RScript, batch et e accent aigü

Bonjour,

j'ai un script R qui fait appel à des fonctions que j'ai écrites dans un fichier séparé.

Ce script affiche l'état d'avancement des opérations grâce à des cat.

Dans le script principal appelé main.R, les accents s'affichent bien. Par exemple, quand on écrit la ligne suivante en Unicode pour "définition des variables" :

Code:

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cat("d\U00E9sfinition des variables")

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On obtient bien

Code:

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définition des variables

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Par contre, dans main.R, j'ai une ligne

Code:

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source("functions.R")

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Si j'écris la même chose dans le fichier functions.R, j'ai un problème d'accents:

Code:

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dÚfinition des variables

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Il est possible que main.R et functions.R n'aient pas le même encodage.
Etant donné que main.R affiche bien les accents, j'aimerais connaître l'encodage du fichier, mais comment le trouver sachant que j'utilise RStudio ?

Bref, je ne sais d'où ça vient..

En vous remerciant par avance de vos réponses,

Mathieu

Bonjour,
il y a quelques mois, vous aviez posé la même question, désolé de vous refaire la même chose : qu'indique les sorties de l'instruction suivante ?

Code:

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sessionInfo()$locale

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Bonjour,

Tout d'abord, je vous prie de m'excuser. Je dois perdre un peu la mémoire, n'ayant pas eu le souvenir d'avoir posté ce sujet il y a quelques mois

Je viens d'avancer dans mon problème mais ne suis pas parvenu malgré tout à le résoudre.

Voici ce que donne sessionInfo()

Code:

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1 2	> sessionInfo()$locale [1] "LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252"

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En fait, j'ai remarqué que le chargement de certains paquets provoquait ce problème d'encodage. C'est le cas d'un paquet appelé RStoolbox et d'igraph

Si, dans mon main.R, j'écris les lignes ci-dessous et si je les exécute via Rscript :

Code:

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cat("first \U00E9 \n") cat("--before--\n") cat(paste("encoding = ", getOption("encoding"), "\n")) cat(paste("locale = ", Sys.getlocale(), "\n")) require("RStoolbox") cat("\n") cat("--after--\n") cat(paste("encoding = ", getOption("encoding"),"\n")) cat(paste("locale = ", Sys.getlocale(), "\n")) cat(" second \U00E9")

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J'obtiens :

Code:

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1 2 3 4 5 6 7 8 9 10 11 12 13 14

first é --before-- encoding = native.enc locale = LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY= French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252 Le chargement a nécessité le package : RStoolbox Message d'avis : le package 'RStoolbox' a ÚtÚ compilÚ avec la version R 3.1.3   --after-- encoding = native.enc locale = LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY= French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252 second Ú

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A noter que si j'exécute tout ça sans Rscript, il n'y a pas d'erreur.

Ce qui est perturbant, c'est que rien ne change niveau encodage, comme les instructions cat() le démontrent. Par contre, le caractère n'est plus reconnu à la fin. Quelque chose change, mais je ne sais quoi..

Je n'ai pas assez d'éléments pour donner une réponse satisfaisante ; je vais donc vous redemander d'autres sorties, celles de ces instructions :

Code:

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sessionInfo()   Sys.getlocale("LC_MESSAGES")   cat("--before--\n") cat(paste0("encoding = ", getOption("encoding"), "\n"), sep = "") cat(paste0("locale = ", Sys.getlocale(), "\n"), sep = "") l10n_info() cat("first \U00E9 \n") require("RStoolbox") cat("\n") cat("--after--\n") cat(paste0("encoding = ", getOption("encoding"),"\n"), sep = "") cat(paste0("locale = ", Sys.getlocale(), "\n"), sep = "") l10n_info() cat(" second \U00E9")

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P.S. Peut-être que je me méprends, il me semble toujours que ce message était le vôtre. Mais qu'à cela ne tienne, essayons de résoudre(message modifié ici) corriger l'erreur cette fois-ci.

Bonjour,

je vous prie de m'excuse de répondre aussi tardivement

J'ai donc mis le code dans un fichier appelé test_accent.R

Puis j'ai lancé la commande

Code:

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Rscript test_accent.R

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: en effet, le problème n'apparaît que lors de l'exécution du code en mode batch et non depuis RStudio

Voici ce que j'obtiens :

Code:

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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31

rscript test_accent.R --before-- encoding = native.enc locale = LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=F rench_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252 $MBCS [1] FALSE   $`UTF-8` [1] FALSE   $`Latin-1` [1] TRUE   $codepage [1] 1252   first é Le chargement a nécessité le package : RStoolbox Message d'avis : le package 'RStoolbox' a ÚtÚ compilÚ avec la version R 3.1.3   --after-- encoding = native.enc locale = LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=F rench_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252 $MBCS [1] FALSE   $`UTF-8` [1] FALSE

---

$`Latin-1`
[1] TRUE

$codepage
[1] 1252

Bonjour,
Il y a maintenant des indications assez précises que les paramètres régionaux du système d'exploitation (ou de l'interpréteur des commandes) diffèrent de ceux de R. C'est d'ailleurs la piste qui était donnée dans la première réponse à l'ancienne discussion.
Comme vous aviez lancé un script, toutes les sorties attendues n'ont pas été générées, il fallait ajouter explicitement des instructions d'affichage. Allons-y alors pour un autre tour : pouvez-vous relancer Rscript test_accent.R et donner les sorties, test_accent.R contenant le code ci-bas ?

