Failed to install Biobase
1
0
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@f8ad121d
Last seen 11 months ago
France

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’
GSVA Biobase • 1.2k views
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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?

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0
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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.

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1
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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.

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@james-w-macdonald-5106
Last seen 4 hours ago
United States

As Guido already noted, Zcaller is blocking access, which isn't something we can help you with. You need to contact your IT people and ask for https://bioconductor.org to be unblocked by Zcaller.

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