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Help! install methylkit package

hello, today I failed to installed methylkit package.

install.packages("methylKit_0.9.2.tar.gz",repos=NULL,type="source")

  • installing source package 'methylKit' ... * R * data * exec * inst ** preparing package for lazy loading

Error : objects 'DataFrame', 'Rle', 'elementMetadata', 'elementMetadata<-' are not exported by 'namespace:IRanges' ERROR: lazy loading failed for package 'methylKit'

  • removing 'C:/Program Files/R/R-3.2.5/library/methylKit'
  • restoring previous 'C:/Program Files/R/R-3.2.5/library/methylKit' Warning messages:

1: running command '"C:/PROGRA~1/R/R-32~1.5/bin/i386/R" CMD INSTALL -l "C:\Program Files\R\R-3.2.5\library" "methylKit_0.9.2.tar.gz"' had status 1

2: In install.packages("methylKit_0.9.2.tar.gz", repos = NULL, type = "source") : installation of package ‘methylKit_0.9.2.tar.gz’ had non-zero exit status

unlink("methylKit_0.9.2.tar.gz")

library("methylkit")

Error in library("methylkit") : there is no package called ‘methylkit’

The methods of install packages were:

install.packages( c("data.table","devtools")) source("http://bioconductor.org/biocLite.R") biocLite(c("GenomicRanges","IRanges")) library(devtools) install_github("al2na/methylKit",build_vignettes=FALSE) download.file("http://methylkit.googlecode.com/files/methylKit_0.9.2.tar.gz",destfile="methylKit_0.9.2.tar.gz") install.packages("methylKit_0.9.2.tar.gz",repos=NULL,type="source") unlink("methylKit_0.9.2.tar.gz")

I dont know which function is wrong. Could you help me in solving it?

r software error chip-seq
• 8,205 views • link
updated by Guangchuang Yu Guangchuang Yu • written by wql_zcq • wql_zcq

3 answers

If your OS is linux, you can copy the following to the terminal and install methylKit. 

mkdir methykit
wget https://cran.rstudio.com/src/contrib/devtools_1.11.0.tar.gz
wget https://cran.rstudio.com/src/contrib/httr_1.1.0.tar.gz
wget https://cran.rstudio.com/src/contrib/memoise_1.0.0.tar.gz
wget https://cran.rstudio.com/src/contrib/whisker_0.3-2.tar.gz
wget https://cran.rstudio.com/src/contrib/rstudioapi_0.5.tar.gz
wget https://cran.rstudio.com/src/contrib/jsonlite_0.9.19.tar.
wget https://cran.rstudio.com/src/contrib/git2r_0.14.0.tar.gz
wget https://cran.rstudio.com/src/contrib/withr_1.0.1.tar.gz

R
install.packages("git2r_0.14.0.tar.gz")
install.packages("httr_1.1.0.tar.gz")
install.packages("memoise_1.0.0.tar.gz")
install.packages("rstudioapi_0.5.tar.gz")
install.packages("whisker_0.3-2.tar.gz")
install.packages("withr_1.0.1.tar.gz")

source("http://bioconductor.org/biocLite.R")
biocLite("httr")
biocLite("memoise")
biocLite("whisker")
biocLite("rstudioapi")
biocLite("jsonlite")
biocLite("git2r")
biocLite("withr")
install.packages("devtools_1.11.0.tar.gz")
library("devtools")
install_github("al2na/methylKit",build_vignettes=FALSE)

After this, Just use the following to check whether it has been successfully installed. 

library("methylKit")

After you install it, you can remove the folder of methykit. It is not useful after the installation.

• 0 views • link
written by Shicheng Guo Shicheng Guo

Installation instructions specified here: https://code.google.com/archive/p/methylkit/ appear different from what you tried.

• 0 views • link
written by WouterDeCoster WouterDeCoster

try this one:

source("http://bioconductor.org/biocLite.R")
biocLite(c('IRanges', 'data.table', 'S4Vectors', 'GenomeInfoDb', 'KernSmooth', 
                 'qvalue', 'emdbook', 'Rsamtools', 'gtools', 'fastseg', 'rtracklayer', 
                 'mclust', 'R.utils', 'limma', 'Rcpp', 'Rhtslib', 'zlibbioc'))
install.packages('methylkit', repos = "http://www.bioconductor.org/packages/devel/bioc")

or the easiest way:

source("http://bioconductor.org/biocLite.R")
useDevel(TRUE)
biocLite("methylKit")
useDevel(FALSE)
• 1 views • link
written by Guangchuang Yu Guangchuang Yu

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