Code:

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cat("\n--before--\n\n") cat("LC_MESSAGES:\n", Sys.getlocale("LC_MESSAGES"), "\n\n", sep = "") cat("encoding:\n", getOption("encoding"), "\n\n", sep = "") cat("locale:\n", Sys.getlocale(), "\n\nl10n_info:\n", sep = "") str(l10n_info()) cat("\n\nà â ï î é è ô ü ç\n\n") str(sessionInfo())   require("RStoolbox")     cat("\n\n\n--after--\n\n") cat("LC_MESSAGES:\n", Sys.getlocale("LC_MESSAGES"), "\n\n", sep = "") cat("encoding:\n", getOption("encoding"), "\n\n", sep = "") cat("locale:\n", Sys.getlocale(), "\n\nl10n_info:\n", sep = "") str(l10n_info()) cat("\n\nà â ï î é è ô ü ç\n\n") str(sessionInfo())

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P.S. Les sorties seront un peu abondantes, les laisser en l'état, il n'y a pas de souci.
P.P.S. Pas de souci pour le temps que ça vous prend pour répondre, il n'y a pas d'urgence me concernant.

Bonjour,

Voici le résultat des commandes. C'est très long.

Merci en tout cas pour votre aide !

Code:

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---

Bonjour,
Les paramètres régionaux du Windows que vous utilisez sont appelés Windows-1252. R n'a aucun moyen de les deviner, on les indique explicitement car par défaut c'est de l'Unicode qui est attendu. Les paquets/bibliothèques/ que vous utilisez ne touchent pas aux paramètres par défaut, le problème ne venait pas de là. Ceci devrait s'exécuter en donnant les bonnes sorties :

1) dans test_accent.R, mettre la seule instruction

Code:

---

cat("\nà â ï î é è ô ü ç\n")

---

2) dans l'interpréteur de commandes (IC) de Windows, lancer

Rscript --encoding=latin1 test_accent.R

3) dans l'IC de R, lancer

Code:

---

source("test_accent.R", encoding = "latin1")

---

P.S. Il y a 5 versions de retard entre le R que vous utilisez et la dernière version en date.

Bonjour,

Merci pour tous les retours.

j'ai donc changé le contenu de test_accent.R en mettant :

Code:

---

cat("\nà â ï î é è ô ü ç\n")

---

j'ai exécuté le code dans l'invite de commandes windows mais j'obtiens toujours des caractères bizarres..

Code:

---

1 2 3

Rscript --encoding=latin1 test_accent.R   Ã* â ï î é è ô ü ç

---

Juste pour mes tests, j'ai alors mis le code suivant dans mon fichier test_accent.R :

Code:

---

1 2 3 4

cat("\nà â ï î é è ô ü ç\n") cat("first \U00E9 \n") require(RStoolbox) cat("second \U00E9 \n")

---

En mettant --encoding=UTF-8, j'obtiens :

Code:

---

1 2 3 4 5 6

à â ï î é è ô ü ç first é Le chargement a nécessité le package : RStoolbox Message d'avis : le package 'RStoolbox' a ÚtÚ compilÚ avec la version R 3.1.3 second Ú

---

En mettant --encoding=ISO-8859-1 :

Code:

---

1 2 3 4 5 6

Ã* â ï î é è ô ü ç first é Le chargement a nécessité le package : RStoolbox Message d'avis : le package 'RStoolbox' a ÚtÚ compilÚ avec la version R 3.1.3 second Ú

---

La situation paraît difficilement soluble..
:roll:

Le problème me paraît réglé : le bon encodage du fichier est UTF-8. En faisant cat("second \U00E9 \n"), vous manipulez directement les points de code, ce qui devrait être fait en bonne connaissance de cause.

Pour Windows, dans la console (en trouvant les bonnes options, la machine (virtuelle) à ma disposition étant configurée différemment de la vôtre)

1) changer les fontes :
Properties ⟶ Font ⟶ Lucida Console ⟶ OK ;

2) saisir la commande (CMD.exe, pas R)

chcp

afin de voir la page de code actuelle ;

3) saisir la commande

chcp 65001

pour passer à l'Unicode ; trouver le bon chiffre pour tout autre encodage.

Quant à R, on peut faire une vérification supplémentaire de l'encodage du fichier : que donne en sortie les instructions suivantes, exécutées avec Rscript --encoding=UTF-8 test_accent.R ?

Code:

---

1 2 3 4 5 6 7 8 9 10 11

library("stringi") xxx <- "\nÉ È é ù ç à\n" yyy <- stri_enc_detect(xxx) str(yyy) cat("\n", yyy[[1L]]$Encoding, "\n", xxx, "\n") require(RStoolbox) vvv <- "\nà â ï î é è ô ü ç\n" www <- stri_enc_detect(vvv) cat("\n\n") str(www) cat("\n\n", vvv, "\n", www[[1L]]$Encoding, "\n")

---

J'ai changé la police en Lucida Console.

j'ai appliqué chcp 65001

J'ai rajouté dans le script test_accent.R la ligne permettant d'afficher les accents car ce qui pose souci, c'est lorsque la librairie RStoolbox est chargée, consécutivement à laquelle lesaccents s'affichent mal..

