DEGreport installation help
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marinaw ▴ 10
@9c8b15cf
Last seen 8 days ago
Canada

Hi everyone,

I'm having trouble installing DEGreport due to a dependency:

> BiocManager::install("DEGreport")

'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details
replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.16 (BiocManager 1.30.18), R 4.2.1 (2022-06-23)
Warning message:
package(s) not installed when version(s) same as current; use `force = TRUE` to re-install: 'DEGreport' 

> library(DEGreport)
Error: package or namespace load failed for ‘DEGreport’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘lasso2’

When I try to install lasso2, the following happens:

> BiocManager::install("lasso2")
'getOption("repos")' replaces Bioconductor standard repositories, see '?repositories' for details

replacement repositories:
    CRAN: https://cran.rstudio.com/

Bioconductor version 3.16 (BiocManager 1.30.18), R 4.2.1 (2022-06-23)
Installing package(s) 'lasso2'
Warning message:
package ‘lasso2’ is not available for Bioconductor version '3.16'

A version of this package for your version of R might be available elsewhere,
see the ideas at
https://cran.r-project.org/doc/manuals/r-patched/R-admin.html#Installing-packages

Lasso2 seems to have been archived. Is there a way to circumvent this so I can install DEGreport? Thanks!

DEGreport • 502 views
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@james-w-macdonald-5106
Last seen 17 hours ago
United States

The lasso2 package has been archived because the maintainer didn't get something done in time. Or something. If you are willing to take the chance, you can download here and then install directly using

install.packages(<path to downloaded file>, repos = NULL)

If you are on Windows, and there is no compiled code, you can add an additional argument of type = "source". If there is compiled code in lasso2 (likely?) and you are on Windows, you need to get Rtools first, and then you can specify type = "source". If you are on a Mac, then you need somebody other than me to help because I know nothing of such things.

Also CAVEAT EMPTOR. You are on your own, no presumption of suitability, who knows what's the deal with lasso2, etc, etc.

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Okay, thank you for the insight! Unfortunately I'm using a Mac.

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Ooof. An M1 Mac? If prior, you might be able to install if you have XCode installed as well. Apparently there is C or C++ code, so you need a compiler.

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install.packages(<path to downloaded file>, type = "source",repos = NULL) worked fine for me on Mac M2

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@munta.jihad I downloaded the latest .tar file and unzipped it, ran the following code:

install.packages('~/Downloads/lasso2/R', type = "source",repos = NULL)

However I still get this

Warning in install.packages :
  installation of package ‘/Users/*(myaccountname)*/Downloads/lasso2/R’ had non-zero exit status
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this worked for me but without unzipping the file!

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I have an M2 Mac!

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