Hello !
I create this post as a big beginner in the world of R because I have to analyze microbiome data for my PhD and I have a lot of trouble understanding how it works. Nobody in my group works with this kind of data, so it's not easy to get help.
At first, I wanted to use Mothur to analyze data in .csv and .tsv format, but a friend advised me to work with R instead, and more specifically with Phyloseq.
Here comes the first problem: I can't install Phyloseq.
I've tried several tutorials (videos/internet posts) but I don't understand the problem.
I'm running version R 4.4.2
Here's what I tried:
sessionInfo()
BiocManager::install("GenomeInfoDbData")
BiocManager::install("GenomeInfoDbData", force = TRUE)
BiocManager::install("phyloseq")
BiocManager::install("phyloseq", force=TRUE)
install. packages(phyloseq)
And what I got as an answer:
sessionInfo()
R version 4.4.2 (2024-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64
Running under: Windows 10 x64 (build 19045)
Matrix products: default
locale:
[1] LC_COLLATE=German_Germany.utf8 LC_CTYPE=German_Germany.utf8 LC_MONETARY=German_Germany.utf8
[4] LC_NUMERIC=C LC_TIME=German_Germany.utf8
time zone: Europe/Berlin
tzcode source: internal
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] phyloseq_1.50.0 BiocManager_1.30.25
loaded via a namespace (and not attached):
[1] stringi_1.8.7 lattice_0.22-6 digest_0.6.37 magrittr_2.0.3
[5] grid_4.4.2 iterators_1.0.14 foreach_1.5.2 plyr_1.8.9
[9] jsonlite_2.0.0 Matrix_1.7-1 ape_5.8-1 GenomeInfoDb_1.42.3
[13] survival_3.7-0 mgcv_1.9-1 httr_1.4.7 UCSC.utils_1.2.0
[17] scales_1.3.0 permute_0.9-7 Biostrings_2.74.1 codetools_0.2-20
[21] ade4_1.7-23 cli_3.6.4 rlang_1.1.5 crayon_1.5.3
[25] XVector_0.46.0 Biobase_2.66.0 splines_4.4.2 munsell_0.5.1
[29] vegan_2.6-10 tools_4.4.2 parallel_4.4.2 reshape2_1.4.4
[33] colorspace_2.1-1 Rhdf5lib_1.28.0 ggplot2_3.5.1 GenomeInfoDbData_1.2.13
[37] multtest_2.62.0 BiocGenerics_0.52.0 vctrs_0.6.5 R6_2.6.1
[41] stats4_4.4.2 lifecycle_1.0.4 rhdf5_2.50.2 zlibbioc_1.52.0
[45] stringr_1.5.1 biomformat_1.34.0 S4Vectors_0.44.0 IRanges_2.40.1
[49] MASS_7.3-61 cluster_2.1.6 pkgconfig_2.0.3 pillar_1.10.2
[53] gtable_0.3.6 glue_1.8.0 data.table_1.17.0 Rcpp_1.0.14
[57] tibble_3.2.1 rhdf5filters_1.18.1 igraph_2.1.4 nlme_3.1-166
[61] compiler_4.4.2
BiocManager::install("GenomeInfoDbData")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")'
for details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.20 (BiocManager 1.30.25), R 4.4.2 (2024-10-31 ucrt)
Installation paths not writeable, unable to update packages
path: C:/Program Files/R/R-4.4.2/library
packages:
class, cluster, foreign, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet, rpart, spatial, survival
Warnmeldung:
package(s) not installed when version(s) same as or greater than current; useforce = TRUEto re-install:
'GenomeInfoDbData'
BiocManager::install("GenomeInfoDbData", force = TRUE)
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")'
for details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.20 (BiocManager 1.30.25), R 4.4.2 (2024-10-31 ucrt)
Installing package(s) 'GenomeInfoDbData'
installiere Quellpaket ‘GenomeInfoDbData’
versuche URL 'https://bioconductor.org/packages/3.20/data/annotation/src/contrib/GenomeInfoDbData_1.2.13.tar.gz'
Content type 'application/x-gzip' length 12924272 bytes (12.3 MB)
downloaded 12.3 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)
Die heruntergeladenen Quellpakete sind in
‘C:\Temp\RtmpqKypLw\downloaded_packages’
Installation paths not writeable, unable to update packages
path: C:/Program Files/R/R-4.4.2/library
packages:
class, cluster, foreign, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet, rpart, spatial, survival
BiocManager::install("phyloseq")
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")'
for details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.20 (BiocManager 1.30.25), R 4.4.2 (2024-10-31 ucrt)
Installation paths not writeable, unable to update packages
path: C:/Program Files/R/R-4.4.2/library
packages:
class, cluster, foreign, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet, rpart, spatial, survival
Warnmeldung:
package(s) not installed when version(s) same as or greater than current; useforce = TRUEto re-install: 'phyloseq'
BiocManager::install("phyloseq", force=TRUE)
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")'
for details.
Replacement repositories:
CRAN: https ://cran.rstudio.com/
Bioconductor version 3.20 (BiocManager 1.30.25), R 4.4.2 (2024-10-31 ucrt)
Installing package(s) 'phyloseq'
Warnung: Paket ‘phyloseq’ wird gerade benutzt und deshab nicht installiert
Installation paths not writeable, unable to update packages
path: C:/Program Files/R/R-4.4.2/library
packages:
class, cluster, foreign, KernSmooth, lattice, MASS, Matrix, mgcv, nlme, nnet, rpart, spatial, survival
install.packages(phyloseq)
Error in install.packages : cannot coerce type 'closure' to vector of type 'any'
Does someone can help me please ? I really don't know what do to more
Thank you very much,
Raphaëlle
