The support.bioconductor.org editor has been updated to markdown! Please see more info at: Tutorial: Updated Support Site Editor

Question: Trouble installing bioconductor
2
gravatar for will.b.porterfield
18 months ago by
will.b.porterfield • 50
will.b.porterfield • 50 wrote:

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 • 761 views
ADD COMMENT • link •
modified 18 months ago by Martin Morgan ♦♦ 22k • written 18 months ago by will.b.porterfield • 50
Answer: Trouble installing bioconductor
2
gravatar for Martin Morgan
18 months ago by
Martin Morgan ♦♦ 22k
United States
Martin Morgan ♦♦ 22k 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 18 months ago by Martin Morgan ♦♦ 22k
1

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 18 months ago • written 18 months ago by will.b.porterfield • 50
1

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 18 months ago by Martin Morgan ♦♦ 22k
2

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 18 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 18 months ago by Martin Morgan ♦♦ 22k
Please log in to add an answer.

Similar posts • Search »

  • Nothing matches yet.
Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 364 users visited in the last hour