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joey711 / phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:
http://joey711.github.io/phyloseq/
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Installation and running problems #915

Open lise2709 opened 6 years ago

lise2709 commented 6 years ago

Hi I've just updated my R studio and now can't run phyloseq, I've tried reinstalling and get the message package ‘nlme’ is not available (for R version 3.3.1) . I've checked in my installed packages and phyloseq is there yet I get this message

library(phyloseq) Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘nlme’ In addition: Warning message: package ‘phyloseq’ was built under R version 3.3.2 Error: package or namespace load failed for ‘phyloseq’

I've tried to look for the nlme package on CRAN and it's not available, any ideas??

Many thanks, Lindsay

spholmes commented 6 years ago

Lindsay, It does seem that https://cran.r-project.org/web/packages/nlme/index.html nlme does exist for all versions, but you should definitely use biocLite to install phyloseq, can you send the sessionInfo() output?

when I do that, I have nlme_3.1-131.1

but there are many updates occurring in real time, it would be good to check that.

On Wed, Apr 11, 2018 at 5:57 AM, lise2709 notifications@github.com wrote:

Hi I've just updated my R studio and now can't run phyloseq, I've tried reinstalling and get the message package ‘nlme’ is not available (for R version 3.3.1) . I've checked in my installed packages and phyloseq is there yet I get this message

library(phyloseq) Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘nlme’ In addition: Warning message: package ‘phyloseq’ was built under R version 3.3.2 Error: package or namespace load failed for ‘phyloseq’

I've tried to look for the nlme package on CRAN and it's not available, any ideas??

Many thanks, Lindsay

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/joey711/phyloseq/issues/915, or mute the thread https://github.com/notifications/unsubscribe-auth/ABJcvQrtw_WcpSpLY5xLB-xU5aPYM9gfks5tnf2hgaJpZM4TP-hG .

-- Susan Holmes John Henry Samter Fellow in Undergraduate Education Professor, Statistics 2017-2018 CASBS Fellow, Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/

lise2709 commented 6 years ago

Thanks so much for the reply, I managed to get it to work by uninstalling R and R studio and reinstalling all the packages with the latest versions using the biocLite install phyloseq instructions on Git Hub. I’m Not really sure what the problem was but reinstalling and updating everything seems to have worked out so I’m putting it down to bad luck!

Thanks so much for the help!

Lindsay

From: Susan Holmes [mailto:notifications@github.com] Sent: 11 April 2018 17:19 To: joey711/phyloseq phyloseq@noreply.github.com Cc: Newbold, Lindsay K. lise@ceh.ac.uk; Author author@noreply.github.com Subject: Re: [joey711/phyloseq] Installation and running problems (#915)

Lindsay, It does seem that https://cran.r-project.org/web/packages/nlme/index.html nlme does exist for all versions, but you should definitely use biocLite to install phyloseq, can you send the sessionInfo() output?

when I do that, I have nlme_3.1-131.1

but there are many updates occurring in real time, it would be good to check that.

On Wed, Apr 11, 2018 at 5:57 AM, lise2709 notifications@github.com<mailto:notifications@github.com> wrote:

Hi I've just updated my R studio and now can't run phyloseq, I've tried reinstalling and get the message package ‘nlme’ is not available (for R version 3.3.1) . I've checked in my installed packages and phyloseq is there yet I get this message

library(phyloseq) Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘nlme’ In addition: Warning message: package ‘phyloseq’ was built under R version 3.3.2 Error: package or namespace load failed for ‘phyloseq’

I've tried to look for the nlme package on CRAN and it's not available, any ideas??

Many thanks, Lindsay

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/joey711/phyloseq/issues/915, or mute the thread https://github.com/notifications/unsubscribe-auth/ABJcvQrtw_WcpSpLY5xLB-xU5aPYM9gfks5tnf2hgaJpZM4TP-hG .

-- Susan Holmes John Henry Samter Fellow in Undergraduate Education Professor, Statistics 2017-2018 CASBS Fellow, Sequoia Hall, 390 Serra Mall Stanford, CA 94305 http://www-stat.stanford.edu/~susan/

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/joey711/phyloseq/issues/915#issuecomment-380511350, or mute the threadhttps://github.com/notifications/unsubscribe-auth/Akg1M-0K36UWvciVl-VSRhgy4oUGP8T6ks5tni0EgaJpZM4TP-hG.

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