Le code de test_accent.R :

Code:

---

1 2 3 4 5 6 7 8 9 10 11

library("stringi") xxx <- "\nÉ È é ù ç à\n" yyy <- stri_enc_detect(xxx) str(yyy) cat("\n", yyy[[1L]]$Encoding, "\n", xxx, "\n") require(RStoolbox) vvv <- "\nà â ï î é è ô ü ç\n" www <- stri_enc_detect(vvv) cat("\n\n") str(www) cat("\n", yyy[[1L]]$Encoding, "\n", xxx, "\n")

---

le résultat :

Code:

---

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28

Message d'avis : le package 'stringi' a été compilé avec la version R 3.1.3 List of 1 $ :List of 3 ..$ Encoding : chr [1:6] "KOI8-R" "ISO-8859-1" "ISO-8859-7" "windows-1251" .. . ..$ Language : chr [1:6] "ru" "fr" "el" "ru" ... ..$ Confidence: num [1:6] 0.42 0.21 0.21 0.21 0.1 0.1   KOI8-R ISO-8859-1 ISO-8859-7 windows-1251 UTF-16BE UTF-16LE   É È é ù ç à   Le chargement a nécessité le package : RStoolbox Message d'avis : le package 'RStoolbox' a �t� compil� avec la version R 3.1.3     List of 1 $ :List of 3 ..$ Encoding : chr [1:6] "ISO-8859-7" "windows-1251" "ISO-8859-1" "KOI8-R" .. . ..$ Language : chr [1:6] "el" "ru" "fr" "ru" ... ..$ Confidence: num [1:6] 0.3 0.3 0.15 0.15 0.1 0.1   KOI8-R ISO-8859-1 ISO-8859-7 windows-1251 UTF-16BE UTF-16LE   � � � � � �

---

Voilà donc le résultat
C'est assez mystérieux

Il y a une fuite de mémoire lors du chargement de RStoolbox. Voici comment la détecter avec Valgrind (sur ma machine, il y a du Linux, je n'ai pas essayé Valgrind sur Windows).

1) script « normal » : normal.R

Code:

---

1 2	cat("\n\nà â ï î é è ô ü ç\n\n") cat("\n\nà â ï î é è ô ü ç\n\n")

---

2) script bogué : bogué.R

Code:

---

1 2 3

cat("\n\nà â ï î é è ô ü ç\n\n") require("RStoolbox") cat("\n\nà â ï î é è ô ü ç\n\n")

---

3) Appels de Valgrind

Code:

---

1 2	R -d "valgrind --leak-check=full --show-reachable=yes --xml=yes --xml-file=valgrind_out_good.xml" -f normal.R R -d "valgrind --leak-check=full --show-reachable=yes --xml=yes --xml-file=valgrind_out.xml" -f bogué.R

---

4) Très bref résumé des sorties de Valgrind

Code:

---

grep '<kind>' valgrind_out.xml valgrind_out_good.xml | uniq

---

valgrind_out.xml:  <kind>Leak_StillReachable</kind>
valgrind_out.xml:  <kind>Leak_DefinitelyLost</kind>
valgrind_out.xml:  <kind>Leak_StillReachable</kind>
valgrind_out.xml:  <kind>Leak_PossiblyLost</kind>
valgrind_out.xml:  <kind>Leak_StillReachable</kind>
valgrind_out_good.xml:  <kind>Leak_StillReachable</kind>
valgrind_out_good.xml:  <kind>Leak_PossiblyLost</kind>
valgrind_out_good.xml:  <kind>Leak_StillReachable</kind>

Leak_DefinitelyLost est une fuite de mémoire assez grave pour être ignorée. Peut-être que l'erreur de l'encodage ne vient pas de cette fuite, mais il faudrait quand même la corriger avant de continuer à utiliser le paquet. Je vous propose donc d'ouvrir un ticket sur le dépôt de RStoolbox afin de signaler le bogue, tout en indiquant que vous avez rencontré également l'erreur d'encodage.

Bonjour,

je vous remercie pour tout ce suivi.

Je viens de poster l'issue sur le site :
https://github.com/bleutner/RStoolbox/issues/5

J'ai remarqué que ce problème d'accent apparaissait également pour le paquet igraph. Si ce pb avait la même origine que pour RSToolbox, cela pourrait être assez grave, étant donnée la popularité d'igraph.

Je considère le post comme résolu

Merci

De rien !
Après une analyse des journaux générés hier, il s'avère que le bogue ne vient pas de RStoolbox mais plutôt de rgeos, un paquet importé dans l'espace des noms de RStoolbox. Je viens d'ouvrir un ticket sur GEOS. Vous pourrez donc signaler cela à Benjamin dans le rapport de bougue que vous avez rédigé tout en lui notifiant que l'issue a été rapportée au bon endroit ; URL : http://trac.osgeo.org/geos/ticket/767
P.S. Vous pouvez également marquer cette discussion comme résolue.

Bonjour Matthieu,
J'ai suivi la discussion que vous avez eu avec Benjamin (le mainteneur de RStoolbox) sut GitHub et dans l'entretemps, Roger (le mainteneur de rgeos) et moi avons échangé par emails interposés car là où j'avais rapporté l'erreur n'était pas le bon endroit. En commun accord avec Roger, je reproduis ici les échanges que nous avons eu. Mais tout d'abord, voici la partie publique des discussions sur GEOS. À noter que GEOS est un ensemble d'outils écrits en C++ tandis que rgeos en est le port (binding) dans R.

