[R-pkg-devel] [External] Re: Packages required and available but unsuitable versions: Error

[Martin Morgan]

The warnings are fixed by changing the NAMESPACE file, not the DESCRIPTION file. Decide which function(s) you would like to import, and import only those using importFrom("Matrix", "sparseMatrix") or import("Matrix", except = "toeplitz")

Martin

On 9/23/19, 8:45 AM, "Agarwal, Divyansh" <Divyansh.Agarwal using pennmedicine.upenn.edu> wrote:

    Hi Martin,
    
    Thanks so much. Removing the version dependencies for those 3 packages fixed the ERROR but I'm now having an issue with these WARNINGS:
    Warning: replacing previous import ‘AnnotationDbi::select’ by ‘MASS::select’ when loading ‘multicross’
    Warning: replacing previous import ‘Matrix::cov2cor’ by ‘stats::cov2cor’ when loading ‘multicross’
    Warning: replacing previous import ‘Matrix::toeplitz’ by ‘stats::toeplitz’ when loading ‘multicross’
    Warning: replacing previous import ‘nbpMatching::quantile’ by ‘stats::quantile’ when loading ‘multicross’
    Warning: replacing previous import ‘Matrix::update’ by ‘stats::update’ when loading ‘multicross’
    
    Looking at a couple of forums I thought putting stats and MASS under "Depends" in the DESCRIPTION file would address these warnings, but they still come up. For reference, my DESCRIPTION file is –
    
    Depends:
              stats (>= 3.5.0),
              MASS (>= 7.3-49),
    Encoding: UTF-8
     Imports:
              nbpMatching (>= 1.5.1),
              crossmatch (>= 1.3-1),
              Matrix (>= 1.2-17),
              org.Hs.eg.db (>= 3.6.0),
              org.Mm.eg.db (>= 3.6.0),
              org.Ce.eg.db (>= 3.6.0),
              Seurat (>= 3.0.0),
              AnnotationDbi (>= 1.42.1)
    
    Please let me know what you'd recommend. Thank you again for taking the time to offer your help, and am really grateful for your suggestions. 
    
    Sincerely,
    Divyansh
    
    
    On 9/23/19, 7:44 AM, "Martin Morgan" <mtmorgan.bioc using gmail.com> wrote:
    
        Probably the easiest 'solution' is to remove the version dependencies, e.g., 'org.Hs.eg.db, org.Mm.eg.db, ...'.
        
        I suspect that the root cause is that the Windows builders do not have the correct version of these packages installed for the version of R in use, perhaps because the version of the package BiocVersion (it should be 3.10.1 in R-devel) is incorrect.
        
        Martin Morgan
        Bioconductor
        
        On 9/23/19, 6:06 AM, "R-package-devel on behalf of Agarwal, Divyansh" <r-package-devel-bounces using r-project.org on behalf of Divyansh.Agarwal using pennmedicine.upenn.edu> wrote:
        
            Dear R developers community,
            
            I’m trying to build and submit an R package to CRAN but keep getting the following error:
            Packages required and available but unsuitable versions:
              'org.Hs.eg.db', 'org.Mm.eg.db', 'org.Ce.eg.db'
            
            The DESCRIPTION file for my package includes the following:
            Depends:
              R (>= 3.5.0),
              stats (>= 3.5.0),
              MASS (>= 7.3-49),
            Encoding: UTF-8
            Imports:
              nbpMatching (>= 1.5.1),
              crossmatch (>= 1.3-1),
              Matrix (>= 1.2-17),
              org.Hs.eg.db (>= 3.6.0),
              org.Mm.eg.db (>= 3.6.0),
              org.Ce.eg.db (>= 3.6.0),
              Seurat (>= 3.0.0),
              AnnotationDbi (>= 1.42.1)
            
            The details of the error log are here: <https://win-builder.r-project.org/incoming_pretest/multicross_2.0.0_20190923_044655/>
            
            I’ve tried a few different things such as specifying an R version under “Depends” or updating the version for the “org.” packages to the latest version (>=3.8) but I haven’t been able to resolve the error and warnings shown in the error log.  I would be really grateful to you if you could kindly advise a potential solution for how to possibly fix this error.
            
            Thanks a lot in advance!
            Divyansh
            
            
            
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