Bonjour,
Serait-il possible d'installer le package R GAPIT3 dans le serveur RStudio ?
J'ai essayé le code suivant mais j'obtiens des erreurs
module load r/4.2.3
R
> install.packages("devtools")
> devtools::install_github("jiabowang/GAPIT", force=TRUE)
Permission denied (publickey)
Warning in i.p(...) :
'lib = "/shared/ifbstor1/software/miniconda/envs/r-4.2.3/lib/R/library"' is not writable
Would you like to use a personal library instead? (yes/No/cancel)
)
Merci !!
Antoine
Bonjour Antoine,
La réponse est dans la question 
Would you like to use a personal library instead? (yes/No/cancel)
Quand vous installez un paquet R via devtools::install_github, si le paquet ne peut pas être installé dans le répertoire dédié (ce qui est le cas sur le cluster), il vous est alors proposé de l'installer dans voter dossier personnel (/home/...).
Il suffit alors de répondre oui.
Bonjour dbenaben,
J'ai déjà essayé avec le yes mais je ne peux pas écrire dans le dossier d'installation :
devtools::install_github("jiabowang/GAPIT", force=TRUE)
Downloading GitHub repo jiabowang/GAPIT@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?
1: All
2: CRAN packages only
3: None
4: tinytex (0.44 -> 0.45 ) [CRAN]
5: fontawesome (0.5.0 -> 0.5.1) [CRAN]
6: ps (1.7.4 -> 1.7.5) [CRAN]
7: processx (3.8.0 -> 3.8.1) [CRAN]
Enter one or more numbers, or an empty line to skip updates: 3
Installing 6 packages: gdata, bigmemory.sri, snowfall, genetics, EMMREML, bigmemory
Warning in i.p(...) :
'lib = "/shared/ifbstor1/software/miniconda/envs/r-4.2.3/lib/R/library"' is not writable
Would you like to use a personal library instead? (yes/No/cancel) yes
trying URL 'https://cloud.r-project.org/src/contrib/gdata_2.18.0.1.tar.gz'
Content type 'application/x-gzip' length 1054317 bytes (1.0 MB)
==================================================
downloaded 1.0 MB
trying URL 'https://cloud.r-project.org/src/contrib/bigmemory.sri_0.1.6.tar.gz'
Content type 'application/x-gzip' length 2186 bytes
==================================================
downloaded 2186 bytes
trying URL 'https://cloud.r-project.org/src/contrib/snowfall_1.84-6.2.tar.gz'
Content type 'application/x-gzip' length 176212 bytes (172 KB)
==================================================
downloaded 172 KB
trying URL 'https://cloud.r-project.org/src/contrib/genetics_1.3.8.1.3.tar.gz'
Content type 'application/x-gzip' length 199227 bytes (194 KB)
==================================================
downloaded 194 KB
trying URL 'https://cloud.r-project.org/src/contrib/EMMREML_3.1.tar.gz'
Content type 'application/x-gzip' length 6556 bytes
==================================================
downloaded 6556 bytes
trying URL 'https://cloud.r-project.org/src/contrib/bigmemory_4.6.1.tar.gz'
Content type 'application/x-gzip' length 72353 bytes (70 KB)
==================================================
downloaded 70 KB
Error: ERROR: no permission to install to directory ‘/shared/ifbstor1/software/miniconda/envs/r-4.2.3/lib/R/library’
Error: ERROR: no permission to install to directory ‘/shared/ifbstor1/software/miniconda/envs/r-4.2.3/lib/R/library’
Error: ERROR: no permission to install to directory ‘/shared/ifbstor1/software/miniconda/envs/r-4.2.3/lib/R/library’
Error: ERROR: no permission to install to directory ‘/shared/ifbstor1/software/miniconda/envs/r-4.2.3/lib/R/library’