Échanges publics
philae (mon pseudo sur l'outil de suivi des bogues)
Thu Feb 4 01:59:22 PST 2016
http://lists.osgeo.org/pipermail/geo...ry/007397.html

Roger
Thu Feb 4 14:15:27 PST 2016
http://lists.osgeo.org/pipermail/geo...ry/007398.html

Roger
Thu Feb 4 14:30:23 PST 2016
http://lists.osgeo.org/pipermail/geo...ry/007399.html

Sandro Santilli (un développeur de GEOS)
Thu Feb 4 23:55:39 PST 2016
http://lists.osgeo.org/pipermail/geo...ry/007400.html

Roger
Fri Feb 5 00:38:19 PST 2016
http://lists.osgeo.org/pipermail/geo...ry/007406.html

strk (un développeur de GEOS)
Fri Feb 5 01:40:13 PST 2016
http://lists.osgeo.org/pipermail/geo...ry/007407.html

philae
Fri Feb 5 03:06:44 PST 2016
http://lists.osgeo.org/pipermail/geo...ry/007408.html



Les mails avec Roger

Eric (votre serviteur)
Fri 2/05/16 1:00 PM

Dear Roger,

This is a second attempt to reply to your first message, hoping it will be delivered in plain text. Below is the verbatim of my first message, slightly edited:

I was reacting to this message: https://lists.osgeo.org/pipermail/ge...ry/007399.html

First of all, I thought that the bug tracker would also be the right place to report about rgeos issues, since it is part of the package DESCRIPTION's file on the same line as your email address. I am sorry for the confusion my first message generated.

I did not personally encounter a bug while using rgeos. I was rather helping an indirect user of the package who was seeking for help on a francophone forum, namely here: (1)

The person is attaching a CRAN package, RStoolbox, that imports rgeos into its namespace. Before attaching RStoolbox, he could print accented characters, for instance using cat and, until that point everything was fine. But then after RStoolbox had been attached, accents formatting was lost. The locale on that machine was:

Code:

---

LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252

---

R is running there on a Windows 64 bits. I suggested him to look at the encoding of CMD.exe as well as setting the "--encoding=" option of Rscript, which were the ways his code was ran. He tried latin1 and UTF-8 as values of the encoding option; it came out UTF-8 was the right file encoding, but he still had formatting clashes after attaching RStoolbox.

After all of that, I debugged his code using Valgrind on a Fedora machine which ended with the memory leak I brought on the bug tracker. The Valgrind logs indicated the leak actually occurred in rgeos and not in RStoolbox. In the meantime, the user I was helping had contacted the RStoolbox's maintainer, please refer to (2) for details. Fair enough, the maintainer replied to him to rather refer to upstream, i.e rgeos maintainers.

To sum up everything:

• a Windows (64 bits) user, in a Latin-1 locale, is having trouble with accents characters. The culprit for the mis-formatting seems to be something happening when RStoolbox is attached on the R search path.
• I am using a Fedora machine. I can't reproduce his bug. I asked Valgrind to tell what might be happening using memcheck, cachegrind, callgrind, helgrind, drd, etc. and thus far, only memcheck complained about something wrong, that being the leakage involved in the current thread.

The original debugged code was:

Code:

---

1 2 3

cat("\n\nà â ï î é è ô ü ç\n\n") #L1 library("RStoolbox") #L2 cat("\n\nà â ï î é è ô ü ç\n\n") #L3

---

The Windows user reported that L1 was displayed as expected and L3 wasn't. All the discussion is publicly available at (1) in French. I am not sure the encoding issue is triggered by that memory leak. All I can say is a bit strange about the above code, provided the OS and R have the same settings as that user's, is the memory leak regardless of its smallness. Maybe its fix would come with the side effect of not ruining the user's locale settings.

Best wishes,
Eric.

(1) http://www.developpez.net/forums/d15...-accent-aigue/
(2) https://github.com/bleutner/RStoolbox/issues/5

P.S. Another confused situation Roger wrote about was the "philae" name: that is the pseudonym I chose on the bug tracker.


Roger
Fri 2/05/16 3:41 PM

Dear Eric,

Replying off-list.

On Windows 7 with (apologies for malformed formatting in outlook webmail):

Code:

---

sessionInfo()

---

R version 3.2.3 (2015-12-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 7 x64 (build 7601) Service Pack 1
locale:
[1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 
[3] LC_MONETARY=French_France.1252 LC_NUMERIC=C 
[5] LC_TIME=French_France.1252 
attached base packages:
[1] stats graphics grDevices utils datasets methods base 
other attached packages:
[1] RStoolbox_0.1.4
loaded via a namespace (and not attached):
[1] Rcpp_0.12.3 raster_2.5-2 magrittr_1.5 splines_3.2.3 
[5] MASS_7.3-45 doParallel_1.0.10 munsell_0.4.2 geosphere_1.5-1 
[9] colorspace_1.2-6 lattice_0.20-33 foreach_1.4.3 minqa_1.2.4 
[13] stringr_1.0.0 car_2.1-1 plyr_1.8.3 tools_3.2.3 
[17] parallel_3.2.3 nnet_7.3-12 pbkrtest_0.4-6 caret_6.0-64 
[21] grid_3.2.3 gtable_0.1.2 nlme_3.1-124 mgcv_1.8-11 
[25] quantreg_5.19 rgeos_0.3-15 MatrixModels_0.4-1 iterators_1.0.8 
[29] lme4_1.1-10 Matrix_1.2-3 nloptr_1.0.4 reshape2_1.4.1 
[33] ggplot2_2.0.0 codetools_0.2-14 sp_1.2-1 stringi_1.0-1 
[37] scales_0.3.0 XML_3.98-1.3 stats4_3.2.3 SparseM_1.7 

the problem is not present and cannot be reproduced. I'm running:

