[Bioc-devel] Imports, depends and warnings

Mon Mar 7 09:21:41 CET 2016

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,
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>>>>>> 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