Error: ERROR: no permission to install to directory ‘/shared/ifbstor1/software/miniconda/envs/r-4.2.3/lib/R/library’
Error: ERROR: no permission to install to directory ‘/shared/ifbstor1/software/miniconda/envs/r-4.2.3/lib/R/library’
The downloaded source packages are in
‘/tmp/RtmpZpmWXe/downloaded_packages’
Updating HTML index of packages in '.Library'
── R CMD build ────────────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file ‘/tmp/RtmpZpmWXe/remotes476a517931ac/jiabowang-GAPIT-e3f00be/DESCRIPTION’ (427ms)
─ preparing ‘GAPIT’:
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
─ building ‘GAPIT_3.1.0.tar.gz’
Warning: invalid uid value replaced by that for user 'nobody'
Warning: invalid gid value replaced by that for user 'nobody'
Warning in i.p(...) :
'lib = "/shared/ifbstor1/software/miniconda/envs/r-4.2.3/lib/R/library"' is not writable
Would you like to use a personal library instead? (yes/No/cancel) yes
Error: ERROR: no permission to install to directory ‘/shared/ifbstor1/software/miniconda/envs/r-4.2.3/lib/R/library’
Warning messages:
1: In i.p(...) : installation of package ‘gdata’ had non-zero exit status
2: In i.p(...) :
installation of package ‘bigmemory.sri’ had non-zero exit status
3: In i.p(...) :
installation of package ‘snowfall’ had non-zero exit status
4: In i.p(...) :
installation of package ‘EMMREML’ had non-zero exit status
5: In i.p(...) :
installation of package ‘genetics’ had non-zero exit status
6: In i.p(...) :
installation of package ‘bigmemory’ had non-zero exit status
7: In file.create(f.tg) :
cannot create file '/shared/ifbstor1/software/miniconda/envs/r-4.2.3/lib/R/doc/html/packages.html', reason 'Permission denied'
8: In make.packages.html(.Library) : cannot update HTML package index
9: In i.p(...) :
installation of package ‘/tmp/RtmpZpmWXe/file476a75700e7c/GAPIT_3.1.0.tar.gz’ had non-zero exit status
Antoine
Cela fonctionne correctement chez moi (excepté une erreur de dépendance sur GAPIT).
Je vous invite à supprimer votre répertoire de librairie personnel et à le recréer:
# Suppression
rm -rf ~/R/x86_64-conda-linux-gnu-library/4.2/
# Reinstallation
module load r/4.2.3
R
> install.packages("devtools")
J'ai obtenue encore une erreur avec votre méthode aussi. Est ce que j'ai mal fait quelque chose ?
Merci encore !!!
> install.packages("devtools")
Warning in install.packages("devtools") :
'lib = "/shared/ifbstor1/software/miniconda/envs/r-4.2.3/lib/R/library"' is not writable
Would you like to use a personal library instead? (yes/No/cancel) yes
Would you like to create a personal library
‘/shared/ifbstor1/home/avajou/R/x86_64-conda-linux-gnu-library/4.2’
to install packages into? (yes/No/cancel) yes
--- Please select a CRAN mirror for use in this session ---
trying URL 'https://mirror.ibcp.fr/pub/CRAN/src/contrib/devtools_2.4.5.tar.gz'
Content type 'application/x-gzip' length 374718 bytes (365 KB)
==================================================
downloaded 365 KB
* installing *source* package ‘devtools’ ...
** package ‘devtools’ successfully unpacked and MD5 sums checked
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (devtools)
The downloaded source packages are in
‘/tmp/RtmpiQ4HL6/downloaded_packages’
> devtools::install_github("jiabowang/GAPIT", force=TRUE)
Downloading GitHub repo jiabowang/GAPIT@HEAD
These packages have more recent versions available.
It is recommended to update all of them.
Which would you like to update?
