1.すぐに利用したい方へ(as soon as)
「RとKerasによるディープラーニング」François Chollet、J. J. Allaire 著
<この項は書きかけです。順次追記します。>
docker
dockerを導入し、Windows, Macではdockerを起動しておいてください。
Windowsでは、BiosでIntel Virtualizationをenableにしないとdockerが起動しない場合があります。
また、セキュリティの警告などが出ることがあります。
##docker pull and run
$ docker pull kaizenjapan/r-sta
$ docker run -it kaizenjapan/r-sta /bin/bash
以下のshell sessionでは
(base) root@473fc1bb505d:/#は入力促進記号(comman prompt)です。実際には数字の部分が違うかもしれません。この行の#の右側を入力してください。
それ以外の行は出力です。出力にエラー、違いがあれば、コメント欄などでご連絡くださると幸いです。
それぞれの章のフォルダに移動します。
dockerの中と、dockerを起動したOSのシェルとが表示が似ている場合には、どちらで捜査しているか間違えることがあります。dockerの入力促進記号(comman prompt)に気をつけてください。
ファイル共有または複写
dockerとdockerを起動したOSでは、ファイル共有をするか、ファイル複写するかして、生成したファイルをブラウザ等表示させてください。参考文献欄にやり方のURLを記載しています。
複写の場合は、dockerを起動したOS側コマンドを実行しました。お使いのdockerの番号で置き換えてください。複写したファイルをブラウザで表示し内容確認しました。
2. dockerを自力で構築する方へ
ここから下は、上記のpullしていただいたdockerをどういう方針で、どういう手順で作ったかを記録します。
上記のdockerを利用する上での参考資料です。本の続きを実行する上では必要ありません。
自力でdocker/anacondaを構築する場合の手順になります。
dockerfileを作る方法ではありません。ごめんなさい。
docker
ubuntu, debianなどのLinuxを、linux, windows, mac osから共通に利用できる仕組み。
利用するOSの設定を変更せずに利用できるのがよい。
同じ仕様で、大量の人が利用することができる。
ソフトウェアの開発元が公式に対応しているものと、利用者が便利に仕立てたものの両方が利用可能である。今回は、公式に配布しているものを、自分で仕立てて、他の人にも利用できるようにする。
docker pull
docker公式配布の利用は、URLからpullすることで実現する。
apt
(base) root@473fc1bb505d:/# apt-get update
(base) root@473fc1bb505d:/# apt install -y procps
(base) root@473fc1bb505d:/# apt install -y vim
(base) root@473fc1bb505d:/# apt install -y apt-utils
(base) root@473fc1bb505d:/# apt install -y r-base
(base) root@473fc1bb505d:/# apt install -y r-cran-hmisc
wget
(base) root@9239fd07cbe8:/# wget https://manning-content.s3.amazonaws.com/download/1/faf36a8-8958-40db-8020-3f106794d8ed/source-code.zip
--2018-10-14 00:07:27-- https://manning-content.s3.amazonaws.com/download/1/faf36a8-8958-40db-8020-3f106794d8ed/source-code.zip
Resolving manning-content.s3.amazonaws.com (manning-content.s3.amazonaws.com)... 52.216.99.155
Connecting to manning-content.s3.amazonaws.com (manning-content.s3.amazonaws.com)|52.216.99.155|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 68634677 (65M) [application/zip]
Saving to: ‘source-code.zip’
source-code.zip 100%[===========================>] 65.46M 5.15MB/s in 15s
2018-10-14 00:07:43 (4.44 MB/s) - ‘source-code.zip’ saved [68634677/68634677]
(base) root@9239fd07cbe8:/# ls
ML_for_Hackers dev lib mnt root source-code.zip sys var
bin etc lib64 opt run srv tmp
boot home media proc sbin statistics-for-data-scientists usr
(base) root@9239fd07cbe8:/# unzip source-code.zip
Archive: source-code.zip
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(base) root@9239fd07cbe8:/# ls
ML_for_Hackers etc mnt sbin tmp
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deep-learning-with-r-notebooks-master lib64 root statistics-for-data-scientists
dev media run sys
