R 4.0.3 compatibility

[tai-mi]

Hello,

I am trying to install the package on R 4.0.3 and am getting the error message "package ‘CellaRepertorium’ is not available for this version of R" Is this another issue on my end or is it not compatible?

[amcdavid]

It's definitely compatible. Did you install with BiocManager::install? install.packages won't work.

[tai-mi]

Yeah I used BiocManager and got an output of (after updating packages):

The downloaded source packages are in
    ‘C:\Users\spamt\AppData\Local\Temp\RtmpQTx8LI\downloaded_packages’
Warning message:
package ‘CellaRepertorium’ is not available for this version of R

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 

[amcdavid]

Can you provide full input and output? It's impossible to debug someone's system without knowing exactly what they typed and what the output was.

I suspect this may be a transient issue with a binary package (that CellaRepertorium depends on) not being available for windows on cran. If you have Rtools installed (can compile R packages source) you could try

BiocManager::install('CellaRepertorium', type = 'source')

[tai-mi]

The full output (with Rtools installed) was

> BiocManager::install('CellaRepertorium', type = 'source')
Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.3
  (2020-10-10)
Installing package(s) 'CellaRepertorium'
Installation path not writeable, unable to update packages: boot,
  class, codetools, foreign, KernSmooth, Matrix, nlme, nnet,
  spatial
Warning message:
package ‘CellaRepertorium’ is not available for this version of R

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 

Even after having successfully updated the listed packages from source with no errors

[amcdavid]

I believe this is because the package has dependencies that require upgraded versions of the "unable to update" packages listed in the error message. Though the error message R gives is certainly not very transparent about this. If you don't want to upgrade them system-wide you could use the renv package, or set R_LIBS_USER (or maybe R_LIBS_SITE) on a per-project basis. See ?.libPaths() and the R administration guide https://cran.r-project.org/doc/manuals/r-release/R-admin.html

On Feb 5, 2021, at 11:56 PM, Taimi notifications@github.com wrote:

The full output (with Rtools installed) was

BiocManager::install('CellaRepertorium', type = 'source') Bioconductor version 3.11 (BiocManager 1.30.10), R 4.0.3 (2020-10-10) Installing package(s) 'CellaRepertorium' Installation path not writeable, unable to update packages: boot, class, codetools, foreign, KernSmooth, Matrix, nlme, nnet, spatial Warning message: package ‘CellaRepertorium’ is not available for this version of R

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 Even after having successfully updated the listed packages from source with no errors

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[tai-mi]

Thanks for your help, it works now! The issue was just that I was using BioConductor 3.11 instead of 3.12

[amcdavid]

Yup, that would do it, too. The error really could be more informative. I'll add a comment about checking BiocManager::valid() to the install instructions to hopefully save others some headache.