1: All
2: CRAN packages only
3: None
4: tinytex (0.44 -> 0.45 ) [CRAN]
5: fontawesome (0.5.0 -> 0.5.1) [CRAN]
6: ps (1.7.4 -> 1.7.5) [CRAN]
7: processx (3.8.0 -> 3.8.1) [CRAN]
Enter one or more numbers, or an empty line to skip updates: 3
Installing 6 packages: gdata, bigmemory.sri, snowfall, genetics, EMMREML, bigmemory
Installing packages into ‘/shared/ifbstor1/home/avajou/R/x86_64-conda-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
trying URL 'https://mirror.ibcp.fr/pub/CRAN/src/contrib/gdata_2.18.0.1.tar.gz'
Content type 'application/x-gzip' length 1054317 bytes (1.0 MB)
==================================================
downloaded 1.0 MB
trying URL 'https://mirror.ibcp.fr/pub/CRAN/src/contrib/bigmemory.sri_0.1.6.tar.gz'
Content type 'application/x-gzip' length 2186 bytes
==================================================
downloaded 2186 bytes
trying URL 'https://mirror.ibcp.fr/pub/CRAN/src/contrib/snowfall_1.84-6.2.tar.gz'
Content type 'application/x-gzip' length 176212 bytes (172 KB)
==================================================
downloaded 172 KB
trying URL 'https://mirror.ibcp.fr/pub/CRAN/src/contrib/genetics_1.3.8.1.3.tar.gz'
Content type 'application/x-gzip' length 199227 bytes (194 KB)
==================================================
downloaded 194 KB
trying URL 'https://mirror.ibcp.fr/pub/CRAN/src/contrib/EMMREML_3.1.tar.gz'
Content type 'application/x-gzip' length 6556 bytes
==================================================
downloaded 6556 bytes
trying URL 'https://mirror.ibcp.fr/pub/CRAN/src/contrib/bigmemory_4.6.1.tar.gz'
Content type 'application/x-gzip' length 72353 bytes (70 KB)
==================================================
downloaded 70 KB
* installing *source* package ‘gdata’ ...
** package ‘gdata’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (gdata)
* installing *source* package ‘bigmemory.sri’ ...
** package ‘bigmemory.sri’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (bigmemory.sri)
* installing *source* package ‘snowfall’ ...
** package ‘snowfall’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (snowfall)
* installing *source* package ‘EMMREML’ ...
** package ‘EMMREML’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (EMMREML)
* installing *source* package ‘genetics’ ...
** package ‘genetics’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
...
The downloaded source packages are in
‘/tmp/RtmpiQ4HL6/downloaded_packages’
── R CMD build ────────────────────────────────────────────────────────────────────────────────────────────────────
✔ checking for file ‘/tmp/RtmpiQ4HL6/remotes5a05dc09701/jiabowang-GAPIT-e3f00be/DESCRIPTION’ (960ms)
─ preparing ‘GAPIT’:
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
─ building ‘GAPIT_3.1.0.tar.gz’
Warning: invalid uid value replaced by that for user 'nobody'
Warning: invalid gid value replaced by that for user 'nobody'
Installing package into ‘/shared/ifbstor1/home/avajou/R/x86_64-conda-linux-gnu-library/4.2’
(as ‘lib’ is unspecified)
ERROR: dependency ‘LDheatmap’ is not available for package ‘GAPIT’
* removing ‘/shared/ifbstor1/home/avajou/R/x86_64-conda-linux-gnu-library/4.2/GAPIT’
Warning message:
In i.p(...) :
installation of package ‘/tmp/RtmpiQ4HL6/file5a0578a99a9d/GAPIT_3.1.0.tar.gz’ had non-zero exit status
Bonjour,
je reviens vers vous pour vous dire que j'ai réussi à installer mes packages. Il y avait plusieurs problèmes de dépendances de GAPIT à d'autres packages. Je suis passé par une installation manuelle via une archive.
Je vous remercie pour votre aide.
Antoine
Bonjour,
C'est noté. Merci pour le retour.
Please help me solving this issue.
Warning message:
In Sys.setlocale("LC_ALL", "NO_NB.utf8") :
OS reports request to set locale to "NO_NB.utf8" cannot be honored
Error: could not find function "install.packages"
Execution halted
Warning message:
In i.p(...) :
installation of package ‘/var/folders/v8/vmtxys7s59x30rwpr15njg2w0000gn/T//RtmpB8TJrQ/filef0f2d952abe/GAPIT_3.1.0.tar.gz’ had non-zero exit status
Hello, je n'arrive pas non plus à installer GAPIT3
par les manières classique il y a trop de dépendance à des packages que je n'arrive pas à résoudre, meme en utilisant
install.packages("devtools", dependencies = TRUE)
devtools::install_github("jiabowang/GAPIT", force=TRUE)
par l'archive cela ne fonctionne pas mieux.
