Question

Problems with installation of 'phyloseq

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Ina • 0

@473928c0

Last seen 3.3 years ago

United States

Hello, I am trying to install 'phyloseq' and followed the instructions I found on the web. However, I did not successfully get 'phyloseq' installed. I would be grateful for suggestions. Thanks a lot, Ina

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

Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18)
Warning message:
package(s) not installed when version(s) same as current; use `force = TRUE` to re-install: 'phyloseq' 

> BiocManager::install("phyloseq", force=TRUE)

Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18)
Installing package(s) 'phyloseq'
trying URL 'https://bioconductor.org/packages/3.13/bioc/bin/macosx/contrib/4.1/phyloseq_1.36.0.tgz'
Content type 'application/x-gzip' length 5994111 bytes (5.7 MB)
==================================================
downloaded 5.7 M
The downloaded binary packages are in
    /var/folders/g_/fg05t4s95z7f8b7l24k3rtnc0000gn/T//RtmpFc8O9O/downloaded_packages

> 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’

phyloseq • 7.3k views

ADD COMMENT • link updated 3.3 years ago by Kevin Blighe ★ 4.0k • written 3.3 years ago by Ina • 0

Kevin Blighe · Answer 1 · 2021-08-01

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Kevin Blighe ★ 4.0k

@kevin

Last seen 21 days ago

Republic of Ireland

What messages do you receive when you try to install the GenomeInfoDbData package?

ADD COMMENT • link 3.3 years ago Kevin Blighe ★ 4.0k

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install.packages("GenomeInfoDbData")

--- Please select a CRAN mirror for use in this session --- Warning message: package ‘GenomeInfoDbData’ is not available for this version of R

A version of this package for your version of R might be available elsewhere, see the ideas at https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages

ADD REPLY • link 3.3 years ago Ina • 0

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GenomeInfoDbData is a Bioconductor package. Please use Bioconductor installation BiocManager::install("GenomeInfoDbData") and report any ERRORs

ADD REPLY • link 3.3 years ago shepherl 4.1k

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Hello, I used the code to install 'GenomeInfoDbData' from Bioconductor- which worked. Then I tried to install 'phyloseq' from Bioconductor as well and was asked to include 'force=TRUE' in my code. Did that and I was able to install 'phyloseq' from Bioconductor. See the details below. THANK YOU VERY MUCH FOR ALL YOUR HELP!!!!!!! Ina

> BiocManager::install("GenomeInfoDbData")

'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://ftp.osuosl.org/pub/cran

Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18)
Installing package(s) 'GenomeInfoDbData'
installing the source package ‘GenomeInfoDbData’

trying URL 'https://bioconductor.org/packages/3.13/data/annotation/src/contrib/GenomeInfoDbData_1.2.6.tar.gz'
Content type 'application/x-gzip' length 10973004 bytes (10.5 MB)
==================================================
downloaded 10.5 MB

* installing *source* package ‘GenomeInfoDbData’ ...
** using staged installation
** data
** inst
** help
*** installing help indices
** building package indices
** 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 (GenomeInfoDbData)

The downloaded source packages are in
    ‘/private/var/folders/g_/fg05t4s95z7f8b7l24k3rtnc0000gn/T/RtmpFc8O9O/downloaded_packages’

> BiocManager::install("phyloseq")

'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://ftp.osuosl.org/pub/cran

Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18)
Warning message:
package(s) not installed when version(s) same as current; use `force = TRUE` to re-install: 'phyloseq' 

> BiocManager::install("phyloseq", force=TRUE)

'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://ftp.osuosl.org/pub/cran

Bioconductor version 3.13 (BiocManager 1.30.16), R 4.1.0 (2021-05-18)
Installing package(s) 'phyloseq'
trying URL 'https://bioconductor.org/packages/3.13/bioc/bin/macosx/contrib/4.1/phyloseq_1.36.0.tgz'
Content type 'application/x-gzip' length 5994111 bytes (5.7 MB)
==================================================
downloaded 5.7 MB


The downloaded binary packages are in
    /var/folders/g_/fg05t4s95z7f8b7l24k3rtnc0000gn/T//RtmpFc8O9O/downloaded_packages

> library(phyloseq)
>

ADD REPLY • link updated 3.3 years ago by Kevin Blighe ★ 4.0k • written 3.3 years ago by Ina • 0

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Great, thanks for the feedback, Ina

ADD REPLY • link 3.3 years ago Kevin Blighe ★ 4.0k