Bonjour,
Je ne parviens pas à installer les packages rjags et infercnv (nécessaire pour lancer la fonction runCNV du package SPATA2), soit disant car la bibliothèque JAGS n'est pas installée.
Savez vous comment je pourrais régler ce problème s'il vous plait ?
Merci !
Pierre-Emmanuel
Bonjour,
Difficile de vous aider sans plus de détail (dont le message d'erreur).
Intuitivement, je dirais qu'il faut installer JAGS 
Et si vous l'avez déjà installé, il faut probablement spécifier les bonnes variables d'environnements pour indiquer où trouver la libraire (par exemple, LD_LIBRARY_PATH=<lib-dossier-jags>).
voila le message :
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.15 (BiocManager 1.30.19), R 4.2.1 (2022-06-23)
Installing package(s) 'rjags'
trying URL 'https://cran.rstudio.com/src/contrib/rjags_4-16.tar.gz'
Content type 'application/x-gzip' length 76035 bytes (74 KB)
==================================================
downloaded 74 KB
* installing *source* package ‘rjags’ ...
** package ‘rjags’ successfully unpacked and MD5 sums checked
** using staged installation
checking for pkg-config... /shared/ifbstor1/software/miniconda/envs/r-4.4.1/bin/pkg-config
configure: WARNING: pkg-config file for jags 4 unavailable
configure: WARNING: Consider adding the directory containing `jags.pc`
configure: WARNING: to the PKG_CONFIG_PATH environment variable
configure: Attempting legacy configuration of rjags
checking for jags... no
configure: error: "automatic detection of JAGS failed. Please use pkg-config to locate the JAGS library. See the INSTALL file for details."
ERROR: configuration failed for package ‘rjags’
* removing ‘/shared/home/pfoy/R/x86_64-conda-linux-gnu-library/4.4/rjags’
The downloaded source packages are in
‘/tmp/RtmpFWOI8g/downloaded_packages’
Installation paths not writeable, unable to update packages
path: /shared/ifbstor1/software/miniconda/envs/r-4.2.1/lib/R/library
packages:
abind, ade4, adegenet, adegraphics, adephylo, adespatial, admisc, agricolae, AlgDesign, amap, anytime, apcluster, ape, aplot, argparse,
aricode, arrow, ashr, askpass, babelwhale, backports, bayesm, bayestestR, bbmle, bdsmatrix, betapart, BH, BiocManager, bit, bit64,
bitops, blob, bookdown, boot, brew, brio, broom, broom.helpers, bslib, BWStest, cachem, Cairo, callr, car, caret, carrier, caTools,
checkmate, circlize, Ckmeans.1d.dp, class, ClassDiscovery, classInt, cli, clock, clue, cluster, clustermq, clustree, clv, coda, codep,
codetools, colorspace, colourpicker, commonmark, compositions, config, conquer, copula, corrplot, countrycode, cowplot, cpp11, crayon,
credentials, crosstalk, curl, data.table, data.tree, datawizard, DBI, dbplyr, dbscan, debugme, deldir, dendextend, densEstBayes,
DEoptimR, Deriv, desc, DiagrammeR, digest, distr, doRNG, dotCall64, downlit, dplyr, dqrng, DT, dtplyr, dynwrap, e1071, easyCODA, ecodist,
effectsize, ellipse, emdbook, emmeans, estimability, evaluate, extrafont, FactoMineR, fansi, farver, fastcluster, fastICA, fastmap,
fastmatch, FD, fdrtool, fields, filelock, findpython, fitdistrplus, float, FNN, fontawesome, forcats, forecast, foreign, formatR,
Formula, fracdiff, fresh, fs, future, future.apply, GA, gargle, gbm, gdtools, GenSA, geodist, geometry, gert, getopt, GGally, ggbeeswarm,
ggdendro, ggeffects, ggExtra, ggfittext, ggforce, ggfun, gggenes, ggiraph, ggnewscale, ggplot2, ggplotify, ggpubr, ggraph, ggrastr,
ggrepel, ggridges, ggsci, ggupset, ggvenn, ggVennDiagram, ggwordcloud, gh, gkmSVM, glmnet, globals, glue, gmm, gmp, googledrive,
googlesheets4, gower, gplots, gprofiler2, graphlayouts, grImport, gsl, gson, gt, gtable, gtools, gtsummary, hardhat, harmony, haven,
hdf5r, heatmaply, hexbin, highr, Hmisc, hms, htmlTable, htmltools, htmlwidgets, httpuv, httr, igraph, influenceR, inline, insight,