Installing package into ‘/shared/ifbstor1/home/mferrand/R/x86_64-redhat-linux-gnu-library/3.5’
(as ‘lib’ is unspecified)
Warning: invalid package ‘GAPIT_3.2.0.9000.tar.gz’
Error: ERROR: no packages specified
Warning in install.packages :
installation of package ‘GAPIT_3.2.0.9000.tar.gz’ had non-zero exit status
Si quelqu'un a une idée ?
merci d'avance
et en passant par les menus du RStudio
Error in install.packages : cannot install Windows binary packages on this platform
Bonjour,
Vu que ca ne fonctionnait pas avec l interphase de R Studio de cette adresse :
https://rstudio.cluster.france-bioinformatique.fr/
avec des packages qui manquaient ou pas dans la bonne version pour installer GAPIT et que je n'arrivais pas à installer pour cette version de R (R version 4.1.1 = Est ce qu'on peut changer de version R dans le Rstudio du cluster ?) comme LDheatmap, snpStat, rlang, etc...
j'ai tenté d'installer directement les packages par la console.
BiocManager::install("snpStats")
BiocManager::install(" LDheatmap ")
install.packages("remotes") remotes::install_github("jiabowang/GAPIT3")
Ca a marché.
Mais maintenant je ne sais pas comment lancer ici mon script sans me le faire killer.
module load r/4.2.1
srun Rscript --vanilla /GAPIT.R
slurmstepd: error: Detected 1 oom-kill event(s) in StepId=34571814.0 cgroup. Some of your processes may have been killed by the cgroup out-of-memory handler.
srun: error: cpu-node-27: task 0: Out Of Memory
qu'est ce que je fais mal ?
Merci d'avance
Bonjour Marina,
"Out Of Memory" indique qu'il n'y a pas assez de mémoire pour exécuter le job.
Il suffit donc de demander plus de mémoire (sans précision, ce sont les valuer par défaut qui s'appliquent: https://ifb-elixirfr.gitlab.io/cluster/doc/slurm/slurm_at/#the-default-values) via --mem ou --mem-per-cpu (https://ifb-elixirfr.gitlab.io/cluster/doc/quick-start/#slurm-commands)
Merci pour ta réponse.
srun Rscript --vanilla /GAPIT.R --mem=32000
srun Rscript --vanilla /GAPIT.R --mem=90000
Même erreur...
Marina,
L'option pour demander plus de mémoire est une option pour srun, il faut donc la placer avant l'appel de RScript:
srun --mem=32G Rscript --vanilla /GAPIT.R
A noter que je vous invite à utiliser plutôt sbatch (et un script dédié). srun étant plutôt pour avoir une interactivité ou lancer des petites commandes.
Le script permets aussi de spécifier au début toutes les directives nécessaires telles que le nombre de CPU, la mémoire, le time (via #SBATCH...). Cela permets de garder une trace des paramètres (très utile quand on revient dessus quelques temps après), de pouvoir lancer des traitements en parallèle via plusieurs jobs, etc.
Bref, pour les traitements (hors mise au point ou petite commande), cela me semble plus adapté.
Ok merci beaucoup dbenaben
c'est effectivement ca l'étape qui me manquait. Maintenant ça se lance.
sbatch scriptbash_GAPIT.sh
#!/bin/bash
#SBATCH -p fast # partition
#SBATCH -N 1 # nombre de nœuds
#SBATCH -n 10 # nombre de cœurs
#SBATCH --mem 32GB # mémoire vive pour l'ensemble des cœurs
#SBATCH -o slurm.%N.%j.out # STDOUT
#SBATCH -e slurm.%N.%j.err # STDERR
module load r/4.2.1
srun Rscript --vanilla /shared/home/mferrand/hapmap/GAPIT/GAPIT.R