Problème installation packages Rstudio

Le problème exposé dans ce sujet a été résolu.

Bonjour,

j’ai installé RStudio. Il y a possibilité dans R d’installer des packages, mais cela ne semble pas se faire pour moi. Voici mon log :

> install.packages(c("tidyverse","cartography","questionr"), dependencies = TRUE)
Installing packages into ‘/home/qwerty/R/x86_64-pc-linux-gnu-library/3.2’
(as ‘lib’ is unspecified)
Warning in install.packages :
  package ‘cartography’ is not available (for R version 3.2.3)
Warning in install.packages :
  dependencies ‘memisc’, ‘spData’ are not available
also installing the dependencies ‘curl’, ‘openssl’, ‘httr’, ‘rvest’, ‘xml2’, ‘classInt’, ‘roxygen2’

--2018-10-20 22:17:05--  https://cran.rstudio.com/src/contrib/curl_3.2.tar.gz
Résolution de cran.rstudio.com (cran.rstudio.com)… 2600:9000:2006:7800:6:c2d3:f940:93a1, 2600:9000:2006:dc00:6:c2d3:f940:93a1, 2600:9000:2006:ae00:6:c2d3:f940:93a1, ...
Connexion à cran.rstudio.com (cran.rstudio.com)|2600:9000:2006:7800:6:c2d3:f940:93a1|:443… connecté.
requête HTTP transmise, en attente de la réponse… 200 OK
Taille : 367047 (358K) [application/x-gzip]
Enregistre : «/tmp/RtmphnRRRn/downloaded_packages/curl_3.2.tar.gz»

     0K .......... .......... .......... .......... .......... 13% 1,36M 0s
    50K .......... .......... .......... .......... .......... 27% 1,98M 0s
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   200K .......... .......... .......... .......... .......... 69% 4,59M 0s
   250K .......... .......... .......... .......... .......... 83% 1,92M 0s
   300K .......... .......... .......... .......... .......... 97% 2,22M 0s
   350K ........                                              100% 59,3M=0,1s

2018-10-20 22:17:06 (2,51 MB/s) - «/tmp/RtmphnRRRn/downloaded_packages/curl_3.2.tar.gz» enregistré [367047/367047]

--2018-10-20 22:17:06--  https://cran.rstudio.com/src/contrib/openssl_1.0.2.tar.gz
Résolution de cran.rstudio.com (cran.rstudio.com)… 2600:9000:2006:a400:6:c2d3:f940:93a1, 2600:9000:2006:800:6:c2d3:f940:93a1, 2600:9000:2006:e600:6:c2d3:f940:93a1, ...
Connexion à cran.rstudio.com (cran.rstudio.com)|2600:9000:2006:a400:6:c2d3:f940:93a1|:443… connecté.
requête HTTP transmise, en attente de la réponse… 200 OK
Taille : 1194883 (1,1M) [application/x-gzip]
Enregistre : «/tmp/RtmphnRRRn/downloaded_packages/openssl_1.0.2.tar.gz»

     0K .......... .......... .......... .......... ..........  4% 2,03M 1s
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  1050K .......... .......... .......... .......... .......... 94% 2,11M 0s
  1100K .......... .......... .......... .......... .......... 98% 2,97M 0s
  1150K .......... ......                                     100% 3,53M=0,4s

2018-10-20 22:17:06 (2,68 MB/s) - «/tmp/RtmphnRRRn/downloaded_packages/openssl_1.0.2.tar.gz» enregistré [1194883/1194883]

--2018-10-20 22:17:06--  https://cran.rstudio.com/src/contrib/httr_1.3.1.tar.gz
Résolution de cran.rstudio.com (cran.rstudio.com)… 2600:9000:2006:7800:6:c2d3:f940:93a1, 2600:9000:2006:a400:6:c2d3:f940:93a1, 2600:9000:2006:800:6:c2d3:f940:93a1, ...
Connexion à cran.rstudio.com (cran.rstudio.com)|2600:9000:2006:7800:6:c2d3:f940:93a1|:443… connecté.
requête HTTP transmise, en attente de la réponse… 200 OK
Taille : 147593 (144K) [application/x-gzip]
Enregistre : «/tmp/RtmphnRRRn/downloaded_packages/httr_1.3.1.tar.gz»

