[Bioc-devel] Imports, depends and warnings

[Marini, Federico]

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