annotaton hub will not load in R4.04 RStudio3.12
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paul28 • 0
@f654a4aa
Last seen 8 months ago

Enter the body of text here

Code should be placed in three backticks as shown below

Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : 
  cannot open the connection
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 1327104 != reported length 1826019
2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file
3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
  cannot open compressed file 'DT/DESCRIPTION', probable reason 'No such file or directory'
AnnotationDbi • 333 views
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You need to provide the entirety of the output, not just a a snippet

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> BiocManager::install("AnnotationHub")
Bioconductor version 3.12 (BiocManager 1.30.10), R 4.0.4
  (2021-02-15)
Installing package(s) 'AnnotationHub'
also installing the dependencies ‘DT’, ‘interactiveDisplayBase’

trying URL 'https://ftp.osuosl.org/pub/cran/bin/windows/contrib/4.0/DT_0.17.zip'
Content type 'application/zip' length 1826019 bytes (1.7 MB)
downloaded 1.2 MB

trying URL 'https://bioconductor.org/packages/3.12/bioc/bin/windows/contrib/4.0/interactiveDisplayBase_1.28.0.zip'
Content type 'application/zip' length 41432 bytes (40 KB)
downloaded 40 KB

trying URL 'https://bioconductor.org/packages/3.12/bioc/bin/windows/contrib/4.0/AnnotationHub_2.22.0.zip'
Content type 'application/zip' length 1480729 bytes (1.4 MB)
downloaded 1.4 MB

Error in read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) : 
  cannot open the connection
In addition: Warning messages:
1: In download.file(url, destfile, method, mode = "wb", ...) :
  downloaded length 1310720 != reported length 1826019
2: In unzip(zipname, exdir = dest) : error 1 in extracting from zip file
3: In read.dcf(file.path(pkgname, "DESCRIPTION"), c("Package", "Type")) :
  cannot open compressed file 'DT/DESCRIPTION', probable reason 'No such file or directory'
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@james-w-macdonald-5106
Last seen 14 hours ago
United States

Seems like this was the problem

trying URL 'https://ftp.osuosl.org/pub/cran/bin/windows/contrib/4.0/DT_0.17.zip'
Content type 'application/zip' length 1826019 bytes (1.7 MB)
downloaded 1.2 MB

You were supposed to get a 1.7 MB file but got a 1.2 MB file. Which won't work. You should try again. I just installed DT directly on my Windows box and it went OK, so it was probably an intermittent issue.

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Although I got mine from CRAN, so maybe the version at osuosl.org is borked? There is a site_repository argument to BiocManager::install that you can use to provide an alternate repo from which to get the package.

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