[Bioc-devel] Imports, depends and warnings

[Marini, Federico]

Thanks!

In the meanwhile I went for a DIY solution - but it would be great to have the image again up(dated) and running.

Federico
________________________________________
From: Dan Tenenbaum <dtenenba at fredhutch.org>
Sent: Friday, March 4, 2016 10:46 PM
To: Marini, Federico
Cc: Martin Morgan; bioc-devel
Subject: Re: [Bioc-devel] Imports, depends and warnings

Yes, it looks like devel_sequencing has not updated for a while. I'll look into that.
Dan


----- Original Message -----
> From: "Federico Marini" <marinif at uni-mainz.de>
> To: "Dan Tenenbaum" <dtenenba at fredhutch.org>
> Cc: "Martin Morgan" <Martin.Morgan at RoswellPark.org>, "bioc-devel" <bioc-devel at r-project.org>
> Sent: Friday, March 4, 2016 1:40:54 PM
> Subject: Re: [Bioc-devel] Imports, depends and warnings

> Hi Dan,
>
> I pulled the devel_sequencing image - took the most up to date a couple of days
> ago.
> Probably even if the rocker/rstudio-daily is indeed updated daily the bioc
> container isn't?
>
> Federico
> ________________________________________
> From: Dan Tenenbaum <dtenenba at fredhutch.org>
> Sent: Friday, March 4, 2016 10:05 PM
> To: Marini, Federico
> Cc: Martin Morgan; bioc-devel
> Subject: Re: [Bioc-devel] Imports, depends and warnings
>
> Can you be more specific about which docker image you pulled?
>
> Dan
>
>
> ----- Original Message -----
>> From: "Federico Marini" <marinif at uni-mainz.de>
>> To: "Martin Morgan" <Martin.Morgan at roswellpark.org>, "bioc-devel"
>> <bioc-devel at r-project.org>
>> Sent: Thursday, March 3, 2016 1:20:46 AM
>> Subject: Re: [Bioc-devel] Imports, depends and warnings
>
>> You're right, sorry for the misunderstanding.
>> By updating to a more recent R devel the warning disappears. I probably
>> should do it more often for development sakes ...
>>
>> Side question but related to this, shouldn't the R version in the
>> current docker container for devel_* be the R devel? On the one I pulled
>> recently, I recall there was the R-3.2.2 - and then I reverted back to
>> the "local" development environment.
>>
>> Federico
>>
>> On 03.03.16 10:08, Morgan, Martin wrote:
>>> Your description is not clear enough. See the github repository branch
>>>
>>> https://github.com/mtmorgan/PkgA/tree/import-conflict
>>>
>>> which imports NMF and ggplot2 without any warning during
>>>
>>> R CMD build PkgA
>>> R CMD check PkgA_0.0.1.tar.gz
>>>
>>> with
>>>
>>> $ R --version|head -n3
>>> R Under development (unstable) (2016-02-27 r70232) -- "Unsuffered Consequences"
>>> Copyright (C) 2016 The R Foundation for Statistical Computing
>>> Platform: x86_64-pc-linux-gnu (64-bit)
>>>
>>>
>>> ________________________________________
>>> From: Federico Marini <marinif at uni-mainz.de>
>>> Sent: Thursday, March 3, 2016 3:44 AM
>>> To: Morgan, Martin; bioc-devel at r-project.org
>>> Subject: Re: [Bioc-devel] Imports, depends and warnings
>>>
>>> With the minimal working example, alone the importing of NMF raises the
>>> warning, so I guess this is due to that particular package.
>>>
>>> Should I contact the author of that in hope he adapts its NAMESPACE to
>>> have some nicer behavior? (or would be *just that* warning "fine" for
>>> the Bioc ecosystem?)
>>>
>>>
>>> Cheers,
>>> Federico
>>>
>>>
>>> On 02.03.16 20:41, Morgan, Martin wrote:
>>>> I think the only unavoidable case is when the package you import 'does it
>>>> wrong'. If that's not the case, then please provide an (easy-to-reproduce --
>>>> start with a simple package.skeleton() and add a couple of Imports: and
>>>> import() statements, rather than providing your current package).
>>>>
>>>> Martin
>>>>
>>>> ________________________________________
>>>> From: Bioc-devel <bioc-devel-bounces at r-project.org> on behalf of Federico Marini
>>>> <marinif at uni-mainz.de>
>>>> Sent: Wednesday, March 2, 2016 10:53 AM
>>>> To: bioc-devel at r-project.org
>>>> Subject: [Bioc-devel] Imports, depends and warnings
