Trouble installing bioconductor

Question: Trouble installing bioconductor

20 months ago by

I am new to R, have minimal experience in python. I have been attempting to install bioconductor, but keep having the same error message after entering:

source("https://bioconductor.org/biocLite.R") biocLite()

Error message:

Error in file(filename, "r", encoding = encoding): internet routines cannot be loaded Traceback:

1. source("https://bioconductor.org/biocLite.R")
2. file(filename, "r", encoding = encoding)

I have attempted many different suggestions on this forum and others to no avail. Tried http vs. https and messing with settings and library location. I do not think it has to do with an institutional proxy either. I believe everything is updated.

Thanks!

Session info:

R version 3.4.1 (2017-06-30)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: OS X El Capitan 10.11.4

Matrix products: default
BLAS: 

/System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/
vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/
vecLib.framework/Versions/A/libLAPACK.dylib

locale:
[1] en_US/en_US/en_US/C/en_US/en_US

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

loaded via a namespace (and not attached):
[1] compiler_3.4.1

biocinstaller installation • 799 views

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modified 20 months ago by Martin Morgan ♦♦ 23k • written 20 months ago by will.b.porterfield • 50

Answer: Trouble installing bioconductor

20 months ago by

Martin Morgan ♦♦ 23k

United States

Martin Morgan ♦♦ 23k wrote:

It would seem like your R has been compiled without internet capabilities, I guess (??) that when you evaluate the command capabilities(), it reports FALSE for http/ftp.

> capabilities()
       jpeg         png        tiff       tcltk         X11        aqua 
       TRUE        TRUE        TRUE        TRUE        TRUE       FALSE 
   http/ftp     sockets      libxml        fifo      cledit       iconv 
       TRUE        TRUE        TRUE        TRUE        TRUE        TRUE 
        NLS     profmem       cairo         ICU long.double     libcurl 
       TRUE        TRUE        TRUE        TRUE        TRUE        TRUE

How did you install R?

ADD COMMENT • link written 20 months ago by Martin Morgan ♦♦ 23k

I actually get true back.

capabilities()
       jpeg         png        tiff       tcltk         X11        aqua 
       TRUE        TRUE        TRUE        TRUE       FALSE        TRUE 
   http/ftp     sockets      libxml        fifo      cledit       iconv 
       TRUE        TRUE        TRUE        TRUE        TRUE        TRUE 
        NLS     profmem       cairo         ICU long.double     libcurl 
       TRUE        TRUE        TRUE        TRUE        TRUE        TRUE

Thanks for the response, interesting. I installed R using jupyter. Best to uninstall and reinstall another way?

ADD REPLY • link modified 20 months ago • written 20 months ago by will.b.porterfield • 50

How do you install R via jupyter? I would follow the installation instructions for your operating system, which I think is just a couple of clicks on the R-3.4.1 link on the MacOS installation page.

ADD REPLY • link written 20 months ago by Martin Morgan ♦♦ 23k

In can be installed through anaconda might be a better way to say it? using:

conda install -c r r-essentials

However your response led me to this link: https://stackoverflow.com/questions/38067322/is-it-possible-to-install-bioconductor-package-rain-in-r-jupyter-notebook

which notes that the r-essentials from anaconda does not contain all the necessary packages. So going through the CRAN R-download, then making it available to jupyter (https://irkernel.github.io/installation/#binary-panel) worked.

Thanks!

ADD REPLY • link written 20 months ago by will.b.porterfield • 50

Apparently the `conda` R is actually missing a part of base R, not just one of the add-on packages. It's probably a (relatively serious) bug in the way R is generated and should be reported to the conda folks.

ADD REPLY • link written 20 months ago by Martin Morgan ♦♦ 23k

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