[Bioc-devel] Imports, depends and warnings

[Dan Tenenbaum]

bioconductor/devel_sequencing is updated now.
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: Monday, March 7, 2016 12:21:41 AM
> Subject: Re: [Bioc-devel] Imports, depends and warnings

> Thanks for looking into it!
> Still saves some time in installing R-devel (and always provides a fresh
> one).
> 
> Federico
> 
> On 04.03.16 23:48, Dan Tenenbaum wrote:
>> 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
>>>>>>> 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
> 
> --
> 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