[Bioc-devel] mcols Function Not Found for Windows Build

[Hervé Pagès]

Hi Dario,

You're missing several imports. The CHECK results on the other platforms
contains "no visible global function definition" notes for several
symbols including 'mcols':

 
https://bioconductor.org/checkResults/3.7/bioc-LATEST/ClassifyR/malbec2-checksrc.html

Not sure why these missing imports only cause problems on Windows but
the error seems to happen in the context of BiocParallel, which could
be doing some platform-dependent business behind the scene. Note that,
generally speaking, code can still work properly even with missing
imports if the package where the missing imports are defined is in
the Depends field. This is the case here for S4Vectors. Because it's
in Depends and not in Imports, it ends up in the search path after
doing library(ClassifyR) so symbols defined in S4Vectors can be found
even if they are not imported. However, you would probably get an
error on all platforms if S4Vectors was in Imports instead of Depends.

Unless you have a good reason for importing selectively from S4Vectors,
I would recommended that you import S4Vectors entirely. This will
make the maintenance of your package easier in the long run and with
no significant downside.

Cheers,
H.


On 03/15/2018 06:00 PM, Dario Strbenac wrote:
> Good day,
> 
> I notice an error happening when the vignette of ClassifyR is checked by tokay2. mcols is not found. I viewed the check reports of S4Vectors, and there are some Warnings for all operating systems, but no platform has Error, so it's unlikely to be related to the problem. Is there a way to make ClassifyR guard against this problem in Windows? I don't know how to begin solving this issue.
> 
> --------------------------------------
> Dario Strbenac
> University of Sydney
> Camperdown NSW 2050
> Australia
> 
> _______________________________________________
> Bioc-devel at r-project.org mailing list
> https://urldefense.proofpoint.com/v2/url?u=https-3A__stat.ethz.ch_mailman_listinfo_bioc-2Ddevel&d=DwICAg&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=2ciFRHT0N-QWOCEhGoXA9xk7mAqAFfd9sj2p159st_U&s=JxXD6gXsz-0euuGL4PsURm-OztXlZm4Ux1RRClPhKwg&e=
> 

-- 
Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Ave. N, M1-B514
P.O. Box 19024
Seattle, WA 98109-1024

E-mail: hpages at fredhutch.org
Phone:  (206) 667-5791
Fax:    (206) 667-1319