     0K .......... .......... .......... .......... .......... 34% 1,34M 0s
    50K .......... .......... .......... .......... .......... 69% 1,32M 0s
   100K .......... .......... .......... .......... ....      100% 3,26M=0,09s

2018-10-20 22:17:06 (1,62 MB/s) - «/tmp/RtmphnRRRn/downloaded_packages/httr_1.3.1.tar.gz» enregistré [147593/147593]

--2018-10-20 22:17:06--  https://cran.rstudio.com/src/contrib/rvest_0.3.2.tar.gz
Résolution de cran.rstudio.com (cran.rstudio.com)… 2600:9000:2006:dc00:6:c2d3:f940:93a1, 2600:9000:2006:7800:6:c2d3:f940:93a1, 2600:9000:2006:a400:6:c2d3:f940:93a1, ...
Connexion à cran.rstudio.com (cran.rstudio.com)|2600:9000:2006:dc00:6:c2d3:f940:93a1|:443… connecté.
requête HTTP transmise, en attente de la réponse… 200 OK
Taille : 1597137 (1,5M) [application/x-gzip]
Enregistre : «/tmp/RtmphnRRRn/downloaded_packages/rvest_0.3.2.tar.gz»

     0K .......... .......... .......... .......... ..........  3% 2,09M 1s
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   700K .......... .......... .......... .......... .......... 48% 2,41M 0s
   750K .......... .......... .......... .......... .......... 51% 2,74M 0s
   800K .......... .......... .......... .......... .......... 54% 1,95M 0s
   850K .......... .......... .......... .......... .......... 57% 5,22M 0s
   900K .......... .......... .......... .......... .......... 60% 3,59M 0s
   950K .......... .......... .......... .......... .......... 64% 3,07M 0s
  1000K .......... .......... .......... .......... .......... 67% 2,14M 0s
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  1100K .......... .......... .......... .......... .......... 73% 1,95M 0s
  1150K .......... .......... .......... .......... .......... 76% 2,30M 0s
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  1250K .......... .......... .......... .......... .......... 83% 3,06M 0s
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  1500K .......... .......... .......... .......... .......... 99% 1,91M 0s
  1550K .........                                             100%  107M=0,6s

2018-10-20 22:17:07 (2,54 MB/s) - «/tmp/RtmphnRRRn/downloaded_packages/rvest_0.3.2.tar.gz» enregistré [1597137/1597137]

--2018-10-20 22:17:07--  https://cran.rstudio.com/src/contrib/xml2_1.2.0.tar.gz
Résolution de cran.rstudio.com (cran.rstudio.com)… 2600:9000:2006:ae00:6:c2d3:f940:93a1, 2600:9000:2006:dc00:6:c2d3:f940:93a1, 2600:9000:2006:7800:6:c2d3:f940:93a1, ...
Connexion à cran.rstudio.com (cran.rstudio.com)|2600:9000:2006:ae00:6:c2d3:f940:93a1|:443… connecté.
requête HTTP transmise, en attente de la réponse… 200 OK
Taille : 251614 (246K) [application/x-gzip]
Enregistre : «/tmp/RtmphnRRRn/downloaded_packages/xml2_1.2.0.tar.gz»

     0K .......... .......... .......... .......... .......... 20% 1,52M 0s
    50K .......... .......... .......... .......... .......... 40% 2,54M 0s
   100K .......... .......... .......... .......... .......... 61% 2,91M 0s
   150K .......... .......... .......... .......... .......... 81% 2,87M 0s
   200K .......... .......... .......... .......... .....     100% 3,65M=0,1s

2018-10-20 22:17:07 (2,46 MB/s) - «/tmp/RtmphnRRRn/downloaded_packages/xml2_1.2.0.tar.gz» enregistré [251614/251614]

--2018-10-20 22:17:07--  https://cran.rstudio.com/src/contrib/classInt_0.2-3.tar.gz
Résolution de cran.rstudio.com (cran.rstudio.com)… 2600:9000:2006:a00:6:c2d3:f940:93a1, 2600:9000:2006:ae00:6:c2d3:f940:93a1, 2600:9000:2006:dc00:6:c2d3:f940:93a1, ...
Connexion à cran.rstudio.com (cran.rstudio.com)|2600:9000:2006:a00:6:c2d3:f940:93a1|:443… connecté.
requête HTTP transmise, en attente de la réponse… 200 OK
Taille : 17315 (17K) [application/x-gzip]
Enregistre : «/tmp/RtmphnRRRn/downloaded_packages/classInt_0.2-3.tar.gz»

