anaconda::openssl-1.1.1-h1de35cc_0 --> pkgs/main::openssl-1.1.1d-h1de35cc_3

Proceed ([y]/n)? y

Downloading and Extracting Packages
certifi-2019.9.11 | 154 KB | ################################################################ | 100%
conda-4.7.12 | 3.0 MB | ################################################################ | 100%
Preparing transaction: done
Verifying transaction: done
Executing transaction: done

> install.packages(c('repr', 'IRdisplay', 'evaluate', 'crayon', 'pbdZMQ', 'devtools', 'uuid', 'digest'))

ld: warning: -pie being ignored. It is only used when linking a main executable
ld: warning: ignoring file /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/System/Library/Frameworks//CoreFoundation.framework/CoreFoundation.tbd
ld: warning: ignoring file /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/lib/libSystem.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/lib/libSystem.tbd
installing via 'install.libs.R' to /anaconda3/lib/R/library/00LOCK-pbdZMQ/00new/pbdZMQ

* installing *source* package ‘uuid’ ...
** パッケージ ‘uuid’ の解凍および MD5 サムの検証に成功しました
** using staged installation
checking for gcc... x86_64-apple-darwin13.4.0-clang
checking whether the C compiler works... no
configure: error: in `/private/var/folders/1j/ykvjgzl54qd3mffmxmk191c40000gn/T/RtmpVLl1WB/R.INSTALLac0e38e90178/uuid':
configure: error: C compiler cannot create executables
See `config.log' for more details
ERROR: configuration failed for package ‘uuid’

ld: warning: ignoring file /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/lib/libSystem.tbd, file was built for unsupported file format ( 0x2D 0x2D 0x2D 0x20 0x21 0x74 0x61 0x70 0x69 0x2D 0x74 0x62 0x64 0x2D 0x76 0x33 ) which is not the architecture being linked (x86_64): /Applications/Xcode.app/Contents/Developer/Platforms/MacOSX.platform/Developer/SDKs/MacOSX.sdk/usr/lib/libSystem.tbd

KojiDoiさんにご指摘頂いたエラーもまだ出ていますので、どこかに問題がある様に感じますが、何をどうすれば良いのが検討がつきません。

[KojiDoi]

やはりgccを再インストールすべきじゃないでしょうか。gcc本体は存在していても環境が完全にはできていないように見えますが。

Answer 2

私はMacは持ってないので直接的な検証はできませんが、

checking for gcc... x86_64-apple-darwin13.4.0-clang
checking whether the C compiler works... no

まずはここに問題がありそうです。とりあえずCコンパイラ環境を整える必要があるでしょう。

Comments

[hassyukidaruma]

お返事ありがとうございます。Cコンパイラ環境を全く触ったことがないのですが、具体的にどのようなことを調べて実行すればよいのでしょうか？

[KojiDoi]

＞具体的にどのようなことを調べて

macos gcc インストール
まずググる。

[hassyukidaruma]

ターミナルからgccがインストールされているかを確認したのですが、
$ gcc -v
Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include/c++/4.2.1
Apple clang version 11.0.0 (clang-1100.0.33.8)
Target: x86_64-apple-darwin18.7.0
Thread model: posix
InstalledDir: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin

gccが存在はしそうなのですが、Target: x86_64-apple-darwin18.7.0がchecking for gcc... x86_64-apple-darwin13.4.0-clangとは違うからエラーが出るのでしょうか？