I can't seem to install the bioconductor package 'monocle' for single cell RNA sequencing analysis. My R version is 3.4.3, Bioconductor is 3.6. I keep getting this error message, and installing DDRTree separately also fails. Do you know how I can solve this? Many thanks.
biocLite("monocle") BioC_mirror: https://bioconductor.org Using Bioconductor 3.6 (BiocInstaller 1.28.0), R 3.4.3 (2017-11-30). Installing package(s) 'monocle' also installing the dependency 'DDRTree'
trying URL 'https://cran.rstudio.com/src/contrib/DDRTree_0.1.5.tar.gz'
Content type 'application/x-gzip' length 13728 bytes (13 KB)
downloaded 13 KB
trying URL 'https://bioconductor.org/packages/3.6/bioc/src/contrib/monocle_2.6.4.tar.gz'
Content type 'application/x-gzip' length 9497904 bytes (9.1 MB)
downloaded 9.1 MB
- installing source package 'DDRTree' ... ** package 'DDRTree' successfully unpacked and MD5 sums checked ** libs /opt/centos/devtoolset-1.1/root/usr/bin/g++ -std=c++11 -I/apps/well/R/3.4.3/lib64/R/include -DNDEBUG -I"/gpfs0/apps/well/R/3.4.3/lib64/R/library/Rcpp/include" -I"/gpfs0/apps/well/R/3.4.3/lib64/R/library/RcppEigen/include" -I"/gpfs0/apps/well/R/3.4.3/lib64/R/library/BH/include" -I/usr/local/include -fpic -g -O2 -c DDRTree.cpp -o DDRTree.o /bin/sh: /opt/centos/devtoolset-1.1/root/usr/bin/g++: No such file or directory make: *** [DDRTree.o] Error 127 ERROR: compilation failed for package 'DDRTree'
- removing '/gpfs0/users/morris/u0302066/R/x86_64-pc-linux-gnu-library/3.4/DDRTree' ERROR: dependency 'DDRTree' is not available for package 'monocle'
- removing '/gpfs0/users/morris/u0302066/R/x86_64-pc-linux-gnu-library/3.4/monocle'
The downloaded source packages are in '/tmp/Rtmpcx6BJi/downloaded_packages' installation path not writeable, unable to update packages: BH, ChIPpeakAnno, ChIPseeker, DBI, DEXSeq, DT, FNN, Formula, GEOquery, GGally, GOSemSim, GWASTools, GenomicAlignments, GenomicFeatures, GenomicRanges, Gviz, HardyWeinberg, Hmisc, ICS, ICSNP, MASS, MCMCpack, Matrix, MultiAssayExperiment, NCmisc, NMF, R6, RCurl, RMySQL, RSQLite, RSpectra, RUnit, Rcpp, RcppArmadillo, RcppEigen, RcppParallel, Rtsne, SPAtest, ShortRead, StanHeaders, VGAM, VariantAnnotation, VennDiagram, XML, ade4, amap, annotate, ape, argparse, bigmemory, bindr, bindrcpp, biomaRt, bit, blob, bookdown, caTools, chron, classInt, cli, cluster, coda, commonmark, cowplot, curl, data.table, desc, devtools, digest, doParallel, dotCall64, dplyr, e1071, edgeR, ellipse, ensembldb, erma, evaluate, ff, ffbase, fgsea, fields, foreign, futile.options, getopt, ggbio, ggfortify, ggplot2, git2r, glmnet, glue, gmp, gtools, hexbin, highr, hms, htmlTable, htmlwidgets, httpuv, igraph, inline, irlba, iterators, knitr, lambda.r, lattice, ldblock, limma, lmtest, logistf, loo, lubridate, maps, matrixStats, mclust, mgcv, mice, microbenchmark, mime, miniUI, mixOmics, munsell, mvtnorm, nlme, openssl, optparse, packrat, phangorn, pheatmap, pillar, pkgconfig, pkgmaker, plogr, plotly, plotrix, progress, psych, purrr, quantreg, rJava, ranger, reshape, rgl, rhandsontable, rjags, rjson, rlang, rmarkdown, rngtools, roxygen2, rpart, rprojroot, rstan, rstudioapi, rtracklayer, rvcheck, sandwich, scales, scater, scatterplot3d, sf, shape, shapes, shiny, shinyWidgets, shinydashboard, shinyjs, sm, snow, sourcetools, spam, spp, stringi, stringr, survey, survival, testthat, tibble, tidyr, tidyselect, truncnorm, units, utf8, viridis, viridisLite, withr, xgboost, xlsx, xml2, xtable, yaml, zoo Warning messages: 1: In install.packages(pkgs = doing, lib = lib, ...) : installation of package 'DDRTree' had non-zero exit status 2: In install.packages(pkgs = doing, lib = lib, ...) : installation of package 'monocle' had non-zero exit status
