chelseajkc commented 6 years ago

Hi there, I am trying to install phyloseq to use the pcoa function. I have the latest version of R (3.4.3) and phyloseq is not supported by it. I have installed R 3.1.3 as well, hoping downgrading would help. But then it says that phyloseq is still not supported. How can I use phyloseq?

spholmes commented 6 years ago

phyloseq is actually supported on all recent versions of R, even the devel one but you must install it through Bioconductor to be sure to get the dependencies right (and not just use install.packages in an RSTudio window which always says : not available. Please try the following two lines and tell us what it says, also please provide more details on your OS and R versions so we can debug properly. Thanks

source("https://bioconductor.org/biocLite.R") biocLite("phyloseq")

On Thu, Feb 8, 2018 at 10:50 PM, chelseajkc notifications@github.com wrote:

Hi there, I am trying to install phyloseq to use the pcoa function. I have the latest version of R (3.4.3) and phyloseq is not supported by it. I have installed R 3.1.3 as well, hoping downgrading would help. But then it says that phyloseq is still not supported. How can I use phyloseq?

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-- 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/

laylaeb commented 6 years ago

Hi!

I have the same problem. I try to install phyloseq with the new version of R.3.4.4. Tried to do what you recommended : source("https://bioconductor.org/biocLite.R") biocLite("phyloseq")

However: I got the following error :

x-gzip' length 3291400 bytes (3.1 MB)

downloaded 3.1 MB

installing source package ‘phyloseq’ ... R data inst preparing package for lazy loading Error : Functions found when exporting methods from the namespace ‘S4Vectors’ which are not S4 generic: ‘sd’, ‘t’, ‘var’ ERROR: lazy loading failed for package ‘phyloseq’
removing ‘/Library/Frameworks/R.framework/Versions/3.4/Resources/library/phyloseq’

The downloaded source packages are in ‘/private/var/folders/fs/vn6w_t8j1nj46ptf0k2gs2cw0000gn/T/Rtmp2BuXQ1/downloaded_packages’ Warning message: In install.packages(pkgs = doing, lib = lib, ...) : installation of package ‘phyloseq’ had non-zero exit status

What should I do ?

Thank you very much in advance..

laylaeb commented 6 years ago

I solved my pb by following the steps for Troubleshooting BiocInstaller! it worked perfectly.

spholmes commented 6 years ago

Thanks for letting us know, there will be a transition period where the new version of R and some of the new versions of BioC packages can create friction, reinstalling a coherent snapshot usually works.

On Sat, Mar 17, 2018 at 9:48 AM, laylaeb notifications@github.com wrote:

I solved my pb by following the steps for Troubleshooting BiocInstaller! it worked perfectly.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/joey711/phyloseq/issues/879#issuecomment-373934837, or mute the thread https://github.com/notifications/unsubscribe-auth/ABJcvQfQf-L6aMIoHV0qs__77BDvmmeRks5tfT55gaJpZM4R_faC .

-- 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/

AdenikeA commented 6 years ago

Hi laylaeb,

I am experiencing the same problem. I have tried following the steps for Troubleshooting BiocInstaller to no avail. Please could you share in details the steps?

megawhims commented 6 years ago

Hi I was trying ti install phyloseq: install.packages("phyloseq") and I got this warning: Warning in install.packages : package ‘phyloseq’ is not available (for R version 3.5.1)

I wanted to use it to save my data that was in biom into xlsx format

carolinzky commented 6 years ago

Hi! I was also trying to load phyloseq for R 5.3.1, and came across the following error:

library(phyloseq) Fehler: package or namespace load failed for ‘phyloseq’: package ‘Biobase’ was installed by an R version with different internals; it needs to be reinstalled for use with this R version

I have tried to reinstall the Biobase dependency from the source, with no success. Reinstalling phyloseq and all dependencies still gives me this problem. How can I get back to work?

lubapardo commented 5 years ago

Hi, Same problem here with source("https://bioconductor.org/biocLite.R")

lubapardo commented 5 years ago

package ‘phyloseq’ is not available (for R version 3.5.1)

Athira-1996 commented 5 years ago

Hi I try to install phyloseq using command

source('http://bioconductor.org/biocLite.R')
biocLite('phyloseq')

typing first command i get like this

Bioconductor version 3.3 (BiocInstaller 1.22.3), ?biocLite for help A newer version of Bioconductor is available for this version of R, ?BiocUpgrade for help

I also try to install using command

`> if (!requireNamespace("BiocManager", quietly = TRUE))

install.packages("BiocManager")

BiocManager::install("phyloseq") `

I get the following error command

`Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26) Installing package(s) 'phyloseq' trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/phyloseq_1.28.0.tar.gz' Content type 'application/x-gzip' length 5474587 bytes (5.2 MB)

downloaded 5.2 MB

installing source package ‘phyloseq’ ... using staged installation R data inst byte-compile and prepare package for lazy loading help * installing help indices building package indices installing vignettes testing if installed package can be loaded from temporary location testing if installed package can be loaded from final location testing if installed package keeps a record of temporary installation path
DONE (phyloseq)

The downloaded source packages are in ‘/tmp/Rtmpk5DdaL/downloaded_packages’ installation path not writeable, unable to update packages: littler, boot, class, cluster, codetools, foreign, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet, spatial, survival `

Can anyone know how to fix this problem ?

FilipeMatteoli commented 5 years ago

Well, I think that the described in phyloseq install page is no longer the way bioclite handles packages nowadays. This worked for me: install.packages("BiocManager") BiocManager::install("phyloseq")

Several other dependencies had to be installed in the first place: sudo apt install libcurl4-openssl-dev libssl-dev libssh2-1-dev libxml2-dev

joey711 / phyloseq

how to install phyloseq into R 3.4.3 #879

essai de l'URL 'https://bioconductor.org/packages/3.4/bioc/src/contrib/phyloseq_1.19.1.tar.gz' Content type 'application/x-gzip' length 3291400 bytes (3.1 MB)

`Bioconductor version 3.9 (BiocManager 1.30.4), R 3.6.0 (2019-04-26) Installing package(s) 'phyloseq' trying URL 'https://bioconductor.org/packages/3.9/bioc/src/contrib/phyloseq_1.28.0.tar.gz' Content type 'application/x-gzip' length 5474587 bytes (5.2 MB)