(base) root@9239fd07cbe8:/# cd deep-learning-with-r-notebooks-master/
(base) root@9239fd07cbe8:/deep-learning-with-r-notebooks-master# ls
LICENSE README.md cats_and_dogs_small_2.h5 notebooks
(base) root@782459e23422:/deep-learning-with-keras-ja/ch01# ls
__pycache__ keras_MINST_V1_Sat_22_Sep_2018_04_48_41 keras_MINST_V2_Sat_22_Sep_2018_05_02_33 keras_MINST_V4.py requirements.txt
keras_MINST_V1.py keras_MINST_V2.py keras_MINST_V3.py make_tensorboard.py requirements_gpu.txt
(base) root@782459e23422:/deep-learning-with-keras-ja/ch01# pip install -r requirements.txt
Collecting keras==2.1.6 (from -r requirements.txt (line 1))
Downloading https://files.pythonhosted.org/packages/54/e8/eaff7a09349ae9bd40d3ebaf028b49f5e2392c771f294910f75bb608b241/Keras-2.1.6-py2.py3-none-any.whl (339kB)
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Collecting tensorflow==1.8.0 (from -r requirements.txt (line 2))
Downloading https://files.pythonhosted.org/packages/22/c6/d08f7c549330c2acc1b18b5c1f0f8d9d2af92f54d56861f331f372731671/tensorflow-1.8.0-cp36-cp36m-manylinux1_x86_64.whl (49.1MB)
100% |████████████████████████████████| 49.1MB 1.1MB/s
Collecting h5py==2.7.1 (from -r requirements.txt (line 3))
Downloading https://files.pythonhosted.org/packages/f2/b8/a63fcc840bba5c76e453dd712dbca63178a264c8990e0086b72965d4e954/h5py-2.7.1-cp36-cp36m-manylinux1_x86_64.whl (5.4MB)
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Requirement already satisfied: scipy>=0.14 in /opt/conda/lib/python3.6/site-packages (from keras==2.1.6->-r requirements.txt (line 1)) (1.1.0)
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Collecting tensorboard<1.9.0,>=1.8.0 (from tensorflow==1.8.0->-r requirements.txt (line 2))
Downloading https://files.pythonhosted.org/packages/59/a6/0ae6092b7542cfedba6b2a1c9b8dceaf278238c39484f3ba03b03f07803c/tensorboard-1.8.0-py3-none-any.whl (3.1MB)
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Collecting html5lib==0.9999999 (from tensorboard<1.9.0,>=1.8.0->tensorflow==1.8.0->-r requirements.txt (line 2))
Downloading https://files.pythonhosted.org/packages/ae/ae/bcb60402c60932b32dfaf19bb53870b29eda2cd17551ba5639219fb5ebf9/html5lib-0.9999999.tar.gz (889kB)
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Collecting bleach==1.5.0 (from tensorboard<1.9.0,>=1.8.0->tensorflow==1.8.0->-r requirements.txt (line 2))
Downloading https://files.pythonhosted.org/packages/33/70/86c5fec937ea4964184d4d6c4f0b9551564f821e1c3575907639036d9b90/bleach-1.5.0-py2.py3-none-any.whl
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Building wheels for collected packages: html5lib
Running setup.py bdist_wheel for html5lib ... done
Stored in directory: /root/.cache/pip/wheels/50/ae/f9/d2b189788efcf61d1ee0e36045476735c838898eef1cad6e29
Successfully built html5lib
twisted 18.7.0 requires PyHamcrest>=1.9.0, which is not installed.
