Question

Update all/some/none? [a/s/n]:

0

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ayeshakaramat • 0

@ayeshakaramat-22832

Last seen 4.3 years ago

hi, I am trying to install ShortRead package but after installation it says ' Update all/some/none? [a/s/n]: ' and after that I am unable to do anything not even simple functions. how can I solve this problem? your help will be highly appreciated.

Installation path not writeable, unable to update packages: boot, foreign, MASS, nlme Old packages: 'blob', 'dplyr', 'GenomicFeatures', 'jsonlite', 'prettyunits', 'RCurl', 'Rhtslib', 'rlang', 'rmarkdown', 'S4Vectors', 'stringi', 'tidyselect', 'vctrs', 'XML', 'yaml' Update all/some/none? [a/s/n]: library(ShortRead) Update all/some/none? [a/s/n]:

software error • 13k views

ADD COMMENT • link updated 4.3 years ago by James W. MacDonald 65k • written 4.3 years ago by ayeshakaramat • 0

score 1 · Answer 1 · 2020-02-03

1

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James W. MacDonald 65k

@james-w-macdonald-5106

Last seen 41 minutes ago

United States

You are being told that there are some old packages, and are being asked if you want to update all/some/none of them. So if you want to update all of them you hit 'a' and enter. If you want to do some of them it's 's' and enter. And if you want to ignore and go on with your life, hit 'n' and enter.

As Steve mentions, you cannot update the base and default packages because you are on Windows and they are installed in a place that requires admin privileges. Also, do note that this message is intended to be pretty clear, and to my eye it is. One of the tricks to using things like R is to practice reading and trying to interpret the meaning of the output that R gives you. It is often pretty terse, but usually everything you need to know is right there in front of you, if only you take the time to read and understand.

ADD COMMENT • link 4.3 years ago James W. MacDonald 65k

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Also, if you just copy/paste things from R without trying to correctly format, you get a blob of text like you show. But the real output looks like this:

> install()
Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05)
Installation path not writeable, unable to update packages: boot, foreign,
  KernSmooth, MASS, Matrix, mgcv, nlme, survival
Old packages: 'blob', 'doRNG', 'dplyr', 'GenomicFeatures', 'gmp', 'Gviz',
  'HDF5Array', 'jsonlite', 'limma', 'PhyloProfile', 'pkgmaker', 'prettyunits',
  'RcppArmadillo', 'RCurl', 'Rhtslib', 'rlang', 'rmarkdown', 'Rmpfr',
  'rngtools', 'S4Vectors', 'tidyr', 'tidyselect', 'vctrs', 'XML', 'yaml'
Update all/some/none? [a/s/n]:

Which sort of tells a different tale, no?

ADD REPLY • link 4.3 years ago James W. MacDonald 65k

score 0 · Answer 2 · 2020-02-03

It looks like you don't have write permissions to the directory on your system that these packages are stored in.

To find out what directories store packages on your system, fire up R and look at the output of lib.paths(). One brute force method is to ensure that you have write permissions to there, and then you can update these packages as you like.

You can find out where a specific package lives by calling find.package("dplyr") (for example, since it needs to be updated, apparently).

If you don't have admin rights to your system, there are other things you can do, but depending on your comfort level with system administration in general, it's hard for me to enumerate all the things you can do before getting some more information from you.

So: I'll start by assuming you are on a personal machine, and you can tweak permissions to the directories enumerated in .libPaths(). Make sure you can write to there, and try to update again.

Even if you can't update the package, you still should be able to perform "simple functions" after moving on from the update prompt. So if you want more help with that, you will have to explain what is happening in a bit more detail (ie. what are you trying and what output do you get).