Question: Help! install methylkit package
3
gravatar for wql_zcq
2.2 years ago by
wql_zcq40
wql_zcq40 wrote:

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?

chip-seq R software error • 3.3k views
ADD COMMENTlink modified 23 months ago by Guangchuang Yu1.8k • written 2.2 years ago by wql_zcq40
1
gravatar for Shicheng Guo
2.2 years ago by
Shicheng Guo4.9k
Shicheng Guo4.9k wrote:

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.

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by Shicheng Guo4.9k

Thank you, I try it.

ADD REPLYlink written 2.2 years ago by wql_zcq40
1
gravatar for WouterDeCoster
2.2 years ago by
Belgium
WouterDeCoster29k wrote:

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

ADD COMMENTlink written 2.2 years ago by WouterDeCoster29k

I installed methylkit package according to the instructions from https://code.google.com/archive/p/methylkit/, but failed.

ADD REPLYlink written 2.2 years ago by wql_zcq40
1
gravatar for Guangchuang Yu
23 months ago by
Guangchuang Yu1.8k
China/Hong Kong/The University of Hong Kong
Guangchuang Yu1.8k wrote:

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)
ADD COMMENTlink modified 23 months ago • written 23 months ago by Guangchuang Yu1.8k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1356 users visited in the last hour