Installing collected packages: h5py, keras, html5lib, bleach, tensorboard, tensorflow
Found existing installation: h5py 2.8.0
Uninstalling h5py-2.8.0:
Successfully uninstalled h5py-2.8.0
Found existing installation: Keras 2.2.2
Uninstalling Keras-2.2.2:
Successfully uninstalled Keras-2.2.2
Found existing installation: html5lib 1.0.1
Uninstalling html5lib-1.0.1:
Successfully uninstalled html5lib-1.0.1
Found existing installation: bleach 2.1.4
Uninstalling bleach-2.1.4:
Successfully uninstalled bleach-2.1.4
Found existing installation: tensorboard 1.9.0
Uninstalling tensorboard-1.9.0:
Successfully uninstalled tensorboard-1.9.0
Found existing installation: tensorflow 1.9.0
Uninstalling tensorflow-1.9.0:
Successfully uninstalled tensorflow-1.9.0
Successfully installed bleach-1.5.0 h5py-2.7.1 html5lib-0.9999999 keras-2.1.6 tensorboard-1.8.0 tensorflow-1.8.0
You are using pip version 10.0.1, however version 18.1 is available.
You should consider upgrading via the 'pip install --upgrade pip' command.
(base) root@782459e23422:/deep-learning-with-keras-ja/ch01# pip install --upgrade pip
Collecting pip
Downloading https://files.pythonhosted.org/packages/c2/d7/90f34cb0d83a6c5631cf71dfe64cc1054598c843a92b400e55675cc2ac37/pip-18.1-py2.py3-none-any.whl (1.3MB)
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twisted 18.7.0 requires PyHamcrest>=1.9.0, which is not installed.
Installing collected packages: pip
Found existing installation: pip 10.0.1
Uninstalling pip-10.0.1:
Successfully uninstalled pip-10.0.1
Successfully installed pip-18.1
(base) root@782459e23422:/deep-learning-with-keras-ja/ch01# pip install -r requirements.txt
Requirement already satisfied: keras==2.1.6 in /opt/conda/lib/python3.6/site-packages (from -r requirements.txt (line 1)) (2.1.6)
Requirement already satisfied: tensorflow==1.8.0 in /opt/conda/lib/python3.6/site-packages (from -r requirements.txt (line 2)) (1.8.0)
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| Description | Notebook | Source Code |
|---|---|---|
| 2.1: A first look at a neural network | Notebook (HTML) | R Markdown (Rmd) |
| 3.5: Classifying movie reviews: a binary classification example | Notebook (HTML) | R Markdown (Rmd) |
| 3.6: Classifying newswires: a multi-class classification example | Notebook (HTML) | R Markdown (Rmd) |
| 3.7: Predicting house prices: a regression example | Notebook (HTML) | R Markdown (Rmd) |
| 4.4: Overfitting and underfitting | Notebook (HTML) | R Markdown (Rmd) |
| 5.1: Introduction to convnets | Notebook (HTML) | R Markdown (Rmd) |
| 5.2: Using convnets with small datasets | Notebook (HTML) | R Markdown (Rmd) |
| 5.3: Using a pre-trained convnet | Notebook (HTML) | R Markdown (Rmd) |
| 5.4: Visualizing what convnets learn | Notebook (HTML) | R Markdown (Rmd) |
| 6.1: One-hot encoding of words or characters | Notebook (HTML) | R Markdown (Rmd) |
| 6.1: Using word embeddings | Notebook (HTML) | R Markdown (Rmd) |
| 6.2: Understanding recurrent neural networks | Notebook (HTML) | R Markdown (Rmd) |
| 6.3: Advanced usage of recurrent neural networks | Notebook (HTML) | R Markdown (Rmd) |
| 6.4: Sequence processing with convnets | Notebook (HTML) | R Markdown (Rmd) |
| 8.1: Text generation with LSTM | Notebook (HTML) | R Markdown (Rmd) |
| 8.2: Deep Dream | Notebook (HTML) | R Markdown (Rmd) |
| 8.3: Neural style transfer | Notebook (HTML) | R Markdown (Rmd) |
| 8.4: Generating images | Notebook (HTML) | R Markdown (Rmd) |
| 8.5: Introduction to generative adversarial networks | Notebook (HTML) | R Markdown (Rmd) |
brary(keras)
mnist <- dataset_mnist()
train_images <- mnist$train$x
train_labels <- mnist$train$y
test_images <- mnist$test$x
test_labels <- mnist$test$y
Error in library(keras) : there is no package called ‘keras’
install.packages("keras")
library(keras)
mnist <- dataset_mnist()
train_images <- mnist$train$x
train_labels <- mnist$train$y
