[Bioc-devel] Imports, depends and warnings

Fri Mar 4 23:48:54 CET 2016

So a preliminary diagnosis is that some packages are not building even though they build in the nightly builds. The problem could be a newer compiler, newer R-devel, slightly different OS (debian vs ubuntu) or something else. Investigating further. However, in the meantime, bioconductor/devel_base is now up to date. Of course this only includes one Bioconductor package (BiocInstaller) and fewer system dependencies, but it might be a helpful stopgap for you.

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 1:48:45 PM
> Subject: Re: [Bioc-devel] Imports, depends and warnings

> 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
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>>>> --
>>>> 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