     0K .......... ......                                     100% 5,87M=0,003s

2018-10-20 22:17:08 (5,87 MB/s) - «/tmp/RtmphnRRRn/downloaded_packages/classInt_0.2-3.tar.gz» enregistré [17315/17315]

--2018-10-20 22:17:08--  https://cran.rstudio.com/src/contrib/roxygen2_6.1.0.tar.gz
Résolution de cran.rstudio.com (cran.rstudio.com)… 2600:9000:2006:6e00:6:c2d3:f940:93a1, 2600:9000:2006:a00:6:c2d3:f940:93a1, 2600:9000:2006:ae00:6:c2d3:f940:93a1, ...
Connexion à cran.rstudio.com (cran.rstudio.com)|2600:9000:2006:6e00:6:c2d3:f940:93a1|:443… connecté.
requête HTTP transmise, en attente de la réponse… 200 OK
Taille : 177264 (173K) [application/x-gzip]
Enregistre : «/tmp/RtmphnRRRn/downloaded_packages/roxygen2_6.1.0.tar.gz»

     0K .......... .......... .......... .......... .......... 28% 2,02M 0s
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   100K .......... .......... .......... .......... .......... 86% 2,86M 0s
   150K .......... .......... ...                             100% 2,22M=0,07s

2018-10-20 22:17:08 (2,43 MB/s) - «/tmp/RtmphnRRRn/downloaded_packages/roxygen2_6.1.0.tar.gz» enregistré [177264/177264]

--2018-10-20 22:17:08--  https://cran.rstudio.com/src/contrib/tidyverse_1.2.1.tar.gz
Résolution de cran.rstudio.com (cran.rstudio.com)… 2600:9000:2006:e600:6:c2d3:f940:93a1, 2600:9000:2006:6e00:6:c2d3:f940:93a1, 2600:9000:2006:a00:6:c2d3:f940:93a1, ...
Connexion à cran.rstudio.com (cran.rstudio.com)|2600:9000:2006:e600:6:c2d3:f940:93a1|:443… connecté.
requête HTTP transmise, en attente de la réponse… 200 OK
Taille : 61647 (60K) [application/x-gzip]
Enregistre : «/tmp/RtmphnRRRn/downloaded_packages/tidyverse_1.2.1.tar.gz»

     0K .......... .......... .......... .......... .......... 83% 1,28M 0s
    50K ..........                                            100% 31,6M=0,04s

2018-10-20 22:17:08 (1,53 MB/s) - «/tmp/RtmphnRRRn/downloaded_packages/tidyverse_1.2.1.tar.gz» enregistré [61647/61647]

--2018-10-20 22:17:08--  https://cran.rstudio.com/src/contrib/questionr_0.6.3.tar.gz
Résolution de cran.rstudio.com (cran.rstudio.com)… 2600:9000:2006:800:6:c2d3:f940:93a1, 2600:9000:2006:e600:6:c2d3:f940:93a1, 2600:9000:2006:6e00:6:c2d3:f940:93a1, ...
Connexion à cran.rstudio.com (cran.rstudio.com)|2600:9000:2006:800:6:c2d3:f940:93a1|:443… connecté.
requête HTTP transmise, en attente de la réponse… 200 OK
Taille : 1392864 (1,3M) [application/x-gzip]
Enregistre : «/tmp/RtmphnRRRn/downloaded_packages/questionr_0.6.3.tar.gz»

     0K .......... .......... .......... .......... ..........  3% 1,37M 1s
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  1350K ..........                                            100% 77,7M=0,6s

2018-10-20 22:17:09 (2,33 MB/s) - «/tmp/RtmphnRRRn/downloaded_packages/questionr_0.6.3.tar.gz» enregistré [1392864/1392864]