test_images <- mnist$test$x
test_labels <- mnist$test$y
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
Error in contrib.url(repos, type) :
trying to use CRAN without setting a mirror
「ミラーを設定せずにCRANを使用しようとしています」というknitr文書でinstall.packagesが失敗する
https://code-examples.net/ja/q/2065380
install.packages("keras",repos = "http://cran.us.r-project.org")
library(keras)
mnist <- dataset_mnist()
train_images <- mnist$train$x
train_labels <- mnist$train$y
test_images <- mnist$test$x
test_labels <- mnist$test$y
(base) root@782459e23422:/deep-learning-with-r-notebooks-master/notebooks/work# r ch2.r
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
also installing the dependencies ‘ps’, ‘glue’, ‘purrr’, ‘jsonlite’, ‘config’, ‘processx’, ‘rstudioapi’, ‘whisker’, ‘tidyselect’, ‘rlang’, ‘reticulate’, ‘tensorflow’, ‘tfruns’, ‘zeallot’, ‘R6’
trying URL 'http://cran.us.r-project.org/src/contrib/ps_1.1.0.tar.gz'
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downloaded 236 KB
trying URL 'http://cran.us.r-project.org/src/contrib/glue_1.3.0.tar.gz'
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trying URL 'http://cran.us.r-project.org/src/contrib/purrr_0.2.5.tar.gz'
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trying URL 'http://cran.us.r-project.org/src/contrib/jsonlite_1.5.tar.gz'
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trying URL 'http://cran.us.r-project.org/src/contrib/config_0.3.tar.gz'
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trying URL 'http://cran.us.r-project.org/src/contrib/whisker_0.3-2.tar.gz'
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trying URL 'http://cran.us.r-project.org/src/contrib/reticulate_1.10.tar.gz'
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trying URL 'http://cran.us.r-project.org/src/contrib/tensorflow_1.9.tar.gz'
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trying URL 'http://cran.us.r-project.org/src/contrib/tfruns_1.4.tar.gz'
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downloaded 1.9 MB
trying URL 'http://cran.us.r-project.org/src/contrib/zeallot_0.1.0.tar.gz'
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trying URL 'http://cran.us.r-project.org/src/contrib/R6_2.3.0.tar.gz'
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downloaded 30 KB
trying URL 'http://cran.us.r-project.org/src/contrib/keras_2.2.0.tar.gz'
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downloaded 4.7 MB
- installing source package ‘ps’ ...
** package ‘ps’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall px.c -o px
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c api-common.c -o api-common.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c common.c -o common.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c extra.c -o extra.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c dummy.c -o dummy.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c posix.c -o posix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c api-posix.c -o api-posix.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c linux.c -o linux.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c api-linux.c -o api-linux.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o ps.so init.o api-common.o common.o extra.o dummy.o posix.o api-posix.o linux.o api-linux.o -L/usr/lib/R/lib -lR
installing via 'install.libs.R' to /usr/local/lib/R/site-library/ps
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded - DONE (ps)
- installing source package ‘glue’ ...
** package ‘glue’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c glue.c -o glue.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c trim.c -o trim.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o glue.so glue.o init.o trim.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/glue/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded - DONE (glue)
- installing source package ‘jsonlite’ ...
