R-Project/Package digest

• installé via install.packages() (voir fullrefmanuel.pdf)
• lire la section du manuel R-admin.pdf
• chown -R bibi /usr/local/lib/R + chgrp -R bibi /usr/local/lib/R , sinon ça le fait pas
• l'install appelle x fois gcc

> install.packages()
Installation du package dans ‘/usr/local/lib/R/site-library’
(car ‘lib’ n'est pas spécifié)
essai de l'URL 'https://pbil.univ-lyon1.fr/CRAN/src/contrib/digest_0.6.12.tar.gz'
Content type 'application/x-gzip' length 120337 bytes (117 KB)
==================================================
downloaded 117 KB

* installing *source* package ‘digest’ ...
** package ‘digest’ correctement décompressé et sommes MD5 vérifiées
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yDv1ct/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c aes.c -o aes.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yDv1ct/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c crc32.c -o crc32.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yDv1ct/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c digest.c -o digest.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yDv1ct/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-yDv1ct/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c md5.c -o md5.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yDv1ct/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c pmurhash.c -o pmurhash.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yDv1ct/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c raes.c -o raes.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yDv1ct/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sha1.c -o sha1.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yDv1ct/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sha2.c -o sha2.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yDv1ct/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sha256.c -o sha256.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yDv1ct/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c xxhash.c -o xxhash.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o digest.so aes.o crc32.o digest.o init.o md5.o pmurhash.o raes.o sha1.o sha2.o sha256.o xxhash.o -L/usr/lib/R/lib -lR
installing to /usr/local/lib/R/site-library/digest/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 (digest)

Les packages source téléchargés sont dans
	‘/tmp/RtmpPHmbQe/downloaded_packages’
> 

> install.packages(lib=lib)
essai de l'URL 'https://pbil.univ-lyon1.fr/CRAN/src/contrib/digest_0.6.12.tar.gz'
Content type 'application/x-gzip' length 120337 bytes (117 KB)
==================================================
downloaded 117 KB

* installing *source* package ‘digest’ ...
** package ‘digest’ correctement décompressé et sommes MD5 vérifiées
** libs
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yDv1ct/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c aes.c -o aes.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yDv1ct/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c crc32.c -o crc32.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yDv1ct/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c digest.c -o digest.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yDv1ct/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-yDv1ct/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c md5.c -o md5.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yDv1ct/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c pmurhash.c -o pmurhash.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yDv1ct/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c raes.c -o raes.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yDv1ct/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sha1.c -o sha1.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yDv1ct/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sha2.c -o sha2.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yDv1ct/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sha256.c -o sha256.o
gcc -std=gnu99 -I/usr/share/R/include -DNDEBUG      -fpic  -g -O2 -fdebug-prefix-map=/build/r-base-yDv1ct/r-base-3.3.3=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c xxhash.c -o xxhash.o
gcc -std=gnu99 -shared -L/usr/lib/R/lib -Wl,-z,relro -o digest.so aes.o crc32.o digest.o init.o md5.o pmurhash.o raes.o sha1.o sha2.o sha256.o xxhash.o -L/usr/lib/R/lib -lR
installing to /usr/lib/R/library/digest/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 (digest)

Les packages source téléchargés sont dans
	‘/tmp/RtmpyzPXRC/downloaded_packages’
mise à jour de la liste HTML des packages dans '.Library'
Warning messages:
1: In file.create(f.tg) :
  impossible de créer le fichier '/usr/share/R/doc/html/packages.html', à cause de 'Permission non accordée'
2: In make.packages.html(.Library) :
  impossible de mettre à jour l'index HTML des packages
> 

• faut faire un chown -R bibi /usr/share/R pour que ça gaze
• à noter que chaque install écrase le répertoire en place sans rien dire

• pour que le package soit enfin chargé, il faut le spécifier dans /etc/R/Renviron.site
  • si on le spécifie plus tard ... c'est trop tard

• voir aussi : Bitcoin