Question

Cannot Install gmapR Bioconductor Package

0

Entering edit mode

kwon.daniel • 0

@kwondaniel-23579

Last seen 4.3 years ago

Hello,

I am having issues installing the gmapR bioconductor package. When I type in the following command:

> BiocManager::install("gmapR")

I receive the following message:

Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.2 (2019-12-12)
Installing package(s) 'gmapR'
Package which is only available in source form, and may need compilation of
  C/C++/Fortran: ‘gmapR’
  These will not be installed
Old packages: 'haven', 'sp', 'tidyr', 'nlme'
Update all/some/none? [a/s/n]:

After updating all, I find that none of these packages are updated and gmapR is not installed.

I've googled this problem and this Stackoverflow post advised to install directly from CRAN; however, how would I do the equivalent using Bioconductor?

https://stackoverflow.com/questions/31249980/error-in-r-package-which-is-only-available-in-source-form-and-may-need-compil

Thanks

software error • 1.2k views

ADD COMMENT • link updated 4.3 years ago by Kevin Blighe ★ 4.0k • written 4.3 years ago by kwon.daniel • 0

1

Entering edit mode

Hi,

Error messages of this form often occur for Windows users when a Windows binary version of the R package is not available. Unfortunately, sometimes packages are simply not built to be compatible with Windows (or particular different operating systems). Note that compatibility details are listed under "Package Archives" in the Bioconductor listing for a package (in this case https://bioconductor.org/packages/release/bioc/html/gmapR.html). I believe a similar case of your issue is here.

If you have access to a Linux or Mac machine, I expect the same installation command should work: BiocManager::install("gmapR") There are also tools to run a Linux/Unix-like environment from a Windows machine- I recommend and personally have used WSL (https://ubuntu.com/wsl). Setting up R and other tools in environments like this may take a bit of work, but I think it can be a worthwhile investment.

I was able to install gMapR with BiocManager::install("gmapR") from R 4.0.2 on Linux. I've provided more details about my set-up at the bottom, if it helps.

Best, -Nick

P.S. I'm currently learning to help others.

> # Reproducibility info
> library('sessioninfo')
> session_info()
─ Session info ───────────────────────────────────────────────────────────────
 setting  value
 version  R version 4.0.2 Patched (2020-06-24 r78746)
 os       CentOS Linux 7 (Core)
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       US/Eastern
 date     2020-10-21

─ Packages ───────────────────────────────────────────────────────────────────
 package     * version date       lib source
 assertthat    0.2.1   2019-03-21 [2] CRAN (R 4.0.0)
 cli           2.0.2   2020-02-28 [2] CRAN (R 4.0.0)
 crayon        1.3.4   2017-09-16 [2] CRAN (R 4.0.0)
 fansi         0.4.1   2020-01-08 [2] CRAN (R 4.0.0)
 glue          1.4.2   2020-08-27 [1] CRAN (R 4.0.2)
 sessioninfo * 1.1.1   2018-11-05 [2] CRAN (R 4.0.0)
 withr         2.2.0   2020-04-20 [2] CRAN (R 4.0.0)

[1] /users/neagles/R/4.0
[2] /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/R/4.0/lib64/R/site-library
[3] /jhpce/shared/jhpce/core/conda/miniconda3-4.6.14/envs/svnR-4.0/R/4.0/lib64/R/library