Entering edit mode
here below my concern during Biobase package installation;
if (!require("BiocManager", quietly = TRUE))
+ install.packages("BiocManager")
>
> BiocManager::install("Biobase", force = TRUE)
'getOption("repos")' replaces Bioconductor standard repositories, see 'help("repositories", package = "BiocManager")' for
details.
Replacement repositories:
CRAN: https://cran.rstudio.com/
Bioconductor version 3.16 (BiocManager 1.30.20), R 4.2.2 (2022-10-31 ucrt)
Installing package(s) 'Biobase'
trying URL 'https://bioconductor.org/packages/3.16/bioc/bin/windows/contrib/4.2/Biobase_2.58.0.zip'
Error in download.file(url, destfile, method, mode = "wb", ...) :
cannot open URL 'https://bioconductor.org/packages/3.16/bioc/bin/windows/contrib/4.2/Biobase_2.58.0.zip'
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
the 'wininet' method is deprecated for http:// and https:// URLs
2: In download.file(url, destfile, method, mode = "wb", ...) :
cannot open URL 'https://bioconductor.org/packages/3.16/bioc/bin/windows/contrib/4.2/Biobase_2.58.0.zip': HTTP status was '403 Forbidden'
Warning in download.packages(pkgs, destdir = tmpd, available = available, :
le téléchargement du package ‘Biobase’ a échoué
Installation paths not writeable, unable to update packages
path: C:/Program Files/R/R-4.2.2/library
packages:
boot, class, codetools, foreign, MASS, Matrix, mgcv, nlme, spatial, survival
>***************************************************************************************************
> R.version.string
[1] "R version 4.2.2 (2022-10-31 ucrt)"
> packageVersion("BiocManager")
[1] ‘1.30.20’
> if (requireNamespace("BiocVersion", quietly = TRUE))
+ packageVersion("BiocVersion")
[1] ‘3.16.0’
> BiocManager::version()
[1] ‘3.16’
If you paste https://bioconductor.org/packages/3.16/bioc/bin/windows/contrib/4.2/Biobase_2.58.0.zip into a browser, does it ask you where to save the file, or does it give you an error about not being able to open the URL?
Hi James When i launched the link via browser, i had message from Zcaller which bloked the access here below the message Access to this website has been blocked due to it’s categorization. Please request a Zscaler Sitereview in case the category is not correct.
I assume you got the message: bluntly said the problem is at your side, since a security tool called Zscaler, that is installed at your network, is blocking access to the Bioconductor repositories. Note that clicking the link above in Firefox immediately prompts me with a question where to store the ZIP file to be downloaded.