Question: Installation problem in IlluminaHumanMethylation450kanno.ilmn12.hg19
0
gravatar for nipabasak
11 weeks ago by
nipabasak0
nipabasak0 wrote:

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?

ADD COMMENTlink modified 11 weeks ago by James W. MacDonald51k • written 11 weeks ago by nipabasak0
Answer: Installation problem in IlluminaHumanMethylation450kanno.ilmn12.hg19
0
gravatar for James W. MacDonald
11 weeks ago by
United States
James W. MacDonald51k wrote:

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)

ADD COMMENTlink written 11 weeks ago by James W. MacDonald51k
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