I am trying to install this on my MacOS Mojave 10.14.3. However, I get this error - see below.
r
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> ipak <- function(pkg, repository = c("CRAN", "Bioconductor", "github")) {
+ new.pkg <- pkg[!(pkg %in% installed.packages()[, "Package"])]
+ # new.pkg <- pkg
+ if (length(new.pkg)) {
+ if (repository == "CRAN") {
+ install.packages(new.pkg, dependencies = TRUE)
+ }
+ if (repository == "Bioconductor") {
+ source("https://bioconductor.org/biocLite.R")
+ biocLite(new.pkg, dependencies = TRUE, ask = FALSE)
+ }
+ if (repository == "github") {
+ devtools::install_github(new.pkg, build_vignettes = FALSE, dependencies = TRUE)
+ }
+ }
+ }
>
> # CRAN PACKAGES
> cranpackages <- c("bbmle", "broom", "cobs", "cowplot", "data.table", "devtools",
+ "doParallel", "dplyr", "drc", "DrImpute", "fastICA", "fitdistrplus", "foreach",
+ "gamlss.dist", "ggExtra", "ggplot2", "ggthemes", "grDevices", "glmnet",
+ "grid", "gtools", "Hmisc", "kernlab", "MASS", "matrixStats", "mclust", "methods",
+ "minpack.lm", "moments", "msir", "NBPSeq", "nonnest2", "parallel", "penalized",
+ "plyr", "pscl", "reshape2", "ROCR", "Rtsne", "scales", "Seurat", "snow",
+ "stats", "tibble", "tidyr", "VGAM", "ZIM")
> ipak(cranpackages, repository = "CRAN")
>
> # BIOCONDUCTOR
> biocpackages <- c("AnnotationDbi", "baySeq", "Biobase", "BiocGenerics", "BiocParallel",
+ "DEDS", "DESeq2", "EBSeq", "edgeR", "IHW", "iCOBRA", "limma", "Linnorm",
+ "MAST", "monocle", "NOISeq", "qvalue", "ROTS", "RUVSeq", "S4Vectors", "scater",
+ "scDD", "scde", "scone", "scran", "SCnorm", "SingleCellExperiment", "SummarizedExperiment",
+ "zinbwave")
> ipak(biocpackages, repository = "Bioconductor")
>
> # GITHUB
> githubpackages <- c("nghiavtr/BPSC", "cz-ye/DECENT", "mohuangx/SAVER", "statOmics/zingeR")
> ipak(githubpackages, repository = "github")
Skipping install of 'BPSC' from a github remote, the SHA1 (5a512e5f) has not changed since last install.
Use `force = TRUE` to force installation
Skipping install of 'DECENT' from a github remote, the SHA1 (dd593069) has not changed since last install.
Use `force = TRUE` to force installation
Skipping install of 'SAVER' from a github remote, the SHA1 (1c124ad8) has not changed since last install.
Use `force = TRUE` to force installation
Skipping install of 'zingeR' from a github remote, the SHA1 (c789ae53) has not changed since last install.
Use `force = TRUE` to force installation
> devtools::install_github("bvieth/powsimR", build_vignettes = TRUE, dependencies = FALSE)
Downloading GitHub repo bvieth/powsimR@master
✔ checking for file ‘/private/var/folders/7r/ns6f04xj55j72y97pvwtwxj0000_2q/T/RtmpnNPrJr/remotesfd02396b0a5c/bvieth-powsimR-c70c819/DESCRIPTION’ ...
─ preparing ‘powsimR’:
✔ checking DESCRIPTION meta-information ...
─ checking for LF line-endings in source and make files and shell scripts
─ checking for empty or unneeded directories
─ looking to see if a ‘data/datalist’ file should be added
─ building ‘powsimR_1.1.4.tar.gz’ (5.3s)
Installing package into ‘/usr/local/lib/R/3.5/site-library’
(as ‘lib’ is unspecified)
* installing *source* package ‘powsimR’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
Error in dyn.load(file, DLLpath = DLLpath, ...) :
unable to load shared object '/usr/local/Cellar/r/3.5.2_2/lib/R/library/lpsymphony/libs/lpsymphony.so':
dlopen(/usr/local/Cellar/r/3.5.2_2/lib/R/library/lpsymphony/libs/lpsymphony.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libRlapack.dylib
Referenced from: /usr/local/Cellar/r/3.5.2_2/lib/R/library/lpsymphony/libs/lpsymphony.so
Reason: image not found
ERROR: lazy loading failed for package ‘powsimR’
* removing ‘/usr/local/lib/R/3.5/site-library/powsimR’
Error in i.p(...) :
(converted from warning) installation of package ‘/var/folders/7r/ns6f04xj55j72y97pvwtwxj0000_2q/T//RtmpnNPrJr/filefd0229d84453/powsimR_1.1.4.tar.gz’ had non-zero exit status