Question: Help! install methylkit package
3
gravatar for wql_zcq
2.7 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 • 3.8k views
ADD COMMENTlink modified 2.4 years ago by Guangchuang Yu2.0k • written 2.7 years ago by wql_zcq40
1
gravatar for Shicheng Guo
2.7 years ago by
Shicheng Guo7.3k
Shicheng Guo7.3k 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 2.7 years ago • written 2.7 years ago by Shicheng Guo7.3k

Thank you, I try it.

ADD REPLYlink written 2.7 years ago by wql_zcq40
1
gravatar for WouterDeCoster
2.7 years ago by
Belgium
WouterDeCoster35k wrote:

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

ADD COMMENTlink written 2.7 years ago by WouterDeCoster35k

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

ADD REPLYlink written 2.7 years ago by wql_zcq40
1
gravatar for Guangchuang Yu
2.4 years ago by
Guangchuang Yu2.0k
China/Hong Kong/The University of Hong Kong
Guangchuang Yu2.0k 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 2.4 years ago • written 2.4 years ago by Guangchuang Yu2.0k
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