** package ‘jsonlite’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c base64.c -o base64.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c collapse_array.c -o collapse_array.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c collapse_object.c -o collapse_object.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c collapse_pretty.c -o collapse_pretty.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c escape_chars.c -o escape_chars.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c integer64_to_na.c -o integer64_to_na.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c is_datelist.c -o is_datelist.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c is_recordlist.c -o is_recordlist.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c is_scalarlist.c -o is_scalarlist.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c modp_numtoa.c -o modp_numtoa.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c null_to_na.c -o null_to_na.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c num_to_char.c -o num_to_char.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c parse.c -o parse.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c prettify.c -o prettify.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c push_parser.c -o push_parser.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c r-base64.c -o r-base64.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c register.c -o register.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c row_collapse.c -o row_collapse.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c transpose_list.c -o transpose_list.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c validate.c -o validate.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c yajl/yajl.c -o yajl/yajl.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c yajl/yajl_alloc.c -o yajl/yajl_alloc.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c yajl/yajl_buf.c -o yajl/yajl_buf.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c yajl/yajl_encode.c -o yajl/yajl_encode.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c yajl/yajl_gen.c -o yajl/yajl_gen.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c yajl/yajl_lex.c -o yajl/yajl_lex.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c yajl/yajl_parser.c -o yajl/yajl_parser.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -Iyajl/api -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c yajl/yajl_tree.c -o yajl/yajl_tree.o
ar rcs libstatyajl.a yajl/yajl.o yajl/yajl_alloc.o yajl/yajl_buf.o yajl/yajl_encode.o yajl/yajl_gen.o yajl/yajl_lex.o yajl/yajl_parser.o yajl/yajl_tree.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o jsonlite.so base64.o collapse_array.o collapse_object.o collapse_pretty.o escape_chars.o integer64_to_na.o is_datelist.o is_recordlist.o is_scalarlist.o modp_numtoa.o null_to_na.o num_to_char.o parse.o prettify.o push_parser.o r-base64.o register.o row_collapse.o transpose_list.o validate.o -L. -lstatyajl -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/jsonlite/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded - DONE (jsonlite)
- installing source package ‘config’ ...
** package ‘config’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded - DONE (config)
- installing source package ‘rstudioapi’ ...
** package ‘rstudioapi’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded - DONE (rstudioapi)
- installing source package ‘whisker’ ...
** package ‘whisker’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded - DONE (whisker)
- installing source package ‘rlang’ ...
** package ‘rlang’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I./lib/ -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c capture.c -o capture.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I./lib/ -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c export.c -o export.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I./lib/ -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c internal.c -o internal.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -I./lib/ -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c lib.c -o lib.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o rlang.so capture.o export.o internal.o lib.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/rlang/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded - DONE (rlang)
- installing source package ‘zeallot’ ...
** package ‘zeallot’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded - DONE (zeallot)
- installing source package ‘R6’ ...
** package ‘R6’ successfully unpacked and MD5 sums checked
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded - DONE (R6)
- installing source package ‘purrr’ ...
** package ‘purrr’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c backports.c -o backports.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c coerce.c -o coerce.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c extract.c -o extract.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c flatten.c -o flatten.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c map.c -o map.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c transpose.c -o transpose.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o purrr.so backports.o coerce.o extract.o flatten.o init.o map.o transpose.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/purrr/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded - DONE (purrr)
- installing source package ‘processx’ ...