Code:

---

Sys.setlocale(locale="French_France.1252")

---

[1] "LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252"

Code:

---

Sys.getlocale()

---

[1] "LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252"

Code:

---

cat("\n\nà â ï î é è ô ü ç\n\n")

---

à â ï î é è ô ü ç

Code:

---

1 2	target <- "\n\nà â ï î é è ô ü ç\n\n" target

---

[1] "\n\nà â ï î é è ô ü ç\n\n"

Code:

---

cat(target)

---

à â ï î é è ô ü ç

Code:

---

1 2	library(RStoolbox) cat(target)

---

à â ï î é è ô ü ç

in the GUI. My Windows locale is also CP1252, so I'm setting to French_France to match the thread on developpez.net.

I also back-transformed the reported output:

Code:

---

1 2	t1 <- "Ã* â ï î é è ô ü ç" t1

---

[1] "Ã* â ï î é è ô ü ç"

Code:

---

1 2	Encoding(t1) <- "UTF-8" t1

---

[1] "\xc3* â ï î é è ô ü ç"

so with the exception of the first character a grave (probably miscoded somewhere with * (hex 2a) rather than hex a0), it is being pushed to UTF-8.

The only difference I can see is that I do not get the startup message about RStoolbox being compiled under an earlier version of R.

I also ran:

Code:

---

Sys.setlocale(locale="French_France.1252")

---

[1] "LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252"

Code:

---

Sys.getlocale()

---

[1] "LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252"

Code:

---

1 2	target <- "\n\nà â ï î é è ô ü ç\n\n" target

---

[1] "\n\nà â ï î é è ô ü ç\n\n"

Code:

---

cat(target)

---

à â ï î é è ô ü ç

Code:

---

library(rgeos)

---

rgeos version: 0.3-15, (SVN revision 515)
GEOS runtime version: 3.4.2-CAPI-1.8.2 r3921 
Linking to sp version: 1.2-1 
Polygon checking: TRUE 

Code:

---

cat(target)

---

à â ï î é è ô ü ç

and once again no problem.

I am not seeing a difference in Rscript either for test.R:

Code:

---

1 2 3 4 5 6 7

Sys.setlocale(locale="French_France.1252") Sys.getlocale() target <- "\n\nà â ï î é è ô ü ç\n\n" cat(target) library(rgeos) cat(target) quit("no")

---

C:\Users\rsb\Documents>"C:/Program Files/R/R-3.2.3/bin/x64/Rscript.exe" test.R
[1] "LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252"
[1] "LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=French_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252"

à â ï î é è ô ü ç
rgeos version: 0.3-15, (SVN revision 515)
GEOS runtime version: 3.4.2-CAPI-1.8.2 r3921
Linking to sp version: 1.2-1
Polygon checking: TRUE

à â ï î é è ô ü ç

So I'm not sure what is happening here. Please consider updating the thread on developpez.net. The original questioner should anyway update packages to the version of R that is being used, which would remove the warning message (the first use of an errant charset).

Best wishes,

Roger

--
Roger Bivand
Norwegian School of Economics
Helleveien 30, 5045 Bergen, Norway
Roger.Bivand@nhh.no


Eric
Fri 2/05/16 6:40 PM

Dear Roger, All that hard work you did to reproduce the Windows workflow, that's great! Thank you so much. And the formatting is OK. So if you please, I would like to just copy-paste your answer to the thread on developpez.net. Would you bother if I did so ?

If you are fluent in French, you can see that in (1) Matthieu (the user) gave three days ago extensive sessionInfo and that I (juliatheric) subsequently warned him in (2) his R was lagging five versions behind the mainline release. The packages are too old to as shown in the enclosed "versionData.tab" file [au lieu de mettre en pièce jointe le fichier en question, je recopie ici son contenu].

Code:

