Hi!

I am trying to use methyLiftover tool, for which I need to unstall IlluminaHumanMethylation450kanno.ilmn12.hg19 library. I am trying to do so with R (both 3.6.0and 3.6.1), but getting following messages-

 BiocManager::install("IlluminaHumanMethylation450kanno.ilmn12.hg19")
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.1 (2019-07-05)
Installing package(s) 'IlluminaHumanMethylation450kanno.ilmn12.hg19'
Warning: unable to access index for repository https://bioconductor.org/packages/3.9/data/annotation/bin/windows/contrib/3.6:
  cannot open URL 'https://bioconductor.org/packages/3.9/data/annotation/bin/windows/contrib/3.6/PACKAGES'
Warning: unable to access index for repository https://bioconductor.org/packages/3.9/data/experiment/bin/windows/contrib/3.6:
  cannot open URL 'https://bioconductor.org/packages/3.9/data/experiment/bin/windows/contrib/3.6/PACKAGES'
installing the source package ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’

trying URL 'https://bioconductor.org/packages/3.9/data/annotation/src/contrib/IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0.tar.gz'
Error in download.file(url, destfile, method, mode = "wb", ...) : 
  cannot open URL 'https://bioconductor.org/packages/3.9/data/annotation/src/contrib/IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0.tar.gz'
In addition: Warning message:
In download.file(url, destfile, method, mode = "wb", ...) :
  InternetOpenUrl failed: ''
Warning in download.packages(pkgs, destdir = tmpd, available = available,  :
  download of package ‘IlluminaHumanMethylation450kanno.ilmn12.hg19’ failed
installation path not writeable, unable to update packages: boot, foreign, nlme

Could you please help?

Sometimes when you try to install things from the internet you end up having some transient connectivity problems. Usually this just means that you need to try again:

> install("IlluminaHumanMethylation450kanno.ilmn12.hg19")
Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.1 (2019-07-05)
Installing package(s) 'BiocVersion',
  'IlluminaHumanMethylation450kanno.ilmn12.hg19'

trying URL 'https://bioconductor.org/packages/3.9/data/annotation/src/contrib/IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0.tar.gz'
Content type 'application/x-gzip' length 57839020 bytes (55.2 MB)
downloaded 55.2 MB

* installing *source* package 'GenomeInfoDbData' ...
** using staged installation
** data
** inst
** help
*** installing help indices
  converting help for package 'GenomeInfoDbData'
    finding HTML links ... done
    GenomeInfoDbData-package                html  
** building package indices
** testing if installed package can be loaded from temporary location
*** arch - i386
*** arch - x64
** testing if installed package can be loaded from final location
*** arch - i386
*** arch - x64
** testing if installed package keeps a record of temporary installation path
* DONE (GenomeInfoDbData)
* installing *source* package 'IlluminaHumanMethylation450kanno.ilmn12.hg19' ...
** using staged installation
** data
*** moving datasets to lazyload DB
** inst
** help
*** installing help indices
  converting help for package 'IlluminaHumanMethylation450kanno.ilmn12.hg19'
    finding HTML links ... done
    IlluminaHumanMethylation450kanno.ilmn12.hg19
                                            html  
    SNPs.CommonSingle                       html  
** building package indices
** testing if installed package can be loaded from temporary location
*** arch - i386
*** arch - x64
** testing if installed package can be loaded from final location
*** arch - i386
*** arch - x64
** testing if installed package keeps a record of temporary installation path
* DONE (IlluminaHumanMethylation450kanno.ilmn12.hg19)