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Hello (this is my first message so, I'm sorry if there is something wrong),

I have been having this problem for a couple of days now. I can't install new packages, I have read a similar question but in my case, the problem only occurs when I try to install a new Bioconductor package (or when I delete an old one and try to reinstall it). The thing is that I always got some variation of the next message (in this example I am trying to install ComplexHeatmap):

BiocManager::install("ComplexHeatmap")

Bioconductor version 3.12 (BiocManager 1.30.13), R 4.0.0 (2020-04-24) Installing package(s) 'BiocVersion', 'ComplexHeatmap' also installing the dependencies �shape�, �rjson�, �BiocGenerics�, �circlize�, �GetoptLong�, �colorspace�, �clue�, �RColorBrewer�, �GlobalOptions�, �png�, �Cairo�, �S4Vectors�, �IRanges�, �matrixStats�

cannot open URL
'https://bioconductor.org/packages/3.12/data/annotation/bin/windows/contrib/4.0/PACKAGES.rds': HTTP status was '404 Not Found'Old packages: 'installr', 'boot', 'class', 'cluster', 'codetools', 'foreign', 'KernSmooth', 'lattice', 'MASS', 'Matrix', 'mgcv', 'nlme', 'nnet', 'spatial', 'survival' Update all/some/none? [a/s/n]: Update all/some/none? [a/s/n]:

It says to me that I must install X packages, so I type "a" and this happens:

Error in readRDS(dest) : error reading from connection

After the first attempt, I only get the second message until I restart R.

I have tried:

  • Start new sessions of Rscripts (or Rmarkdowns)
  • Remove all packages (by deleting the folders, directly)
  • Uninstall and reinstall R and RStudio (trying different versions, down to 4.0 for R)
  • Reboot R and the computer

I tried to install a previous version of BiocManager, but I am not able to do it. Everything is updated. Thank you very much for your attention I would appreciate your help.

elOscatron
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1 Answers1

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This is a known issue with BiocManager 1.30.13. Install the developmental version by running the following:

install.packages("devtools")    
devtools::install_github("Bioconductor/BiocManager", ref="ghost-binary-repo")
  • It worked!! thank you a lot. I have had to reboot R a cople of times to get rid of the message, but it is done. And thank you also for the link, very useful. – elOscatron May 09 '21 at 02:17