Question

Trouble installing bioconductor

2

Entering edit mode

will.b.porterfield ▴ 50

@willbporterfield-13817

Last seen 7.3 years ago

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 • 2.1k views

ADD COMMENT • link updated 7.3 years ago by Martin Morgan 25k • written 7.3 years ago by will.b.porterfield ▴ 50

score 2 · Answer 1 · 2017-08-22

2

Entering edit mode

Martin Morgan 25k

@martin-morgan-1513

Last seen 3 months ago

United States

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 7.3 years ago Martin Morgan 25k

1

Entering edit mode

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 7.3 years ago will.b.porterfield ▴ 50

1

Entering edit mode

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 7.3 years ago Martin Morgan 25k

2

Entering edit mode

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 7.3 years ago will.b.porterfield ▴ 50

0

Entering edit mode

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 7.3 years ago Martin Morgan 25k