---

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43

PackageName MatthieuVersion RogerVersion Mat_vs_Rog RStoolbox 0.1.1 0.1.4 Mat < Rog Rcpp_0.12.3 0.12.0 0.12.3 Mat < Rog raster 2.3-40 2.5-2 Mat < Rog magrittr 1.5 1.5 Mat = Rog splines 3.1.2 3.2.3 Mat < Rog MASS 7.3-35 7.3-45 Mat < Rog doParallel 1.0.8 1.0.10 Mat < Rog munsell 0.4.2 0.4.2 Mat = Rog geosphere 1.4-3 1.5-1 Mat < Rog colorspace 1.2-6 1.2-6 Mat = Rog lattice 0.20-29 0.20-33 Mat < Rog foreach 1.4.2 1.4.3 Mat < Rog minqa 1.2.4 1.2.4 Mat = Rog stringr 1.0.0 1.0.0 Mat = Rog car 2.0-25 2.1-1 Mat < Rog plyr 1.8.3 1.8.3 Mat = Rog tools 3.1.2 3.2.3 Mat < Rog parallel 3.1.2 3.2.3 Mat < Rog nnet 7.3-8 7.3-12 Mat < Rog pbkrtest 0.4-2 0.4-6 Mat < Rog caret 6.0-57 6.0-64 Mat < Rog grid 3.1.2 3.2.3 Mat < Rog gtable 0.1.2 0.1.2 Mat = Rog nlme 3.1-118 3.1-124 Mat < Rog mgcv 1.8-3 1.8-11 Mat < Rog quantreg 5.19 5.19 Mat = Rog rgeos 0.3-8 0.3-15 Mat < Rog MatrixModels 0.4-1 0.4-1 Mat = Rog iterators 1.0.7 1.0.8 Mat < Rog lme4 1.1-10 1.1-10 Mat = Rog Matrix 1.2-2 1.2-3 Mat < Rog nloptr 1.0.4 1.0.4 Mat = Rog reshape2 1.4.1 1.4.1 Mat = Rog ggplot2 1.0.1 2.0.0 Mat < Rog codetools 0.2-9 0.2-14 Mat < Rog sp 1.0-17 1.2-1 Mat < Rog stringi 0.5-5 1.0-1 Mat < Rog scales 0.2.5 0.3.0 Mat < Rog XML 3.98-1.3 3.98-1.3 Mat = Rog stats4 3.1.2 3.2.3 Mat < Rog SparseM 1.7 1.7 Mat = Rog

---

Code:

---

1 2	versionData <- read.delim("versionData.tab", quote = "", stringsAsFactors = FALSE) table(versionData$Mat_vs_Rog)

---

Mat < Rog Mat = Rog
            27             14

Matthieu should update his packages and everything will be fine since you reproduced his entire environment and locale settings remained as they had been before. Once more, thank you so much.

The best,
Eric.

(1) http://www.developpez.net/forums/d15...e/#post8520099
(2) http://www.developpez.net/forums/d15...e/#post8520288


Roger
Fri 2/05/16 8:29 PM

> Dear Roger,
>
> All that hard work you did to reproduce the Windows workflow, that's
> great! Thank you so much. And the formatting is OK. So if you please, I
> would like to just copy-paste your answer to the thread on
> developpez.net. Would you bother if I did so ?

Of course - followers of the thread will benefit from a resolution.
However, please ask that Matthieu confirms that this does resolve the
problem for him after upgrading.

>
> If you are fluent in French, you can see that in (1) Matthieu (the user)
> gave three days ago extensive sessionInfo and that I (juliatheric)
> subsequently warned him in (2) his R was lagging five versions behind
> the mainline release. The packages are too old to as shown in the
> enclosed "versionData.tab" file.

Not fluent, but the code helped to follow the arguments. The charset
switching is still odd. I tried to install rgeos from R 3.0 and 3.1 in R
3.2.3 to see if I could generate the warnings without success, so it
wasn't a complete reconstruction.

>> table(versionData$Mat_vs_Rog)
> Mat < Rog Mat = Rog
> 27 14
>
> Matthieu should update his packages and everything will be fine since
> you reproduced his entire environment and locale settings remained as
> they had been before. Once more, thank you so much.
>

I do try to check reported issues, as this would have been serious. We see
some valgrind false positives when it takes snapshots as optimized code
exits, and R's garbage collector can I believe confuse it. All CRAN
package C/C++ code is also run through clang, which is much less forgiving
than gcc - rgeos is clean there:

https://cran.r-project.org/web/check...lts_rgeos.html

(the error for osx-mavericks is because of missing GEOS on the testing
system).

Best wishes,

Roger

> The best,
> Eric.
>
> (1) http://www.developpez.net/forums/d15...e/#post8520099
> (2) http://www.developpez.net/forums/d15...e/#post8520288

--
Roger Bivand
Department of Economics, Norwegian School of Economics,
Helleveien 30, N-5045 Bergen, Norway.
voice: +47 55 95 93 55; fax +47 55 95 91 00
e-mail: Roger.Bivand@nhh.no
http://orcid.org/0000-0003-2392-6140
https://scholar.google.no/citations?...hB0AAAAJ&hl=en
http://depsy.org/person/434412



Alors, je vous propose de mettre à jour

1. R si ce n'est déjà fait, en téléchargeant le dernier binaire en date et en désinstallant l'ancien ;
2. tous vos paquets en lançant la commande

Code:

---

update.packages(ask = FALSE)

---

Il existe des outils qui automatisent les deux étapes, mais peut-être que vous avez d'autres habitudes. L'essentiel est qu'à la fin, les sorties de sessionInfo() sur votre machine devraient être les mêmes que celles obtenues sur celle de Roger. Comme vous l'avez lu, ce dernier est très intéressé de savoir ce que donnera en sortie le code qui échouait une fois que les mises à jour auront été faites. Merci d'indiquer donc ces sorties.

Bon weekend,
Eric.

P.S. J'espère que les modératrices & modérateurs auront la mansuétude de tolérer ce pavé comportant de larges portions écrites dans une autre langue que le français. À mon avis, la sollicitude de Roger oblige. Pour information, Roger BIVAND, en plus de sa très brève présentation faite au début de ce message, est aussi membre de la fondation R (ça sent peut-être l'argument d'autorité mais j'ai noté utile de le signaler).