* installing *source* package ‘curl’ ...
** package ‘curl’ correctement décompressé et sommes MD5 vérifiées
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Package libcurl was not found in the pkg-config search path.
Perhaps you should add the directory containing `libcurl.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libcurl' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lcurl
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libcurl was not found. Try installing:
 * deb: libcurl4-openssl-dev (Debian, Ubuntu, etc)
 * rpm: libcurl-devel (Fedora, CentOS, RHEL)
 * csw: libcurl_dev (Solaris)
If libcurl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libcurl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘curl’
* removing ‘/home/qwerty/R/x86_64-pc-linux-gnu-library/3.2/curl’
Warning in install.packages :
  installation of package ‘curl’ had non-zero exit status
* installing *source* package ‘openssl’ ...
** package ‘openssl’ correctement décompressé et sommes MD5 vérifiées
Using PKG_CFLAGS=
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because openssl was not found. Try installing:
 * deb: libssl-dev (Debian, Ubuntu, etc)
 * rpm: openssl-devel (Fedora, CentOS, RHEL)
 * csw: libssl_dev (Solaris)
 * brew: openssl@1.1 (Mac OSX)
If openssl is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a openssl.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘openssl’
* removing ‘/home/qwerty/R/x86_64-pc-linux-gnu-library/3.2/openssl’
Warning in install.packages :
  installation of package ‘openssl’ had non-zero exit status
* installing *source* package ‘xml2’ ...
** package ‘xml2’ correctement décompressé et sommes MD5 vérifiées
Package libxml-2.0 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libxml-2.0.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libxml-2.0' found
Package libxml-2.0 was not found in the pkg-config search path.
Perhaps you should add the directory containing `libxml-2.0.pc'
to the PKG_CONFIG_PATH environment variable
No package 'libxml-2.0' found
Using PKG_CFLAGS=
Using PKG_LIBS=-lxml2
------------------------- ANTICONF ERROR ---------------------------
Configuration failed because libxml-2.0 was not found. Try installing:
 * deb: libxml2-dev (Debian, Ubuntu, etc)
 * rpm: libxml2-devel (Fedora, CentOS, RHEL)
 * csw: libxml2_dev (Solaris)
If libxml-2.0 is already installed, check that 'pkg-config' is in your
PATH and PKG_CONFIG_PATH contains a libxml-2.0.pc file. If pkg-config
is unavailable you can set INCLUDE_DIR and LIB_DIR manually via:
R CMD INSTALL --configure-vars='INCLUDE_DIR=... LIB_DIR=...'
--------------------------------------------------------------------
ERROR: configuration failed for package ‘xml2’
* removing ‘/home/qwerty/R/x86_64-pc-linux-gnu-library/3.2/xml2’
Warning in install.packages :
  installation of package ‘xml2’ had non-zero exit status
ERROR: dependency ‘spData’ is not available for package ‘classInt’
* removing ‘/home/qwerty/R/x86_64-pc-linux-gnu-library/3.2/classInt’
Warning in install.packages :
  installation of package ‘classInt’ had non-zero exit status
ERROR: dependencies ‘curl’, ‘openssl’ are not available for package ‘httr’
* removing ‘/home/qwerty/R/x86_64-pc-linux-gnu-library/3.2/httr’
Warning in install.packages :
  installation of package ‘httr’ had non-zero exit status
ERROR: dependency ‘xml2’ is not available for package ‘roxygen2’
* removing ‘/home/qwerty/R/x86_64-pc-linux-gnu-library/3.2/roxygen2’
Warning in install.packages :
  installation of package ‘roxygen2’ had non-zero exit status
ERROR: dependency ‘classInt’ is not available for package ‘questionr’
* removing ‘/home/qwerty/R/x86_64-pc-linux-gnu-library/3.2/questionr’
Warning in install.packages :
  installation of package ‘questionr’ had non-zero exit status
ERROR: dependencies ‘xml2’, ‘httr’ are not available for package ‘rvest’
* removing ‘/home/qwerty/R/x86_64-pc-linux-gnu-library/3.2/rvest’
Warning in install.packages :
  installation of package ‘rvest’ had non-zero exit status
ERROR: dependencies ‘httr’, ‘rvest’, ‘xml2’ are not available for package ‘tidyverse’
* removing ‘/home/qwerty/R/x86_64-pc-linux-gnu-library/3.2/tidyverse’
Warning in install.packages :
  installation of package ‘tidyverse’ had non-zero exit status

The downloaded source packages are in
    ‘/tmp/RtmphnRRRn/downloaded_packages’

Une idée de comment résoudre ça ? Cdt

+0 -0

Manifestement, il manque des packets que R ne peut installer.
Notamment curl, openssl et un plus bizarre nommé spData (le problème pour lui vient très certainement de la libxml).

