Error while installing BiocManager::install("org.Vdahliae.eg.db")
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Patadù ▴ 10
@ff20d7e7
Last seen 9 days ago
The Netherlands

Hi all,

I have just created my db using makeOrgPackageFromNCBI() for Verticillium dahliae. I have used the following code:

if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("AnnotationHub")

if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("AnnotationForge")

if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")
BiocManager::install("biomaRt")

install.packages("devtools") 
devtools::install_version("dbplyr", version = "2.3.4") #downgrade dbplyr

library(AnnotationHub)
library(AnnotationForge)

hub <- AnnotationHub()
query(hub, c("Verticillium"))

makeOrgPackageFromNCBI(version = "0.1",
                       author = "L. Fiorentino <luigi.fiorentnino@wur.nl>",
                       maintainer = "L. Fiorentino",
                       outputDir = "C:/Users/Luigi/Desktop/WUR/R_Directory/org.Vd",
                       tax_id = "498257 ",
                       genus = "Verticillium",
                       species = "dahliae")

I could obtain the org.Vdahliae.eg.db Now, I am running clusterProfiler and AnnnotationDb to perform GO analysis but when I try to install the db package I get the following error:

> if (!require("BiocManager", quietly = TRUE))
+   install.packages("BiocManager")
> BiocManager::install("org.Vdahliae.eg.db", force = TRUE)
'getOption("repos")' replaces Bioconductor standard repositories, see
'help("repositories", package = "BiocManager")' for details.
Replacement repositories:
    CRAN: https://cran.rstudio.com/
Bioconductor version 3.18 (BiocManager 1.30.23), R 4.3.0 (2023-04-21 ucrt)
Installing package(s) 'org.Vdahliae.eg.db'
Installation paths not writeable, unable to update packages
  path: C:/Program Files/R/R-4.3.0/library
  packages:
    boot, class, cluster, codetools, foreign, KernSmooth, lattice, mgcv, nlme,
    nnet, rpart, spatial, survival
Messaggio di avvertimento:
the package "org.Vdahliae.eg.db" is not available for this version of R

Please, do you have any idea on how to solve this problem? Is there a specific code to use to install the db package I created or is it just with the code used above?

I have already tried to upgrade BiocManager to version 3.18, R to 4.3 and RStudio to the latest version.

Thanks, Luigi

org.vdahlaie.eg.db Bioconductor • 281 views
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FWIW: based on previous posts it is suggested to install like this:

install.packages(pkgs="./org.Vdahliae.eg.db", repos=NULL, type="source")

Also very important, did you see this message?

Installation paths not writeable, unable to update packages

this means that you don't have sufficient user rights to install/update packages on that location, and this may interfere with installing the OrgDb. I suggest you fix that!

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Thanks again Guido, I will try to run the script you have suggested and see if I can install the package.

Yes, I have seen this message as well (Installation paths not writeable, unable to update packages) but when I load libraries it seems to work well. Would you have any idea on how to solve it? I am working on my own computer, I do not understand why there should not be sufficient user rights.

Thanks again, Luigi

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0
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I have arranged the code again following the other post and also the script you suggested. Now, I managed to install org.Vdahliae.eg.db. Yet, it still appears the Installation paths not writeable, unable to update packages warning message.

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@marcel-ramos-7325
Last seen 11 days ago
United States

BiocManager does not install local packages. It only installs Bioconductor, CRAN, and GitHub ones.

You should install local packages with either remotes::install_local or with install.packages :

## as mentioned by Guido
install.packages("./org.Vdahliae.eg.db", repos = NULL, type = "source")
## OR
remotes::install_local("./org.Vdahliae.eg.db", dependencies = TRUE, repos = BiocManager::repositories())

As for the Installation paths not writeable warning, it is an artifact of folder permissions on Windows.

This can be ignored as long as the .libPaths()[1] looks correct, i.e., the folder is write-able.

Best regards,

Marcel

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Hi Marcel Ramos

Thanks for the clarification. Yes, I have installed org.Vdahlaie.eg.db using the code you and Guido suggested and now is working correctly and could perform GO analysis with clusterProfiler.

I will try to check if the .libPaths()[1] is correct.

Thanks,

Luigi

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