>>>>
>>>> Hi Bioconductors,
>>>>
>>>> I'm on a good way to finalize the pcaExplorer package I presented at the
>>>> recent Bioc Developers Meeting.
>>>>
>>>> Trying to keep check and BiocCheck always in the background of my head,
>>>> as well as trying to be a good 'package neighbour', I am dealing with
>>>> the issue of some "Warning: replacing previous import by..." messages,
>>>> when building/loading/checking.
>>>>
>>>>    From my understanding, there might be some cases where this can not be
>>>> fixed, probably because an imported package in turn imports itself
>>>> another one entirely, making my own import redundant (e.g., ggplot2 for
>>>> plotting and NMF for aheatmap give this part:
>>>>
>>>> Warnung: replacing previous import by ‘ggplot2::unit’ when loading ‘NMF’
>>>> Warnung: replacing previous import by ‘ggplot2::arrow’ when loading ‘NMF’
>>>>
>>>> This happens even if I specifically just use importFrom in the NAMESPACE.
>>>>
>>>> I'm kind of puzzled on this, so I thought I'd better ask out for some
>>>> expert advice on the ML. If required, I could put the package in a
>>>> GitHub repository.
>>>>
>>>> Thank you in advance for any help you can provide!
>>>>
>>>> Federico
>>>>
>>>> --
>>>> Federico Marini, M.Sc.
>>>> Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI)
>>>> Division Biostatistics and Bioinformatics
>>>> University Medical Center of the Johannes Gutenberg University Mainz
>>>> Postal address: 55101 Mainz
>>>> Office and delivery address: Obere Zahlbacher Str. 69, 55131 Mainz
>>>>
>>>> Phone: +49 (0) 6131 17-8108
>>>> Fax: +49 (0) 6131 17-2968
>>>> Web: www.imbei.uni-mainz.de
>>>> E-Mail: marinif at uni-mainz.de
>>>>
>>>> _______________________________________________
>>>> Bioc-devel at r-project.org mailing list
>>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>>
>>>>
>>>> This email message may contain legally privileged and/or confidential
>>>> information.  If you are not the intended recipient(s), or the employee or
>>>> agent responsible for the delivery of this message to the intended
>>>> recipient(s), you are hereby notified that any disclosure, copying,
>>>> distribution, or use of this email message is prohibited.  If you have received
>>>> this message in error, please notify the sender immediately by e-mail and
>>>> delete this email message from your computer. Thank you.
>>> --
>>> Federico Marini, M.Sc.
>>> Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI)
>>> Division Biostatistics and Bioinformatics
>>> University Medical Center of the Johannes Gutenberg University Mainz
>>> Postal address: 55101 Mainz
>>> Office and delivery address: Obere Zahlbacher Str. 69, 55131 Mainz
>>>
>>> Phone: +49 (0) 6131 17-8108
>>> Fax: +49 (0) 6131 17-2968
>>> Web: www.imbei.uni-mainz.de
>>> E-Mail: marinif at uni-mainz.de
>>>
>>>
>>> This email message may contain legally privileged and/or confidential
>>> information.  If you are not the intended recipient(s), or the employee or
>>> agent responsible for the delivery of this message to the intended
>>> recipient(s), you are hereby notified that any disclosure, copying,
>>> distribution, or use of this email message is prohibited.  If you have received
>>> this message in error, please notify the sender immediately by e-mail and
>>> delete this email message from your computer. Thank you.
>>
>> --
>> Federico Marini, M.Sc.
>> Institute of Medical Biostatistics, Epidemiology and Informatics (IMBEI)
>> Division Biostatistics and Bioinformatics
>> University Medical Center of the Johannes Gutenberg University Mainz
>> Postal address: 55101 Mainz
>> Office and delivery address: Obere Zahlbacher Str. 69, 55131 Mainz
>>
>> Phone: +49 (0) 6131 17-8108
>> Fax: +49 (0) 6131 17-2968
>> Web: www.imbei.uni-mainz.de
>> E-Mail: marinif at uni-mainz.de
>>
>> _______________________________________________
>> Bioc-devel at r-project.org mailing list
> > https://stat.ethz.ch/mailman/listinfo/bioc-devel