Bonjour,

J'ai MAJ R, ainsi que mes librairies.

J'ai créé un script avec le code de Roger Bivand, avec en plus un petit sessionInfo() :

Code:

---

1 2 3 4 5 6 7 8

Sys.setlocale(locale="French_France.1252") Sys.getlocale() target <- "\n\nà â ï î é è ô ü ç\n\n" cat(target) library(RStoolbox) print(sessionInfo()) cat(target) quit("no")

---

J'ai lancé la commande avec R nouvelle version :

Code:

---

C:\R\R-3.2.3\bin\rscript test_accent.R

---

Et j'obtiens :

Code:

---

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48

[1] "LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=Frenc h_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252" [1] "LC_COLLATE=French_France.1252;LC_CTYPE=French_France.1252;LC_MONETARY=Frenc h_France.1252;LC_NUMERIC=C;LC_TIME=French_France.1252"     à â ï î é è ô ü ç   R version 3.2.3 (2015-12-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1   locale: [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 [3] LC_MONETARY=French_France.1252 LC_NUMERIC=C [5] LC_TIME=French_France.1252   attached base packages: [1] stats graphics grDevices utils datasets base   other attached packages: [1] RStoolbox_0.1.4   loaded via a namespace (and not attached): [1] Rcpp_0.12.3 raster_2.5-2 magrittr_1.5 splines_3.2.3   [5] MASS_7.3-45 doParallel_1.0.10 munsell_0.4.2 geosphere_1.5-1   [9] colorspace_1.2-6 lattice_0.20-33 foreach_1.4.3 minqa_1.2.4   [13] stringr_1.0.0 car_2.1-1 plyr_1.8.3 tools_3.2.3   [17] parallel_3.2.3 nnet_7.3-12 pbkrtest_0.4-6 caret_6.0-64   [21] grid_3.2.3 gtable_0.1.2 nlme_3.1-124 mgcv_1.8-11   [25] quantreg_5.19 rgeos_0.3-15 MatrixModels_0.4-1 iterators_1.0.8   [29] lme4_1.1-10 Matrix_1.2-3 nloptr_1.0.4 reshape2_1.4.1   [33] ggplot2_2.0.0 codetools_0.2-14 sp_1.2-2 stringi_1.0-1   [37] methods_3.2.3 scales_0.3.0 XML_3.98-1.3 stats4_3.2.3   [41] SparseM_1.7     Ó Ô ´ ¯ Ú Þ ¶ ³ þ

---

Par contre, pas de souci rencontré avec rgeos où tous les accents s'affichent bien, y compris avec la version précédente de R que j'avais, la 3.1.2

Je penche donc plus sur un souci localisé au niveau de RStoolbox, peut-être non liée à la fuite de mémoire révélée par valgrind.

Bonjour,
Pourriez-vous faire une série de vérifications supplémentaires avant d'envisager d'autres solutions ?

1) Afin de s'assurer que tous les packages de toutes les libraries ont été mis à jour :

Code:

---

1 2	chooseCRANmirror() # Choisir le 0-Cloud upgrade(packageStatus(), ask = FALSE)

---

2) Dans CMD.exe, ne pas oublier de changer le point de code en UTF-8 (ça permet de réutiliser de façon reproductible les sorties lors du débogage même quand elles n'ont pas été bien affichées) :

Code:

---

chcp 65001

---

3) Sans toucher aux paramètres régionaux de R, relancer Rscript --encoding=UTF-8 test_accent.R où test_accent.R contient le code suivant :

Code:

---

1 2 3 4 5

target <- "\n\nà â ï î é è ô ü ç\n\n" cat(target) library("RStoolbox") cat(target) print(sessionInfo())

---

Qu'avez-vous en sortie ?

Voilà ce que j'obtiens :

Code:

---

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47

rscript test_accent.R     à â ï î é è ô ü ç   Message d'avis : le package 'RStoolbox' a �t� compil� avec la version R 3.1.3     � � � � � � � � �   R version 3.1.2 (2014-10-31) Platform: i386-w64-mingw32/i386 (32-bit)   locale: [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 [3] LC_MONETARY=French_France.1252 LC_NUMERIC=C [5] LC_TIME=French_France.1252   attached base packages: [1] stats graphics grDevices utils datasets base   other attached packages: [1] RStoolbox_0.1.4   loaded via a namespace (and not attached): [1] car_2.0-25 caret_6.0-64 codetools_0.2-14 colorspace_1.2-6   [5] doParallel_1.0.10 foreach_1.4.3 geosphere_1.5-1 ggplot2_2.0.0   [9] grid_3.1.2 gtable_0.1.2 iterators_1.0.8 lattice_0.20-33   [13] lme4_1.1-10 magrittr_1.5 MASS_7.3-45 Matrix_1.2-3   [17] MatrixModels_0.4-1 methods_3.1.2 mgcv_1.8-11 minqa_1.2.4   [21] munsell_0.4.2 nlme_3.1-124 nloptr_1.0.4 nnet_7.3-12   [25] parallel_3.1.2 pbkrtest_0.4-4 plyr_1.8.3 quantreg_5.19   [29] raster_2.5-2 Rcpp_0.12.3 reshape2_1.4.1 rgeos_0.3-15   [33] scales_0.3.0 sp_1.2-2 SparseM_1.7 splines_3.1.2   [37] stats4_3.1.2 stringi_1.0-1 stringr_1.0.0 tools_3.1.2   [41] XML_3.98-1.3

---

:?