R ne peut les installer tout seul.

Du coup, ben essaye les Try installing, tu ne les as peut-être pas remarqué mais il y a une procédure pour résoudre le problème. C’est d’installer les packets cités aux lignes 221, 238 et 265. Tu dois pouvoir les installer depuis la logitech. Sinon, tu peux le faire grâce à un apt install [...]

+0 -0

L’erreur semble persister… Une idée ?

> install.packages(c("tidyverse","cartography","questionr"), dependencies = TRUE)
Installing packages into ‘/home/qwerty/R/x86_64-pc-linux-gnu-library/3.2’
(as ‘lib’ is unspecified)
Warning in install.packages :
  package ‘cartography’ is not available (for R version 3.2.3)
Warning in install.packages :
  dependencies ‘memisc’, ‘spData’ are not available
also installing the dependency ‘classInt’

--2018-10-21 10:25:53--  https://cran.rstudio.com/src/contrib/classInt_0.2-3.tar.gz
Résolution de cran.rstudio.com (cran.rstudio.com)… 2600:9000:2006:8000:6:c2d3:f940:93a1, 2600:9000:2006:5400:6:c2d3:f940:93a1, 2600:9000:2006:9a00:6:c2d3:f940:93a1, ...
Connexion à cran.rstudio.com (cran.rstudio.com)|2600:9000:2006:8000:6:c2d3:f940:93a1|:443… connecté.
requête HTTP transmise, en attente de la réponse… 200 OK
Taille : 17315 (17K) [application/x-gzip]
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requête HTTP transmise, en attente de la réponse… 200 OK
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--2018-10-21 10:25:53--  https://cran.rstudio.com/src/contrib/questionr_0.6.3.tar.gz
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requête HTTP transmise, en attente de la réponse… 200 OK
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ERROR: dependency ‘spData’ is not available for package ‘classInt’
* removing ‘/home/qwerty/R/x86_64-pc-linux-gnu-library/3.2/classInt’
Warning in install.packages :
  installation of package ‘classInt’ had non-zero exit status
* installing *source* package ‘tidyverse’ ...
** package ‘tidyverse’ correctement décompressé et sommes MD5 vérifiées
** R
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘tibble::as_tibble’ when loading ‘broom’
Warning: replacing previous import by ‘tibble::tibble’ when loading ‘broom’
Note: the specification for S3 class “difftime” in package ‘lubridate’ seems equivalent to one from package ‘hms’: not turning on duplicate class definitions for this class.
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘tibble::as_tibble’ when loading ‘broom’
Warning: replacing previous import by ‘tibble::tibble’ when loading ‘broom’
Note: the specification for S3 class “difftime” in package ‘lubridate’ seems equivalent to one from package ‘hms’: not turning on duplicate class definitions for this class.
* DONE (tidyverse)
ERROR: dependency ‘classInt’ is not available for package ‘questionr’
* removing ‘/home/qwerty/R/x86_64-pc-linux-gnu-library/3.2/questionr’
Warning in install.packages :
  installation of package ‘questionr’ had non-zero exit status

The downloaded source packages are in
    ‘/tmp/Rtmp01EL2u/downloaded_packages’
+0 -0

:( le package spData est un jeu de donné.

Essaye de l’installer autrement que via R.

Il semble que le package correspondant soit 'r-cran-spdata’. Un apt install r-cran-spdata peut peut-être marcher.

+0 -0

En général, quand un package n’est pas trouvé, c’est que ta version de R n’est plus à jour et que le package en question demande une version plus récente (ce qui est signe d’un package a jour, donc plutôt un bon point !).

D’aprés le package cartography, il te faut une version de R 3.3 ou plus. Donc il faut que tu mettes à jour ta version de R, qui est une 3.2.x ! Sachant qu’on est en 3.5.x, tu es un peu en retard ! ;)

Je pense que cela devrait résoudre tous tes problèmes de packages !

+0 -0

Non malheureusement je suis sous Windows, je n’ai pas la moindre idée de comment R fonctionne sous Linux… a part que ça à l’air compliqué. :p

Le site du cran ne t’aide pas à trouver des dépôts à jour dans la partie linux ? https://cloud.r-project.org/

La version pour Ubuntu semble récente, donc elle devrait convenir si tu arrives à l’installer.

+1 -0
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