Skip to content

[Bioc-devel] Missing dependency errors on nebbiolo1 (Bioc 3.17)

4 messages · Rainer Johannes, Oleksii Nikolaienko, Henrik Bengtsson

Rainer Johannes
# 
Dear all,

I'm continuing to see some strange dependency problems for packages on the linux build system for Bioconductor 3.17. First time I've seen them where on the build report for snapshot 2023-03-31, and they are still there for snapshot date 2023-04-02 (build report from 2023-04-03). What I've seen so far is that most are related to `BiocStyle` missing.

Some examples are:
- ROC (missing BiocStyle)
- SCATE (missing BiocStyle)
- SC3 (missing BiocStyle)
- scTHI (missing BiocStyle)

Since they are only present on the linux build system - maybe that's something related to the setup on that particular server? Or the R version used there does not properly get all dependencies of packages?

cheers, jo

---
Johannes Rainer, PhD

Eurac Research
Institute for Biomedicine
Via A.-Volta 21, I-39100 Bolzano, Italy

email: johannes.rainer at eurac.edu
github: jorainer
mastodon: jorainer at fosstodon.org
Oleksii Nikolaienko
# 
Hi,
maybe because BiocStyle is not listed as a dependency or suggested package
in DESCRIPTION?
More info here: https://github.com/Bioconductor/BBS/issues/248

Best,
Oleksii

On Tue, 4 Apr 2023 at 11:22, Rainer Johannes <Johannes.Rainer at eurac.edu>
wrote:

  
  


  


      

    

    

      
      

        


  

        

      Henrik Bengtsson
    

    

      
      #
    

  


  

      
On Tue, Apr 4, 2023 at 2:44?AM Oleksii Nikolaienko

        
<oleksii.nikolaienko at gmail.com> wrote:

            

      
      
      
    

        
Yes, this is why. The package needs 'BiocStyle' to build the vignette,
and therefore it needs to be declared. Some other packages forgot to
declare 'RUnit' needed for the unit tests. We'll also see packages
that rely on non-declared annotation packages. These new checks were
introduced for Bioc devel(*) checks and aligns with how this already
works on CRAN since a long time.

(*) I'm not 100% sure, but I believe the reason you only see it on the
Linux server is that that's the only one that runs 'R CMD check' on
vignettes. Checking vignettes takes time, so the decision was to do
that only one platform. Since 'BiocStyle' is only involved for
vignettes, this is why that particular package gets flagged only
there.  Packages that forgot to add 'RUnit' to suggests, will get an
error on all platforms.

Adding 'BiocStyle' to Suggests: in the package DESCRIPTION file solves
this problem.

/Henrik

            

      
      
      
    

        

      
      
    

            

      
      
      
    

        

      
      
    

  
  


  


      

    

    

      
      

        


  

        

      Rainer Johannes
    

    

      
      #
    

  


  

      
thanks to all for the explanations and feedback.

I'll reach out to the respective developers of these packages - hoping they respond and fix the issue timely.

cheers, jo

---
Johannes Rainer, PhD

Eurac Research
Institute for Biomedicine
Via A.-Volta 21, I-39100 Bolzano, Italy

email: johannes.rainer at eurac.edu
github: jorainer
mastodon: jorainer at fosstodon.org

        
Henrik Bengtsson wrote:

        
On Tue, Apr 4, 2023 at 2:44?AM Oleksii Nikolaienko

        
<oleksii.nikolaienko at gmail.com> wrote:

            

      
      
      
    

        
Yes, this is why. The package needs 'BiocStyle' to build the vignette,
and therefore it needs to be declared. Some other packages forgot to
declare 'RUnit' needed for the unit tests. We'll also see packages
that rely on non-declared annotation packages. These new checks were
introduced for Bioc devel(*) checks and aligns with how this already
works on CRAN since a long time.

(*) I'm not 100% sure, but I believe the reason you only see it on the
Linux server is that that's the only one that runs 'R CMD check' on
vignettes. Checking vignettes takes time, so the decision was to do
that only one platform. Since 'BiocStyle' is only involved for
vignettes, this is why that particular package gets flagged only
there.  Packages that forgot to add 'RUnit' to suggests, will get an
error on all platforms.

Adding 'BiocStyle' to Suggests: in the package DESCRIPTION file solves
this problem.

/Henrik