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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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Problems with installing 'phyloseq' #1490

Open itimling opened 3 years ago

itimling commented 3 years ago

Hello, I am having trouble installing 'phyloseq'. I used the following code:

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'

Based on the warning message, I tried:

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

However, when I wanted to load 'phyloseq' I got the following message:

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’

It would be great if someone had some recommendations what I need to do differently in order to install ' phyloseq'. I am looking forward to installing 'phyloseq' !!!!! Thanks, Ina

ycl6 commented 3 years ago

AFAIK, phyloseq does not require GenomeInfoDbData. Can you run sessionInfo() and show its output?

itimling commented 3 years ago

sessionInfo()

R version 4.1.0 (2021-05-18) Platform: x86_64-apple-darwin17.0 (64-bit) Running under: macOS Mojave 10.14.6

Matrix products: default BLAS: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRblas.dylib LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

Random number generation: RNG: Mersenne-Twister Normal: Inversion Sample: Rounding

locale: [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages: [1] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached): [1] Rcpp_1.0.7 IRanges_2.26.0 codetools_0.2-18 foreach_1.5.1 crayon_1.4.1
[6] bitops_1.0-7 plyr_1.8.6 stats4_4.1.0 magrittr_2.0.1 stringi_1.7.3
[11] reshape2_1.4.4 S4Vectors_0.30.0 iterators_1.0.13 tools_4.1.0 stringr_1.4.0
[16] Biobase_2.52.0 RCurl_1.98-1.3 parallel_4.1.0 compiler_4.1.0 BiocGenerics_0.38.0 [21] BiocManager_1.30.16

ycl6 commented 3 years ago

Hi @itimling, I've see similar reports online regarding GenomeInfoDbData when installing other packages, it seems to happens on Windows or Mac OS. Can you try installing GenomeInfoDbData first and see if that work.

BiocManager::install("GenomeInfoDbData")
itimling commented 3 years ago

Hi, I installed '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 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)

ycl6 commented 3 years ago

Hi @itimling, I am glad the issue is now resolved.

slambrechts commented 1 year ago

I'm having the same problem. Additionally, when I try to install BiocManager::install("GenomeInfoDbData") to solve it, I get:

Warning message:
package ‘GenomeInfoDbData’ is not available as a binary package for Bioconductor version '3.17'