old.packages で、更新可能なパッケージが確認できる。
> old.packages()
Package LibPath Installed Built ReposVer Repository
cluster "cluster" "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "2.0.6" "3.4.4" "2.0.7" "https://cran.ism.ac.jp/src/contrib"
lmtest "lmtest" "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "0.9-35" "3.4.0" "0.9-36" "https://cran.ism.ac.jp/src/contrib"
Matrix "Matrix" "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "1.2-12" "3.4.4" "1.2-13" "https://cran.ism.ac.jp/src/contrib"
nlme "nlme" "/Library/Frameworks/R.framework/Versions/3.4/Resources/library" "3.1-131.1" "3.4.4" "3.1-137" "https://cran.ism.ac.jp/src/contrib"
update.packages で、全てアップデートできるが、パッケージ毎に確認を求められる。
> update.packages() cluster : Version 2.0.6 installed in /Library/Frameworks/R.framework/Versions/3.4/Resources/library Version 2.0.7 available at https://cran.ism.ac.jp Update (y/N/c)? lmtest : Version 0.9-35 installed in /Library/Frameworks/R.framework/Versions/3.4/Resources/library Version 0.9-36 available at https://cran.ism.ac.jp Update (y/N/c)? Matrix : Version 1.2-12 installed in /Library/Frameworks/R.framework/Versions/3.4/Resources/library Version 1.2-13 available at https://cran.ism.ac.jp Update (y/N/c)? nlme : Version 3.1-131.1 installed in /Library/Frameworks/R.framework/Versions/3.4/Resources/library Version 3.1-137 available at https://cran.ism.ac.jp Update (y/N/c)?
ask = F とすると確認不要になるが、ソースからのインストールについては、確認を求められる。
> update.packages(ask = F)
利用できるバイナリー版がありますがソース版は後者です:
binary source needs_compilation
nlme 3.1-131.1 3.1-137 TRUE
パッケージのソースからインストールを行いますか? (コンパイルが必要です)
y/n: y
URL 'https://cran.ism.ac.jp/bin/macosx/el-capitan/contrib/3.4/cluster_2.0.7.tgz' を試しています
Content type 'application/x-gzip' length 565608 bytes (552 KB)
==================================================
downloaded 552 KB
URL 'https://cran.ism.ac.jp/bin/macosx/el-capitan/contrib/3.4/lmtest_0.9-36.tgz' を試しています
Content type 'application/x-gzip' length 277347 bytes (270 KB)
==================================================
downloaded 270 KB
URL 'https://cran.ism.ac.jp/bin/macosx/el-capitan/contrib/3.4/Matrix_1.2-13.tgz' を試しています
Content type 'application/x-gzip' length 3009024 bytes (2.9 MB)
==================================================
downloaded 2.9 MB
ダウンロードされたパッケージは、以下にあります
/var/folders/20/8dj2jpm90s381fqpsv9sxk740000gn/T//RtmphvnDKG/downloaded_packages
ソースパッケージ ‘nlme’ をインストール中です
URL 'https://cran.ism.ac.jp/src/contrib/nlme_3.1-137.tar.gz' を試しています
Content type 'application/x-gzip' length 786769 bytes (768 KB)
==================================================
downloaded 768 KB
* installing *source* package ‘nlme’ ...
** パッケージ ‘nlme’ の解凍および MD5 サムの検証に成功しました
** libs
gfortran -fPIC -g -O2 -c chol.f -o chol.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c corStruct.c -o corStruct.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c gnls.c -o gnls.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c init.c -o init.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c matrix.c -o matrix.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c nlOptimizer.c -o nlOptimizer.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c nlme.c -o nlme.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c nlmefit.c -o nlmefit.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c pdMat.c -o pdMat.o
clang -I/Library/Frameworks/R.framework/Resources/include -DNDEBUG -I/usr/local/include -fPIC -Wall -g -O2 -c pythag.c -o pythag.o
gfortran -fPIC -g -O2 -c rs.f -o rs.o
clang++ -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/lib -o nlme.so chol.o corStruct.o gnls.o init.o matrix.o nlOptimizer.o nlme.o nlmefit.o pdMat.o pythag.o rs.o -L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: warning: directory not found for option '-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin15/6.1.0'
installing to /Library/Frameworks/R.framework/Versions/3.4/Resources/library/nlme/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (nlme)
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/20/8dj2jpm90s381fqpsv9sxk740000gn/T/RtmphvnDKG/downloaded_packages’
>
Comments