Cannot install this package "ben-laufer / DMRichR" with error information

[DengEr-1993]

Hi Sir,

I just want to use this package to visualise the methylation calling result.

I think your sample visualization for CpG count matrix is beautiful.

But when I tried to install it with below tutorial:

if(!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
if(!requireNamespace("remotes", quietly = TRUE))
  install.packages("remotes")
Sys.setenv("R_REMOTES_NO_ERRORS_FROM_WARNINGS" = TRUE)
BiocManager::install("ben-laufer/DMRichR")

The error information appeared:

> BiocManager::install("ben-laufer/DMRichR")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")'
for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.1 (2022-06-23 ucrt)
Installing github package(s) 'ben-laufer/DMRichR'
Downloading GitHub repo ben-laufer/DMRichR@HEAD
Error in utils::download.file(url, path, method = method, quiet = quiet,  : 
  cannot open URL 'https://api.github.com/repos/ben-laufer/DMRichR/tarball/HEAD'
Installation paths not writeable, unable to update packages
  path: C:/Program Files/R/R-4.2.1/library
  packages:
    boot, class, cluster, codetools, foreign, MASS, Matrix, mgcv, nlme, nnet, rpart, spatial, survival
Old packages: 'BiocParallel', 'cli', 'XML'
Update all/some/none? [a/s/n]: 
n

I also failed to install it manually.

Can you give me some advice. I don't know if it is OK for me to use the source code of this package only.

[ben-laufer]

This error doesn't seem to be specific to DMRichR. It looks to me like you weren't able to download from GitHub. Can you test this by trying to download a different package from GitHub?

[DengEr-1993]

This error doesn't seem to be specific to DMRichR. It looks to me like you weren't able to download from GitHub. Can you test this by trying to download a different package from GitHub?

@ben-laufer Thanks, I can install this pacakge on my mac. Maybe I don't have the permission on windows PC.

[DengEr-1993]

This error doesn't seem to be specific to DMRichR. It looks to me like you weren't able to download from GitHub. Can you test this by trying to download a different package from GitHub?

Thank you. I finally installed this package manually. But I don't know the exact reason.

Here is my installation code:

if(!requireNamespace("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
if(!requireNamespace("remotes", quietly = TRUE))
  install.packages("remotes")

###########b
Bioconductor_packages<-c('Boruta', 'CMplot', 'ChIPseeker', 'GOfuncR', 'gt', 'lsmeans', 'rGREAT', 'sigFeature', 'R2HTML', 'LOLA', 'PerformanceAnalytics', 'hablar', 'ggsci', 'minfi', 'plyranges', 'rrvgo', 'Glimma', 'genefilter', 'methylCC')

for (pkg in Bioconductor_packages) {
  if (!require(pkg,character.only = T)) {
   BiocManager::install(pkg,ask = F,update = F)
    require(pkg,character.only = T)

  }

}

#############

Sys.setenv("R_REMOTES_NO_ERRORS_FROM_WARNINGS" = TRUE)
BiocManager::install("ben-laufer/DMRichR")  ##  Here I installed package manually instead
## library("ben-laufer/DMRichR")
library(RCurl)
#library(devtools)
## install_github("ben-laufer/DMRichR")
## library("ben-laufer/DMRichR")
library(DMRichR)   ## this worked.
##########################

Warning in untar2(tarfile, files, list, exdir, restore_times) :
  skipping pax global extended headers
* installing *source* package 'DMRichR' ...
** using staged installation
** R
** exec
** inst
** byte-compile and prepare package for lazy loading
Warning messages:
1: package 'GenomicRanges' was built under R version 4.2.2 
2: package 'S4Vectors' was built under R version 4.2.2 
3: package 'GenomeInfoDb' was built under R version 4.2.2 
4: package 'matrixStats' was built under R version 4.2.2 
Note: wrong number of arguments to '*' 
Note: wrong number of arguments to '/' 
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Warning: package 'GenomicRanges' was built under R version 4.2.2
Warning: package 'S4Vectors' was built under R version 4.2.2
Warning: package 'GenomeInfoDb' was built under R version 4.2.2
Warning: package 'matrixStats' was built under R version 4.2.2
** testing if installed package can be loaded from final location
Warning: package 'GenomicRanges' was built under R version 4.2.2
Warning: package 'S4Vectors' was built under R version 4.2.2
Warning: package 'GenomeInfoDb' was built under R version 4.2.2
Warning: package 'matrixStats' was built under R version 4.2.2
** testing if installed package keeps a record of temporary installation path
* DONE (DMRichR)
> #library(devtools)
> # install_github("ben-laufer/DMRichR")
> library("ben-laufer/DMRichR")
Error in library("ben-laufer/DMRichR") : 
  there is no package called ‘ben-laufer/DMRichR’
> library(DMRichR)
Loading required package: dmrseq
Loading required package: bsseq

Attaching package: ‘bsseq’

The following object is masked from ‘package:minfi’:

    getMeth

DMRichR v1.7.1 has loaded. If you use DMRichR in published research please cite Laufer et al. 2020, Korthauer et al. 2018, and Hansen et al. 2012.

Attaching package: 'DMRichR'

The following object is masked from 'package:minfi':

    densityPlot

The following object is masked from 'package:Biostrings':

    windows

The following object is masked from 'package:XVector':

    windows

The following object is masked from 'package:GenomicRanges':

    windows

The following object is masked from 'package:IRanges':

    windows

The following object is masked from 'package:grDevices':

    windows

> library(DMRichR)