interp, iotools, ipred, IRkernel, isoband, jpeg, jsonlite, kableExtra, keras, kernlab, KernSmooth, klaR, knitr, kohonen, ks, kSamples,
labdsv, labeling, labelled, later, lattice, lava, leaps, leiden, leidenbase, LiblineaR, lifecycle, limSolve, listenv, lme4, locfit,
locpol, longitudinalData, loo, lpSolve, lubridate, magic, magick, MALDIquant, mapplots, maps, markdown, MatrixExtra, MatrixModels,
matrixStats, mclust, memuse, metap, metR, mgcv, minqa, mixsqp, mixtools, modelr, multcomp, multcompView, multicool, multipanelfigure,
munsell, mutoss, mvtnorm, ncdf4, network, nlme, nloptr, NLP, nls2, NMF, nnet, nnls, norm, oompaData, openssl, openxlsx, optparse,
packrat, parallelly, parameters, parsedate, parsnip, patchwork, pbapply, pbdZMQ, pbkrtest, pcaPP, performance, phangorn, phylobase,
pillar, pinfsc50, pingr, pixmap, pkgbuild, pkgcache, pkgdown, pkgload, plot3D, plotly, plotrix, plyr, PMCMRplus, png, polyclip, poweRlaw,
pracma, prettyunits, pROC, processx, prodlim, profvis, progress, progressr, promises, proxyC, pryr, ps, pspline, psych, purrr, qlcMatrix,
qqconf, qqman, quantmod, quantreg, questionr, R.oo, R.utils, ragg, randomForest, ranger, RANN, rbibutils, rcdd, rclipboard, Rcpp,
RcppAnnoy, RcppArmadillo, RcppCNPy, RcppEigen, RcppHNSW, RcppNumerical, RcppParallel, RcppRoll, RcppThread, RcppTOML, RCurl, Rdpack,
readODS, readr, readxl, recipes, reldist, rematch, remotes, renv, repr, reprex, reticulate, RGCCA, rgl, RhpcBLASctl, rintrojs, rio,
rjags, rJava, rjson, RJSONIO, rlang, RMariaDB, rmarkdown, Rmpfr, rncl, RNeXML, robustbase, roxygen2, rpart, rpart.plot, rprojroot,
rsample, rsparse, RSpectra, RSQLite, rstan, rstantools, rstatix, rstudioapi, rsvg, Rtsne, Rttf2pt1, RUnit, rvest, s2, sandwich, sass,
scales, scam, scattermore, scatterpie, scatterplot3d, sctransform, segmented, seqinr, seqminer, seriation, Seurat, SeuratObject, sf,
sfsmisc, shadowtext, shape, shiny, shinyAce, shinyalert, shinycssloaders, shinydashboardPlus, shinytest, shinyWidgets, Signac, sjmisc,
sjPlot, sjstats, slam, slider, sm, sn, SnowballC, SOMbrero, sourcetools, sp, spam, SparseM, sparsesvd, spatstat.data, spatstat.explore,
spatstat.geom, spatstat.random, spatstat.sparse, spatstat.utils, spData, spdep, stabledist, StanHeaders, startupmsg, StatMatch, statmod,
statnet.common, stringi, stringr, styler, SuppDists, survey, survival, svglite, svMisc, sys, systemfonts, tensorA, tensorflow, tester,
testthat, text2vec, textshaping, tfruns, TH.data, tibble, tictoc, tidygraph, tidyr, tidyselect, tidytree, tidyverse, timechange,
timeDate, tinytex, TITAN2, tm, tmvtnorm, treemap, truncnorm, tseries, TSP, TTR, tweenr, tzdb, umap, units, urca, usethis, utf8, uuid,
uwot, V8, VAM, vcfR, vctrs, vegan, venn, VGAM, vioplot, vipor, viridis, viridisLite, vroom, waldo, warp, webshot, WGCNA, whisker, withr,
wk, xfun, xgboost, XML, xml2, xopen, xts, yaml, yardstick, yulab.utils, zip, zoo
Warning message:
In install.packages(...) :
installation of package ‘rjags’ had non-zero exit status
Comme JAGS n'est pas un package R je ne sais pas comment l'installer dans mon espace IFBcore ...
Merci pour votre aide.
Il faut donc bien installer JAGS (https://mcmc-jags.sourceforge.net/) dans votre environnement.
Cela peut être fait notamment via conda (Jags | Anaconda.org).
Nous avons lancé pour vous l'installation de JAGS. C'est en cours:
JAGS est maintenant disponible. Comme d'habitude:
module load jags/4.3.2
Une fois dans R, on peut aussi faire:
source("/shared/software/modules/4.6.1/init/r.R")
module("load jags/4.3.2")
Mais cela ne semble pas fonctionner dans RStudio.
En attendant de trouver une solution, il faut peut-être jouer avec les variables d'environnements (jags est installé dans /shared/ifbstor1/software/miniconda/envs/jags-4.3.2/)