[Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

Fri, Mar 20, 2020 1:39 PM

Hi Martin,

That is probably what happened.

Thank you again for your help!

Sincerely,
Charles

-----Original Message-----
From: Martin Morgan <mtmorgan.bioc at gmail.com> 
Sent: Friday, March 20, 2020 1:38 PM
To: Charles Warden <cwarden at coh.org>; Alexey Sergushichev <alsergbox at gmail.com>
Cc: bioc-devel at r-project.org
Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

yes, use 1.33.1. Maybe you had a space between the '.' and the '1' or similar, '1.33. 1' ? This generates an error

** using staged installation
Error : Invalid DESCRIPTION file

Malformed package version.

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.

ERROR: installing package DESCRIPTION failed for package ...

Martin

?On 3/20/20, 4:28 PM, "Charles Warden" <cwarden at coh.org> wrote:

Hi Martin,
    
    I am currently having difficulty reproducing my earlier error (which I think didn?t even get to the step of testing the demo code).  So, I think the short answer is that I should just use version 1.33.1.
    
    In my search history, I can tell that I Googled "R Malformed package version," so I think that was part of the earlier message that I got.
    
    For what is worth, I think this is what gave me the idea to change the version numbering system:
    
    https://urldefense.com/v3/__https://cran.r-project.org/doc/manuals/r-release/R-exts.html*The-DESCRIPTION-file__;Iw!!Fou38LsQmgU!54yJgFhe0LVN6Sfb91X3m3HjH3zyeO6TroDujXtNKpwV4g0kwCruJ9yJaP_S$ 
    
    However, if I am not currently getting an error message, then I won't worry about it.
    
    Thank you very much for your help!
    
    Sincerely,
    Charles
    
    -----Original Message-----
    From: Martin Morgan <mtmorgan.bioc at gmail.com> 
    Sent: Friday, March 20, 2020 1:09 PM
    To: Charles Warden <cwarden at coh.org>; Alexey Sergushichev <alsergbox at gmail.com>
    Cc: bioc-devel at r-project.org
    Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message
    
    Can you be precise about the concern about 1.33.1 as a version number (what precise note / error / warning you received)? This scheme is very standard for package versions, and as you see enforced (for many years!) by Bioconductor.
    
    Martin
    
    ?On 3/20/20, 4:03 PM, "Bioc-devel on behalf of Charles Warden" <bioc-devel-bounces at r-project.org on behalf of cwarden at coh.org> wrote:
    
        Hi Everybody,
        
        I think changing that read.table() parameter fixed the main issue.
        
        However, when I tested my code, R used a different way to note versions in R-v.4.0.0.
        
        For example, in order to clear a message from ?R CMD check? or ?R CMD build?, I had to say the version was 1.33-1 (instead of 1.33.1).
        
        I uploaded those changes to GitHub and tested an R-3.6 installation, and that was OK.
        
        However, when I am working on merging the GitHub and Bioconductor branches, I get the following error message:
        
        ?Remote: Error: Illegal version bump from ?1.33.0? to ?1.33-1??
        
        Is this going to be changed in Bioconductor, or should I see if this is only a NOTE or WARNING (and submit the package as version 1.33.1)?
        
        Thank You,
        Charles
        
        From: Alexey Sergushichev <alsergbox at gmail.com>
        Sent: Thursday, March 19, 2020 3:00 PM
        To: Charles Warden <cwarden at coh.org>
        Cc: Shepherd, Lori <Lori.Shepherd at roswellpark.org>; bioc-devel at r-project.org
        Subject: Re: [Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message
        
        I think one of the major changes recently is setting stringsAsFactors option to FALSE by default.
        
        Best,
        Alexey

On Fri, Mar 20, 2020 at 12:48 AM Charles Warden <cwarden at coh.org<mailto:cwarden at coh.org>> wrote:

Hi Lori,
        
        Thank you very much.
        
        If I use R-4.0 (instead of R-3.6), then I can reproduce the error message.
        
        I will work in figuring out why the code works with R-3.6 but not R-4.0, but it seems like this might affect other packages as well (since I received error messages for 2 out of 2 of the Bioconductor packages that I contributed to).
        
        Do you have any general suggestions of what types of new errors might be encountered from using R-4.0?
        
        Thanks Again,
        Charles
        
        From: Shepherd, Lori [mailto:Lori.Shepherd at RoswellPark.org<mailto:Lori.Shepherd at RoswellPark.org>]
        Sent: Thursday, March 19, 2020 1:41 PM
        To: bioc-devel at r-project.org<mailto:bioc-devel at r-project.org>; Charles Warden <cwarden at coh.org<mailto:cwarden at coh.org>>
        Subject: Re: Issue Reproducing BioC 3.11 COHCAP Error Message
        
        Yes that is the correct version of R to use. Thank you for taking the time to make sure everything is correct to debug. We appreciate your effort and contributors to bioconductor.
        Get Outlook for Android<https://urldefense.com/v3/__https:/aka.ms/ghei36__;!!Fou38LsQmgU!5kLQzxLFDLkE15tideOn6Lfj4ouKaT1CB36y5FZreJ7HHHtZgHjVns3uz4qi$>

[Bioc-devel] Issue Reproducing BioC 3.11 COHCAP Error Message

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