Problem installing

[meiruv]

Hi there I'm trying to install Phyloseq but whenever I run require(phyloseq) I get the following error: Loading required package: phyloseq Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘Rcpp’

I tried to install according to the instructions here : https://joey711.github.io/phyloseq/install.html

and tried to solve my problem according to the tips here: http://stackoverflow.com/questions/31717850/error-package-or-namespace-load-failed-for-ggplot2-and-for-data-table

but still fail :/

any help will be appreciated, Thanks - Meirav

[spholmes]

Try using

install.packages("phyloseq", dependencies=TRUE)

or in RStudio with the packages tab use click on the install dependencies when you choose phyloseq,

it should also install Rcpp which is required.

It may be you are having trouble because you are using an old operating system and your Rcpp failed, but you should tell us what your system is.

Best Susan

On Sun, Apr 9, 2017 at 5:09 AM, meiruv notifications@github.com wrote:

Hi there I'm trying to install Phyloseq but whenever I run require(phyloseq) I get the following error: Loading required package: phyloseq Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : there is no package called ‘Rcpp’

I tried to install according to the instructions here : https://joey711.github.io/phyloseq/install.html

and tried to solve my problem according to the tips here: http://stackoverflow.com/questions/31717850/error- package-or-namespace-load-failed-for-ggplot2-and-for-data-table

but still fail :/

any help will be appreciated, Thanks - Meirav

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[camo18]

I am also having the same problem as @meiruv, and when I try to install dependencies I get the following error: install.packages("phyloseq", dependencies=TRUE) Installing package into ‘C:/Users/camplamo/Documents/R/win-library/3.4’ (as ‘lib’ is unspecified) Warning in install.packages : package ‘phyloseq’ is not available (for R version 3.4.3)

It doesn't make sense that phyloseq wouldn't be supported by this version, but if so, how would I install the package of phyloseq that I could access?

[spholmes]

Please pay attention to the following, it is essential:

Always always install phyloseq with the biocLite command:

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

never ever with install.packages()

On Thu, Apr 5, 2018 at 4:17 PM, camo18 notifications@github.com wrote:

I am also having the same problem as @meiruv https://github.com/meiruv, and when I try to install dependencies I get the following error: install.packages("phyloseq", dependencies=TRUE) Installing package into ‘C:/Users/camplamo/Documents/R/win-library/3.4’ (as ‘lib’ is unspecified) Warning in install.packages : package ‘phyloseq’ is not available (for R version 3.4.3)

It doesn't make sense that phyloseq wouldn't be supported by this version, but if so, how would I install the package of phyloseq that I could access?

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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/

[soluna1]

Hi,

the same problem happens to me. I've used the recommended code:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("phyloseq", version = "3.8")

The problem arises with the 'graph' package. I tried to install it from different sources, but still got the error:

library(phyloseq) Error: package or namespace load failed for ‘phyloseq’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘igraph’

and at least out_table() functions is not available.

Any possible solution/alternative?

thanks a lot

Sisi

[Mrudhulaks]

Hi,

Same issue with me as well.

I installed phyloseq using if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("phyloseq")

And when I try to run the phyloseq. I get following error.

library(phyloseq) Error: package or namespace load failed for ‘phyloseq’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]): there is no package called ‘glue’

Could you please help me resolve this.

Thank you.

[DanaBJohnson]

I am getting a similar error when I try to run phyloseq.

library(phyloseq) Error: package or namespace load failed for ‘phyloseq’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]): there is no package called ‘GenomeInfoDbData’ In addition: Warning message: package ‘phyloseq’ was built under R version 4.1.1

All my attempts to install GenomeInfoDbData have failed.

[julietaalvarez]

My phyloseq was working until my R Studio crashed. I tried again to run it and now I have this error:

Error: package or namespace load failed for ‘phyloseq’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 namespace ‘vctrs’ 0.4.2 is being loaded, but >= 0.5.0 is required

The last package I installed was "microViz", I don't know if this is the reason. Can someone help me?

[david-barnett]

updating the vctrs package should fix your issue, it's a dependency of e.g. dplyr, which is a dependency of microViz

as a better fix, I'll have a look why this dependency version isn't being automatically upgraded upon microViz install, probably I'll just have to explicitly declare vctrs version 0.5 is needed

For my interest, before you do anything else in R could you share the output of the following code?

packageVersion(microViz)
packageVersion(dplyr)
packageVersion(ggplot2)

[julietaalvarez]

packageVersion(microViz) Error in packageDescription(pkg, lib.loc = lib.loc, fields = "Version") : object 'microViz' not found But I already solve the problem with the re-installing "vctrs". Thank you!!