Je pense qu'à défaut de réussir à résoudre ça, autant passer la main au dév de RStoolbox d'autant plus qu'il est courant du souci.

J'ai mis tous mes print avec des e sans accent. Ce n'est pas grave

Bonjour,
Vous n'avez pas fait toutes les mises à jour. La situation attendue était que

1. R soit mis à jour ;
2. les paquets le soient également.

Vous avez accompli le deuxième point mais pas le premier. La version à jour de R est 3.2.3. De votre côté, il y a encore la 3.1.2. Avant que les mainteneurs des paquets ne soient re-contactés, veuillez encore une fois

1. télécharger et ré-installer R, par exemple à partir d'ici : https://cran.r-project.org/bin/windows/base/
2. dans le nouvel environnement de R, évaluer

Code:

---

1 2 3 4 5 6 7

chooseCRANmirror() # Choisir le 0-Cloud upgrade(packageStatus(), ask = FALSE) target <- "\n\nà â ï î é è ô ü ç\n\n" cat(target) library("RStoolbox") cat(target) print(sessionInfo())

---

Bonjour,

Oui, autant pour moi, c'est juste que j'avais oublié de mettre la dernière version dans le PATH..

J'ai donc relancé les commandes de mise à jour, mis chcp 65001 dans la fenêtre DOS

Et j'obtiens :

Code:

---

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46

C:\R\R-3.2.3\bin\Rscript.exe test_accent.R     à â ï î é è ô ü ç       � � � � � � � � �   R version 3.2.3 (2015-12-10) Platform: x86_64-w64-mingw32/x64 (64-bit) Running under: Windows 7 x64 (build 7601) Service Pack 1   locale: [1] LC_COLLATE=French_France.1252 LC_CTYPE=French_France.1252 [3] LC_MONETARY=French_France.1252 LC_NUMERIC=C [5] LC_TIME=French_France.1252   attached base packages: [1] stats graphics grDevices utils datasets base   other attached packages: [1] RStoolbox_0.1.4   loaded via a namespace (and not attached): [1] Rcpp_0.12.3 raster_2.5-2 magrittr_1.5 splines_3.2.3   [5] MASS_7.3-45 doParallel_1.0.10 munsell_0.4.2 geosphere_1.5-1   [9] colorspace_1.2-6 lattice_0.20-33 foreach_1.4.3 minqa_1.2.4   [13] stringr_1.0.0 car_2.1-1 plyr_1.8.3 tools_3.2.3   [17] parallel_3.2.3 nnet_7.3-12 pbkrtest_0.4-6 caret_6.0-64   [21] grid_3.2.3 gtable_0.1.2 nlme_3.1-124 mgcv_1.8-11   [25] quantreg_5.19 rgeos_0.3-15 MatrixModels_0.4-1 iterators_1.0.8   [29] lme4_1.1-10 Matrix_1.2-3 nloptr_1.0.4 reshape2_1.4.1   [33] ggplot2_2.0.0 codetools_0.2-14 sp_1.2-2 stringi_1.0-1   [37] methods_3.2.3 scales_0.3.0 XML_3.98-1.3 stats4_3.2.3   [41] SparseM_1.7

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Bonjour,
Après re-vérification sur un Windows, quoique légèrement différent du vôtre* du point de vue de R, il s'avère que le souci existe bien : il est localisé dans les paramètres par défaut de CMD.exe ; R et les paquets que nous avons abordés jusqu'ici n'ont rien à voir avec le problème, ils ne sont que des révélateurs. Par ailleurs, ce n'est ni rgeos (vous aviez déjà remarqué cela) ni RStoolbox qui sont des révélateurs mais plutôt les paquets car, caret et quantreg, ceux-ci faisant partie de l'arbre des dépendances de RStoolbox.
Alors, il suffit de changer convenablement les paramètres d'encodage de CMD.exe pour que le programme tourne comme on s'y attend (du moins de ce côté-ci). Je vous avais proposé de les mettre en 65001, ce n'était pas la bonne option, mea culpa. Il s'agit plutôt de 1252 et, à regarder attentivement les sorties de sessionInfo()$locale, l'indication était déjà là. Pratiquement donc, ceci fonctionne :

Code:

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chcp 1252

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Code:

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target <- "\n\nà â ï î é è ô ü ç\n\n" cat(target) library("car") # ou library("caret") ou encore library("quantreg") cat(target)

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Une liste détaillée des valeurs possibles pour les points de code de Windows se trouve sur cette page de Wikipédia (en anglais).

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(*) Les sorties de sessionInfo()$platform sont les mêmes que celles obtenues sur votre machine, mais

Code:

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Sys.info()["release"]

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 release
"10 x64"

Super, ça fonctionne.

Merci beaucoup.

C'est vraiment exceptionnel d'avoir une telle aide :)

Merci à vous aussi d'avoir persévéré.
Je transmettrai à R. Bivand les détails de l'issue finale ; l'erreur que détectait Valgrind était sans doute un faux-positif.

C'est surtout vous qui avez persévéré.

Tout le mérite vous revient

Merci encore :)