** package ‘processx’ successfully unpacked and MD5 sums checked
** libs
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -Wall tools/px.c -o tools/px
gcc -std=gnu99 -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g supervisor/supervisor.c supervisor/utils.c
-o supervisor/supervisor
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c init.c -o init.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c poll.c -o poll.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c processx-connection.c -o processx-connection.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c processx-vector.c -o processx-vector.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c create-time.c -o create-time.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unix/childlist.c -o unix/childlist.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unix/connection.c -o unix/connection.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unix/processx.c -o unix/processx.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unix/sigchld.c -o unix/sigchld.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unix/utils.c -o unix/utils.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c unix/named_pipe.c -o unix/named_pipe.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o processx.so init.o poll.o processx-connection.o processx-vector.o create-time.o unix/childlist.o unix/connection.o unix/processx.o unix/sigchld.o unix/utils.o unix/named_pipe.o -L/usr/lib/R/lib -lR
installing via 'install.libs.R' to /usr/local/lib/R/site-library/processx
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded - DONE (processx)
- installing source package ‘reticulate’ ...
** package ‘reticulate’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c event_loop.cpp -o event_loop.o
g++ -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c libpython.cpp -o libpython.o
g++ -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c output.cpp -o output.o
g++ -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c python.cpp -o python.o
g++ -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c readline.cpp -o readline.o
g++ -shared -L/usr/lib/R/lib -Wl,-z,relro -o reticulate.so RcppExports.o event_loop.o libpython.o output.o python.o readline.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/reticulate/libs
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded - DONE (reticulate)
- installing source package ‘tidyselect’ ...
** package ‘tidyselect’ successfully unpacked and MD5 sums checked
** libs
g++ -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c RcppExports.cpp -o RcppExports.o
g++ -I/usr/share/R/include -DNDEBUG -I"/usr/lib/R/site-library/Rcpp/include" -fpic -g -O2 -fdebug-prefix-map=/build/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g -c combine_variables.cpp -o combine_variables.o
g++ -shared -L/usr/lib/R/lib -Wl,-z,relro -o tidyselect.so RcppExports.o combine_variables.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/tidyselect/libs
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded - DONE (tidyselect)
- installing source package ‘tfruns’ ...
** package ‘tfruns’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded - DONE (tfruns)
- installing source package ‘tensorflow’ ...
** package ‘tensorflow’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded - DONE (tensorflow)
- installing source package ‘keras’ ...
** package ‘keras’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded - DONE (keras)
The downloaded source packages are in
‘/tmp/downloaded_packages’
/opt/conda/lib/python3.6/site-packages/h5py/init.py:36: FutureWarning: Conversion of the second argument of issubdtype from float to np.floating is deprecated. In future, it will be treated as np.float64 == np.dtype(float).type.
from ._conv import register_converters as _register_converters
Using TensorFlow backend.
(base) root@782459e23422:/deep-learning-with-r-notebooks-master/notebooks/work# r ch2.r
Installing package into ‘/usr/local/lib/R/site-library’
(as ‘lib’ is unspecified)
trying URL 'http://cran.us.r-project.org/src/contrib/keras_2.2.0.tar.gz'
Content type 'application/x-gzip' length 4903324 bytes (4.7 MB)
downloaded 4.7 MB
- installing source package ‘keras’ ...
** package ‘keras’ successfully unpacked and MD5 sums checked
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded - DONE (keras)
The downloaded source packages are in
‘/tmp/downloaded_packages’
/opt/conda/lib/python3.6/site-packages/h5py/init.py:36: FutureWarning: Conversion of the second argument of issubdtype from float to np.floating is deprecated. In future, it will be treated as np.float64 == np.dtype(float).type.
from ._conv import register_converters as _register_converters
Using TensorFlow backend.
参考文献(reference)
R ScriptやR Markdownからinstall.packages()を呼び出す場合はレポジトリを指定しないとエラーになる
https://qiita.com/maech/items/03b9566fb0fe940e1736
Rでtrying to use CRAN without setting a mirrorと言われたら
https://qiita.com/manabuishiirb/items/88fb9d5207e6802da4b7
＜この記事は個人の過去の経験に基づく個人の感想です。現在所属する組織、業務とは関係がありません。＞
文書履歴(document history)
ver. 0.10 初稿 20181014
ver. 0.11 番号変更,参考文献追記 20181028
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